molstar 3.3.1 → 3.4.0

package/lib/commonjs/mol-math/geometry/boundary-helper.js

@@ -88,7 +88,7 @@ var BoundaryHelper = /** @class */ (function () {
         this.centroidHelper.radiusSphereStep(center, radius);
     };
     BoundaryHelper.prototype.getSphere = function (sphere) {
-        return geometry_1.Sphere3D.setExtrema(this.centroidHelper.getSphere(sphere), (0, tslib_1.__spreadArray)([], this.extrema, true));
+        return geometry_1.Sphere3D.setExtrema(this.centroidHelper.getSphere(sphere), tslib_1.__spreadArray([], this.extrema, true));
     };
     BoundaryHelper.prototype.getBox = function (box) {
         return box3d_1.Box3D.fromVec3Array(box || (0, box3d_1.Box3D)(), this.extrema);
@@ -109,16 +109,16 @@ function getEposDir(quality) {
     var dir;
     switch (quality) {
         case '6':
-            dir = (0, tslib_1.__spreadArray)([], Type001, true);
+            dir = tslib_1.__spreadArray([], Type001, true);
             break;
         case '14':
-            dir = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], Type001, true), Type111, true);
+            dir = tslib_1.__spreadArray(tslib_1.__spreadArray([], Type001, true), Type111, true);
             break;
         case '26':
-            dir = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], Type001, true), Type111, true), Type011, true);
+            dir = tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([], Type001, true), Type111, true), Type011, true);
             break;
         case '98':
-            dir = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], Type001, true), Type111, true), Type011, true), Type012, true), Type112, true), Type122, true);
+            dir = tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([], Type001, true), Type111, true), Type011, true), Type012, true), Type112, true), Type122, true);
             break;
     }
     return dir.map(function (a) {

package/lib/commonjs/mol-math/geometry/gaussian-density/cpu.js

@@ -12,7 +12,7 @@ var linear_algebra_1 = require("../../linear-algebra");
 var int_1 = require("../../../mol-data/int");
 var approx_1 = require("../../approx");
 function GaussianDensityCPU(ctx, position, box, radius, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         function accumulateRange(begI, endI) {
             for (var i = begI; i < endI; ++i) {
                 var j = int_1.OrderedSet.getAt(indices, i);
@@ -63,9 +63,9 @@ function GaussianDensityCPU(ctx, position, box, radius, props) {
             }
         }
         function accumulate() {
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
                 var i;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             i = 0;
@@ -87,7 +87,7 @@ function GaussianDensityCPU(ctx, position, box, radius, props) {
             });
         }
         var resolution, radiusOffset, smoothness, scaleFactor, indices, x, y, z, id, n, radii, maxRadius, i, r, pad, expandedBox, min, scaledBox, dim, space, data, field, idData, idField, dimX, dimY, dimZ, iu, iv, iuv, gridx, gridy, gridz, densData, alpha, updateChunk, transform;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     resolution = props.resolution, radiusOffset = props.radiusOffset, smoothness = props.smoothness;

package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js

@@ -287,7 +287,7 @@ function createGaussianDensityRenderable(webgl, drawCount, positions, radii, gro
         dGridTexType: mol_util_1.ValueCell.create(minDistanceTexture.getDepth() > 0 ? '3d' : '2d'),
         dCalcType: mol_util_1.ValueCell.create('density'),
     };
-    var schema = (0, tslib_1.__assign)({}, GaussianDensitySchema);
+    var schema = tslib_1.__assign({}, GaussianDensitySchema);
     var shaderCode = (0, shader_code_1.ShaderCode)(GaussianDensityName, gaussian_density_vert_1.gaussianDensity_vert, gaussian_density_frag_1.gaussianDensity_frag);
     var renderItem = (0, render_item_1.createComputeRenderItem)(webgl, 'points', shaderCode, schema, values);
     return (0, renderable_1.createComputeRenderable)(renderItem, values);

package/lib/commonjs/mol-math/geometry/gaussian-density.js

@@ -17,8 +17,8 @@ exports.DefaultGaussianDensityProps = {
 };
 function computeGaussianDensity(position, box, radius, props) {
     var _this = this;
-    return task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return task_1.Task.create('Gaussian Density', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, (0, cpu_1.GaussianDensityCPU)(ctx, position, box, radius, props)];
                 case 1: return [2 /*return*/, _a.sent()];
@@ -41,8 +41,8 @@ function computeGaussianDensityTexture3d(position, box, radius, props, webgl, te
 exports.computeGaussianDensityTexture3d = computeGaussianDensityTexture3d;
 function _computeGaussianDensityTexture(type, position, box, radius, props, webgl, texture) {
     var _this = this;
-    return task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return task_1.Task.create('Gaussian Density', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, type === '2d' ?
                     (0, gpu_1.GaussianDensityTexture2d)(webgl, position, box, radius, false, props, texture) :
                     (0, gpu_1.GaussianDensityTexture3d)(webgl, position, box, radius, props, texture)];

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

@@ -44,12 +44,12 @@ function getAngleTables(probePositions) {
 //
 exports.MolecularSurfaceCalculationParams = {
     probeRadius: param_definition_1.ParamDefinition.Numeric(1.4, { min: 0, max: 10, step: 0.1 }, { description: 'Radius of the probe tracing the molecular surface.' }),
-    resolution: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.01, max: 20, step: 0.01 }, (0, tslib_1.__assign)({ description: 'Grid resolution/cell spacing.' }, base_1.BaseGeometry.CustomQualityParamInfo)),
-    probePositions: param_definition_1.ParamDefinition.Numeric(36, { min: 12, max: 90, step: 1 }, (0, tslib_1.__assign)({ description: 'Number of positions tested for probe target intersection.' }, base_1.BaseGeometry.CustomQualityParamInfo)),
+    resolution: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.01, max: 20, step: 0.01 }, tslib_1.__assign({ description: 'Grid resolution/cell spacing.' }, base_1.BaseGeometry.CustomQualityParamInfo)),
+    probePositions: param_definition_1.ParamDefinition.Numeric(36, { min: 12, max: 90, step: 1 }, tslib_1.__assign({ description: 'Number of positions tested for probe target intersection.' }, base_1.BaseGeometry.CustomQualityParamInfo)),
 };
 exports.DefaultMolecularSurfaceCalculationProps = param_definition_1.ParamDefinition.getDefaultValues(exports.MolecularSurfaceCalculationParams);
 function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         /**
          * Is the point at x,y,z obscured by any of the atoms specifeid by indices in neighbours.
          * Ignore indices a and b (these are the relevant atoms in projectPoints/Torii)
@@ -157,9 +157,9 @@ function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
             }
         }
         function projectPoints() {
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
                 var i;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             i = 0;
@@ -267,9 +267,9 @@ function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
             }
         }
         function projectTorii() {
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
                 var i;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             i = 0;
@@ -291,7 +291,7 @@ function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
             });
         }
         var lastClip, atob, mid, n1, n2, resolution, probeRadius, probePositions, scaleFactor, ngTorus, cellSize, lookup3d, neighbours, indices, px, py, pz, id, radius, n, pad, expandedBox, _a, minX, minY, minZ, scaledBox, dim, dimX, dimY, dimZ, iu, iv, iuv, _b, cosTable, sinTable, space, data, idData, gridx, gridy, gridz, updateChunk, field, idField, transform;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     lastClip = -1;

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

@@ -183,7 +183,7 @@ exports.Sphere3D = Sphere3D;
         linear_algebra_1.Vec3.copy(out.center, sphere.center);
         out.radius = Math.max(sphere.radius, linear_algebra_1.Vec3.distance(sphere.center, by.center) + by.radius);
         if (hasExtrema(sphere) && hasExtrema(by)) {
-            setExtrema(out, (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], sphere.extrema.map(function (e) { return linear_algebra_1.Vec3.clone(e); }), true), by.extrema.map(function (e) { return linear_algebra_1.Vec3.clone(e); }), true));
+            setExtrema(out, tslib_1.__spreadArray(tslib_1.__spreadArray([], sphere.extrema.map(function (e) { return linear_algebra_1.Vec3.clone(e); }), true), by.extrema.map(function (e) { return linear_algebra_1.Vec3.clone(e); }), true));
         }
         return out;
     }

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

@@ -7,11 +7,11 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./geometry/common"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/symmetry-operator"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/spacegroup/construction"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/lookup3d/common"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/lookup3d/grid"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/primitives/box3d"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/primitives/sphere3d"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/primitives/axes3d"), exports);
+tslib_1.__exportStar(require("./geometry/common"), exports);
+tslib_1.__exportStar(require("./geometry/symmetry-operator"), exports);
+tslib_1.__exportStar(require("./geometry/spacegroup/construction"), exports);
+tslib_1.__exportStar(require("./geometry/lookup3d/common"), exports);
+tslib_1.__exportStar(require("./geometry/lookup3d/grid"), exports);
+tslib_1.__exportStar(require("./geometry/primitives/box3d"), exports);
+tslib_1.__exportStar(require("./geometry/primitives/sphere3d"), exports);
+tslib_1.__exportStar(require("./geometry/primitives/axes3d"), exports);

package/lib/commonjs/mol-math/graph/inter-unit-graph.js

@@ -30,7 +30,7 @@ var InterUnitGraph = /** @class */ (function () {
                             vertexKeyIndex.set(vertexKey, [edges.length]);
                         else
                             e.push(edges.length);
-                        edges.push((0, tslib_1.__assign)((0, tslib_1.__assign)({}, edgeInfo), { indexA: indexA, unitA: unitA, unitB: unitB }));
+                        edges.push(tslib_1.__assign(tslib_1.__assign({}, edgeInfo), { indexA: indexA, unitA: unitA, unitB: unitB }));
                     });
                 });
             });

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

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./graph/int-adjacency-graph"), exports);
+tslib_1.__exportStar(require("./graph/int-adjacency-graph"), exports);

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

@@ -6,5 +6,5 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./linear-algebra/3d"), exports);
-(0, tslib_1.__exportStar)(require("./linear-algebra/tensor"), exports);
+tslib_1.__exportStar(require("./linear-algebra/3d"), exports);
+tslib_1.__exportStar(require("./linear-algebra/tensor"), exports);

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

@@ -15,7 +15,7 @@ var DefaultAlignmentOptions = {
 };
 function align(seqA, seqB, options) {
     if (options === void 0) { options = {}; }
-    var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultAlignmentOptions), options);
+    var o = tslib_1.__assign(tslib_1.__assign({}, DefaultAlignmentOptions), options);
     var alignment = new Alignment(seqA, seqB, o);
     alignment.calculate();
     return alignment.trace();

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

@@ -9,6 +9,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.Sequence = void 0;
 var constants_1 = require("./constants");
 var db_1 = require("../../mol-data/db");
+var type_helpers_1 = require("../../mol-util/type-helpers");
 var Sequence;
 (function (Sequence) {
     function getSequenceString(seq) {
@@ -43,7 +44,7 @@ var Sequence;
             case "generic" /* Generic */:
                 code = function () { return 'X'; };
                 break;
-            default: throw new Error("unknown kind '".concat(kind, "'"));
+            default: (0, type_helpers_1.assertUnreachable)(kind);
         }
         if (map && map.size > 0) {
             return function (name) {

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

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./sequence/sequence"), exports);
+tslib_1.__exportStar(require("./sequence/sequence"), exports);

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

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./shape/shape"), exports);
+tslib_1.__exportStar(require("./shape/shape"), exports);

package/lib/commonjs/mol-model/structure/coordinates.js

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./coordinates/coordinates"), exports);
+tslib_1.__exportStar(require("./coordinates/coordinates"), exports);

package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js

@@ -38,7 +38,7 @@ function compare_ssr(x, y) {
     return a.sheet_id < b.sheet_id ? -1 : a.sheet_id === b.sheet_id ? x.start.element - y.start.element : 1;
 }
 ;
-var struct_conf_fields = function () { return (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
+var struct_conf_fields = function () { return tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([
     CifField.str('conf_type_id', function (i, data) { return data[i].element.type_id; }),
     CifField.str('id', function (i, data, idx) { return "".concat(data[i].element.type_id).concat(idx + 1); })
 ], (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [
@@ -48,7 +48,7 @@ var struct_conf_fields = function () { return (0, tslib_1.__spreadArray)((0, tsl
     }),
     CifField.int('pdbx_PDB_helix_length', function (i, data) { return data[i].length; })
 ], false); };
-var struct_sheet_range_fields = function () { return (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
+var struct_sheet_range_fields = function () { return tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([
     CifField.str('sheet_id', function (i, data) { return data[i].element.sheet_id; }),
     CifField.index('id')
 ], (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [

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

@@ -33,7 +33,7 @@ var Model;
         var coarseGrained = isCoarseGrained(model);
         for (var i = 0, il = frames.length; i < il; ++i) {
             var f = frames[i];
-            var m = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, model), { id: uuid_1.UUID.create22(), modelNum: i, atomicConformation: coordinates_1.Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray), 
+            var m = tslib_1.__assign(tslib_1.__assign({}, model), { id: uuid_1.UUID.create22(), modelNum: i, atomicConformation: coordinates_1.Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray), 
                 // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates?
                 // coarseConformation: coarse.conformation,
                 customProperties: new custom_property_1.CustomProperties(), _staticPropertyData: Object.create(null), _dynamicPropertyData: Object.create(null) });
@@ -53,9 +53,9 @@ var Model;
     Model.trajectoryFromModelAndCoordinates = trajectoryFromModelAndCoordinates;
     function trajectoryFromTopologyAndCoordinates(topology, coordinates) {
         var _this = this;
-        return mol_task_1.Task.create('Create Trajectory', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Create Trajectory', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var models, model, trajectory, bondData, indexPairBonds, coarseGrained, index, _a, trajectory_2, m;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0: return [4 /*yield*/, (0, parser_1.createModels)(topology.basic, topology.sourceData, ctx)];
                     case 1:

package/lib/commonjs/mol-model/structure/model/properties/atomic.js

@@ -6,6 +6,6 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./atomic/conformation"), exports);
-(0, tslib_1.__exportStar)(require("./atomic/hierarchy"), exports);
-(0, tslib_1.__exportStar)(require("./atomic/measures"), exports);
+tslib_1.__exportStar(require("./atomic/conformation"), exports);
+tslib_1.__exportStar(require("./atomic/hierarchy"), exports);
+tslib_1.__exportStar(require("./atomic/measures"), exports);

package/lib/commonjs/mol-model/structure/model/properties/coarse.js

@@ -6,5 +6,5 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./coarse/conformation"), exports);
-(0, tslib_1.__exportStar)(require("./coarse/hierarchy"), exports);
+tslib_1.__exportStar(require("./coarse/conformation"), exports);
+tslib_1.__exportStar(require("./coarse/hierarchy"), exports);

package/lib/commonjs/mol-model/structure/model/types/saccharides.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+export declare const SaccharideNames: Set<string>;

package/lib/commonjs/mol-model/structure/model/types/saccharides.js

@@ -0,0 +1,11 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SaccharideNames = void 0;
+exports.SaccharideNames = new Set(['145', '147', '149', '289', '291', '293', '445', '475', '491', '510', '604', '045', '05L', '07E', '07Y', '08U', '09X', '0AT', '0BD', '0H0', '0HX', '0LP', '0MK', '0NZ', '0TS', '0UB', '0V4', '0WK', '0XY', '0YT', '10M', '12E', '14T', '15L', '16F', '16G', '16O', '17T', '18D', '18O', '18T', '1AR', '1BW', '1CF', '1FT', '1GL', '1GN', '1JB', '1LL', '1NA', '1S3', '1S4', '1SD', '1X4', '20S', '20X', '22O', '22S', '23V', '24S', '25E', '26M', '26O', '26Q', '26R', '26V', '26W', '26Y', '27C', '2DG', '2DR', '2F8', '2FG', '2FL', '2FP', '2GL', '2GS', '2H5', '2HA', '2M4', '2M5', '2M8', '2OS', '2WP', '2WS', '32O', '34V', '38J', '3BU', '3CM', '3DO', '3DY', '3FM', '3GR', '3HD', '3J3', '3J4', '3LJ', '3LR', '3MF', '3MG', '3MK', '3R3', '3S6', '3SA', '3YW', '40J', '42D', '44S', '46D', '46M', '46Z', '48Z', '49A', '49S', '49T', '49V', '4AM', '4CQ', '4GC', '4GL', '4GP', '4JA', '4N2', '4NN', '4QY', '4R1', '4RS', '4SG', '4U0', '4U1', '4U2', '4UZ', '4V5', '50A', '51N', '56N', '57S', '5DI', '5GF', '5GO', '5II', '5KQ', '5KS', '5KT', '5KV', '5L2', '5L3', '5LS', '5LT', '5MM', '5N6', '5QP', '5RP', '5SA', '5SP', '5TH', '5TJ', '5TK', '5TM', '61J', '62I', '64K', '66O', '6BG', '6C2', '6DM', '6GB', '6GP', '6GR', '6K3', '6KH', '6KL', '6KS', '6KU', '6KW', '6LA', '6LS', '6LW', '6MJ', '6MN', '6PG', '6PY', '6PZ', '6S2', '6SA', '6UD', '6Y6', '6YR', '6ZC', '73E', '79J', '7CV', '7D1', '7GP', '7JZ', '7K2', '7K3', '7NU', '7SA', '83Y', '89Y', '8B7', '8B9', '8EX', '8GA', '8GG', '8GP', '8LM', '8LR', '8OQ', '8PK', '8S0', '8YV', '95Z', '96O', '9AM', '9C1', '9CD', '9GP', '9KJ', '9MR', '9OK', '9PG', '9QG', '9QZ', '9S7', '9SG', '9SJ', '9SM', '9SP', '9T1', '9T7', '9VP', '9WJ', '9WN', '9WZ', '9YW', 'A0K', 'A1Q', 'A2G', 'A5C', 'A6P', 'AAL', 'AAO', 'ABC', 'ABD', 'ABE', 'ABF', 'ABL', 'AC1', 'ACG', 'ACR', 'ACX', 'ADA', 'ADG', 'ADR', 'AF1', 'AFD', 'AFL', 'AFO', 'AFP', 'AFR', 'AGC', 'AGH', 'AGL', 'AGR', 'AH2', 'AH8', 'AHG', 'AHM', 'AHR', 'AIG', 'ALL', 'ALX', 'AMG', 'AMN', 'AMU', 'AMV', 'ANA', 'AOG', 'AOS', 'AQA', 'ARA', 'ARB', 'ARE', 'ARI', 'ARW', 'ASC', 'ASG', 'ASO', 'AXP', 'AXR', 'AY9', 'AZC', 'B0D', 'B16', 'B1H', 'B1N', 'B2G', 'B4G', 'B6D', 'B7G', 'B8D', 'B9D', 'BBK', 'BBV', 'BCD', 'BCW', 'BDF', 'BDG', 'BDP', 'BDR', 'BDZ', 'BEM', 'BFN', 'BFP', 'BG6', 'BG8', 'BGC', 'BGL', 'BGN', 'BGP', 'BGS', 'BHG', 'BM3', 'BM7', 'BMA', 'BMX', 'BND', 'BNG', 'BNX', 'BO1', 'BOG', 'BQY', 'BRI', 'BS7', 'BTG', 'BTU', 'BWG', 'BXF', 'BXP', 'BXX', 'BXY', 'BZD', 'C3B', 'C3G', 'C3X', 'C4B', 'C4W', 'C4X', 'C5X', 'CAP', 'CBF', 'CBI', 'CBK', 'CDR', 'CE5', 'CE6', 'CE8', 'CEG', 'CEX', 'CEY', 'CEZ', 'CGF', 'CJB', 'CKB', 'CKP', 'CNP', 'CR1', 'CR6', 'CRA', 'CT3', 'CTO', 'CTR', 'CTT', 'D0N', 'D1M', 'D5E', 'D6G', 'DAF', 'DAG', 'DAN', 'DDA', 'DDB', 'DDL', 'DEG', 'DEL', 'DFR', 'DFX', 'DG0', 'DGC', 'DGD', 'DGM', 'DGO', 'DGS', 'DGU', 'DIG', 'DJB', 'DJE', 'DK4', 'DKX', 'DKZ', 'DL6', 'DLD', 'DLF', 'DLG', 'DMU', 'DNO', 'DO8', 'DOM', 'DP5', 'DPC', 'DQQ', 'DQR', 'DR2', 'DR3', 'DR4', 'DR5', 'DRI', 'DSR', 'DT6', 'DVC', 'DYM', 'E3M', 'E4P', 'E5G', 'EAG', 'EBG', 'EBQ', 'EEN', 'EEQ', 'EGA', 'EJT', 'EMP', 'EMZ', 'EPG', 'EQP', 'EQV', 'ERE', 'ERI', 'ETT', 'EUS', 'F1P', 'F1X', 'F55', 'F58', 'F6P', 'F8X', 'FBP', 'FCA', 'FCB', 'FCT', 'FDP', 'FDQ', 'FFC', 'FFX', 'FIF', 'FIX', 'FK9', 'FKD', 'FMF', 'FMO', 'FNG', 'FNY', 'FRU', 'FSA', 'FSI', 'FSM', 'FSR', 'FSW', 'FU4', 'FUB', 'FUC', 'FUD', 'FUF', 'FUL', 'FUY', 'FVQ', 'FX1', 'FYJ', 'G0S', 'G16', 'G1P', 'G20', 'G28', 'G2F', 'G3F', 'G3I', 'G4D', 'G4S', 'G6D', 'G6P', 'G6S', 'G7P', 'G8Z', 'GAA', 'GAC', 'GAD', 'GAF', 'GAL', 'GAT', 'GBH', 'GC1', 'GC4', 'GC9', 'GCB', 'GCD', 'GCN', 'GCO', 'GCS', 'GCT', 'GCU', 'GCV', 'GCW', 'GDA', 'GDL', 'GE1', 'GE3', 'GFP', 'GIV', 'GL0', 'GL1', 'GL2', 'GL4', 'GL5', 'GL6', 'GL7', 'GL9', 'GLA', 'GLB', 'GLC', 'GLD', 'GLF', 'GLG', 'GLO', 'GLP', 'GLS', 'GLT', 'GLW', 'GM0', 'GMB', 'GMH', 'GMT', 'GMZ', 'GN1', 'GN4', 'GNS', 'GNX', 'GP0', 'GP1', 'GP4', 'GPH', 'GPK', 'GPM', 'GPO', 'GPQ', 'GPU', 'GPV', 'GPW', 'GQ1', 'GRF', 'GRX', 'GS1', 'GS4', 'GS9', 'GSA', 'GSD', 'GTE', 'GTH', 'GTK', 'GTM', 'GTR', 'GU0', 'GU1', 'GU2', 'GU3', 'GU4', 'GU5', 'GU6', 'GU8', 'GU9', 'GUF', 'GUL', 'GUP', 'GUZ', 'GXL', 'GXV', 'GYE', 'GYG', 'GYP', 'GYU', 'GYV', 'GZL', 'H1M', 'H1S', 'H2P', 'H3S', 'H53', 'H6Q', 'H6Z', 'HBZ', 'HD4', 'HDL', 'HMS', 'HNV', 'HNW', 'HSG', 'HSH', 'HSJ', 'HSQ', 'HSR', 'HSU', 'HSX', 'HSY', 'HSZ', 'HTG', 'HTM', 'I57', 'IAB', 'IDC', 'IDF', 'IDG', 'IDR', 'IDS', 'IDT', 'IDU', 'IDX', 'IDY', 'IEM', 'IN1', 'IPT', 'ISD', 'ISL', 'ISX', 'IXD', 'J5B', 'JFZ', 'JHM', 'JLT', 'JRV', 'JS2', 'JSV', 'JV4', 'JVA', 'JVS', 'JZR', 'K5B', 'K99', 'KBA', 'KBG', 'KD5', 'KDA', 'KDB', 'KDD', 'KDE', 'KDF', 'KDM', 'KDN', 'KDO', 'KDR', 'KFN', 'KG1', 'KGM', 'KHP', 'KME', 'KO1', 'KO2', 'KOT', 'KTU', 'L1L', 'L6S', 'L6T', 'LAG', 'LAH', 'LAI', 'LAK', 'LAO', 'LAT', 'LB2', 'LBS', 'LBT', 'LCN', 'LDY', 'LEC', 'LER', 'LFC', 'LFR', 'LGC', 'LGU', 'LKA', 'LKS', 'LM2', 'LMO', 'LMT', 'LMU', 'LNV', 'LOG', 'LOX', 'LPK', 'LRH', 'LSM', 'LTG', 'LTM', 'LVO', 'LVZ', 'LXB', 'LXC', 'LXZ', 'LZ0', 'M1F', 'M1P', 'M2F', 'M3M', 'M3N', 'M55', 'M6D', 'M6P', 'M7B', 'M7P', 'M8C', 'MA1', 'MA2', 'MA3', 'MA8', 'MAB', 'MAF', 'MAG', 'MAL', 'MAN', 'MAT', 'MAV', 'MAW', 'MBE', 'MBF', 'MBG', 'MCU', 'MDA', 'MDP', 'MFA', 'MFB', 'MFU', 'MG5', 'MGA', 'MGC', 'MGL', 'MGS', 'MJJ', 'MLB', 'MLR', 'MMA', 'MMN', 'MN0', 'MNA', 'MQG', 'MQT', 'MRH', 'MRP', 'MSX', 'MTT', 'MUB', 'MUG', 'MUR', 'MVP', 'MXY', 'MXZ', 'MYG', 'N1L', 'N9S', 'NA1', 'NAA', 'NAG', 'NBG', 'NBX', 'NBY', 'NDG', 'NED', 'NFG', 'NG1', 'NG6', 'NGA', 'NGB', 'NGC', 'NGE', 'NGF', 'NGK', 'NGL', 'NGR', 'NGS', 'NGY', 'NGZ', 'NHF', 'NLC', 'NM6', 'NM9', 'NNG', 'NPF', 'NSQ', 'NT1', 'NTF', 'NTO', 'NTP', 'NXD', 'NYT', 'O1G', 'OAK', 'OEL', 'OI7', 'OPM', 'ORP', 'OSU', 'OTG', 'OTN', 'OTU', 'OX2', 'P53', 'P6P', 'P8E', 'PA1', 'PA5', 'PAV', 'PDX', 'PH5', 'PKM', 'PNA', 'PNG', 'PNJ', 'PNW', 'PPC', 'PRP', 'PSG', 'PSJ', 'PSV', 'PTQ', 'PUF', 'PZU', 'QDK', 'QIF', 'QKH', 'QPS', 'QV4', 'R1P', 'R1X', 'R2B', 'R2G', 'R5P', 'RAA', 'RAE', 'RAF', 'RAM', 'RAO', 'RAT', 'RB5', 'RBL', 'RCD', 'RDP', 'REL', 'RER', 'RF5', 'RG1', 'RGG', 'RHA', 'RHC', 'RI2', 'RIB', 'RIP', 'RM4', 'RNS', 'RNT', 'ROB', 'ROR', 'RP3', 'RP5', 'RP6', 'RPA', 'RR7', 'RRJ', 'RRY', 'RST', 'RTG', 'RTV', 'RUB', 'RUG', 'RUU', 'RV7', 'RVG', 'RVM', 'RWI', 'RY7', 'RZM', 'S6P', 'S7P', 'S81', 'SA0', 'SCG', 'SCR', 'SDD', 'SDY', 'SEJ', 'SF6', 'SF9', 'SFJ', 'SFU', 'SG4', 'SG5', 'SG6', 'SG7', 'SGA', 'SGC', 'SGD', 'SGN', 'SGS', 'SHB', 'SHD', 'SHG', 'SI3', 'SIA', 'SID', 'SIO', 'SIZ', 'SLB', 'SLM', 'SLT', 'SMD', 'SN5', 'SNG', 'SOE', 'SOG', 'SOL', 'SOR', 'SR1', 'SSG', 'SSH', 'STW', 'STZ', 'SUC', 'SUP', 'SUS', 'SWE', 'SZZ', 'T68', 'T6D', 'T6P', 'T6T', 'TA6', 'TAG', 'TCB', 'TCG', 'TDG', 'TEU', 'TF0', 'TFU', 'TGA', 'TGK', 'TGR', 'TGY', 'TH1', 'TM5', 'TM6', 'TM9', 'TMR', 'TMX', 'TNX', 'TOA', 'TOC', 'TQY', 'TRE', 'TRV', 'TS8', 'TT7', 'TTV', 'TTZ', 'TU4', 'TUG', 'TUJ', 'TUP', 'TUR', 'TVD', 'TVG', 'TVM', 'TVS', 'TVV', 'TVY', 'TW7', 'TWA', 'TWD', 'TWG', 'TWJ', 'TWY', 'TXB', 'TYV', 'U1Y', 'U2A', 'U2D', 'U63', 'U8V', 'U97', 'U9A', 'U9D', 'U9G', 'U9J', 'U9M', 'UAP', 'UCD', 'UDC', 'UEA', 'V3M', 'V3P', 'V71', 'VG1', 'VJ1', 'VJ4', 'VKN', 'VTB', 'W9T', 'WIA', 'WOO', 'WUN', 'WZ1', 'WZ2', 'WZ4', 'X0X', 'X1P', 'X1X', 'X2F', 'X2Y', 'X34', 'X4S', 'X5S', 'X6X', 'X6Y', 'XBP', 'XDP', 'XDX', 'XGP', 'XIL', 'XKJ', 'XLF', 'XLS', 'XMM', 'XS2', 'XUL', 'XXM', 'XXR', 'XXX', 'XYB', 'XYF', 'XYL', 'XYP', 'XYS', 'XYT', 'XYZ', 'YDR', 'YIO', 'YJM', 'YKR', 'YO5', 'YX0', 'YX1', 'YYB', 'YYH', 'YYJ', 'YYK', 'YYM', 'YYQ', 'YYR', 'YZ0', 'Z0F', 'Z15', 'Z16', 'Z2D', 'Z2T', 'Z3K', 'Z3L', 'Z3Q', 'Z3U', 'Z4K', 'Z4R', 'Z4S', 'Z4U', 'Z4V', 'Z4W', 'Z4Y', 'Z57', 'Z5J', 'Z5L', 'Z61', 'Z6H', 'Z6J', 'Z6W', 'Z8H', 'Z8T', 'Z9D', 'Z9E', 'Z9H', 'Z9K', 'Z9L', 'Z9M', 'Z9N', 'Z9W', 'ZB0', 'ZB1', 'ZB2', 'ZB3', 'ZCD', 'ZCZ', 'ZD0', 'ZDC', 'ZDM', 'ZDO', 'ZEE', 'ZEL', 'ZGE', 'ZMR', 'UMQ', 'SQD']);

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

@@ -9,11 +9,11 @@ exports.StructureSequence = exports.Symmetry = exports.Types = exports.Model = v
 var tslib_1 = require("tslib");
 var model_1 = require("./model/model");
 Object.defineProperty(exports, "Model", { enumerable: true, get: function () { return model_1.Model; } });
-var Types = (0, tslib_1.__importStar)(require("./model/types"));
+var Types = tslib_1.__importStar(require("./model/types"));
 exports.Types = Types;
 var symmetry_1 = require("./model/properties/symmetry");
 Object.defineProperty(exports, "Symmetry", { enumerable: true, get: function () { return symmetry_1.Symmetry; } });
 var sequence_1 = require("./model/properties/sequence");
 Object.defineProperty(exports, "StructureSequence", { enumerable: true, get: function () { return sequence_1.StructureSequence; } });
-(0, tslib_1.__exportStar)(require("./model/properties/custom/indexed"), exports);
-(0, tslib_1.__exportStar)(require("./model/indexing"), exports);
+tslib_1.__exportStar(require("./model/properties/custom/indexed"), exports);
+tslib_1.__exportStar(require("./model/indexing"), exports);

package/lib/commonjs/mol-model/structure/query/queries/generators.js

@@ -19,9 +19,9 @@ var none = function (ctx) { return selection_1.StructureSelection.Sequence(ctx.i
 exports.none = none;
 var all = function (ctx) { return selection_1.StructureSelection.Singletons(ctx.inputStructure, ctx.inputStructure); };
 exports.all = all;
-function residues(params) { return atoms((0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { groupBy: function (ctx) { return structure_1.StructureProperties.residue.key(ctx.element); } })); }
+function residues(params) { return atoms(tslib_1.__assign(tslib_1.__assign({}, params), { groupBy: function (ctx) { return structure_1.StructureProperties.residue.key(ctx.element); } })); }
 exports.residues = residues;
-function chains(params) { return atoms((0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { groupBy: function (ctx) { return structure_1.StructureProperties.chain.key(ctx.element); } })); }
+function chains(params) { return atoms(tslib_1.__assign(tslib_1.__assign({}, params), { groupBy: function (ctx) { return structure_1.StructureProperties.chain.key(ctx.element); } })); }
 exports.chains = chains;
 function _true(ctx) { return true; }
 function _zero(ctx) { return 0; }

package/lib/commonjs/mol-model/structure/query/queries/modifiers.js

@@ -129,7 +129,7 @@ function includeSurroundings(query, params) {
     return function query_includeSurroundings(ctx) {
         var inner = query(ctx);
         if (params.elementRadius) {
-            var prms = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { elementRadius: params.elementRadius, elementRadiusClosure: createElementRadiusFn(ctx, params.elementRadius), sourceMaxRadius: findStructureRadius(ctx, params.elementRadius) });
+            var prms = tslib_1.__assign(tslib_1.__assign({}, params), { elementRadius: params.elementRadius, elementRadiusClosure: createElementRadiusFn(ctx, params.elementRadius), sourceMaxRadius: findStructureRadius(ctx, params.elementRadius) });
             if (selection_1.StructureSelection.isSingleton(inner)) {
                 var surr = getIncludeSurroundingsWithRadius(ctx, ctx.inputStructure, inner.structure, prms);
                 var ret = selection_1.StructureSelection.Singletons(ctx.inputStructure, surr);
@@ -600,7 +600,7 @@ var StructConnGraph = /** @class */ (function () {
                 added.add(b);
                 var v = this.vertices.get(b);
                 if (u.operator_name === v.operator_name) {
-                    set.add((0, tslib_1.__assign)((0, tslib_1.__assign)({}, v), { operator_name: start.operator_name }));
+                    set.add(tslib_1.__assign(tslib_1.__assign({}, v), { operator_name: start.operator_name }));
                 }
                 else {
                     set.add(v);

package/lib/commonjs/mol-model/structure/query.js

@@ -11,12 +11,12 @@ var selection_1 = require("./query/selection");
 Object.defineProperty(exports, "StructureSelection", { enumerable: true, get: function () { return selection_1.StructureSelection; } });
 var query_1 = require("./query/query");
 Object.defineProperty(exports, "StructureQuery", { enumerable: true, get: function () { return query_1.StructureQuery; } });
-(0, tslib_1.__exportStar)(require("./query/context"), exports);
-var generators = (0, tslib_1.__importStar)(require("./query/queries/generators"));
-var modifiers = (0, tslib_1.__importStar)(require("./query/queries/modifiers"));
-var filters = (0, tslib_1.__importStar)(require("./query/queries/filters"));
-var combinators = (0, tslib_1.__importStar)(require("./query/queries/combinators"));
-var internal = (0, tslib_1.__importStar)(require("./query/queries/internal"));
+tslib_1.__exportStar(require("./query/context"), exports);
+var generators = tslib_1.__importStar(require("./query/queries/generators"));
+var modifiers = tslib_1.__importStar(require("./query/queries/modifiers"));
+var filters = tslib_1.__importStar(require("./query/queries/filters"));
+var combinators = tslib_1.__importStar(require("./query/queries/combinators"));
+var internal = tslib_1.__importStar(require("./query/queries/internal"));
 var predicates_1 = require("./query/predicates");
 exports.Queries = {
     generators: generators,

package/lib/commonjs/mol-model/structure/structure/carbohydrates/compute.js

@@ -304,7 +304,7 @@ function computeCarbohydrates(structure) {
             });
         });
     }
-    return (0, tslib_1.__assign)({ links: links, terminalLinks: terminalLinks, elements: elements, partialElements: partialElements }, buildLookups(elements, links, terminalLinks));
+    return tslib_1.__assign({ links: links, terminalLinks: terminalLinks, elements: elements, partialElements: partialElements }, buildLookups(elements, links, terminalLinks));
 }
 exports.computeCarbohydrates = computeCarbohydrates;
 function buildLookups(elements, links, terminalLinks) {

package/lib/commonjs/mol-model/structure/structure/carbohydrates/constants.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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/commonjs/mol-model/structure/structure/carbohydrates/constants.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -9,6 +9,7 @@ var _a, _b;
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SaccharideCompIdMap = exports.MonosaccharidesColorTable = exports.SaccharidesSnfgMap = exports.UnknownSaccharideComponent = exports.getSaccharideShape = exports.getSaccharideName = exports.SaccharideColors = void 0;
 var color_1 = require("../../../../mol-util/color");
+var saccharides_1 = require("../../model/types/saccharides");
 exports.SaccharideColors = (0, color_1.ColorMap)({
     Blue: 0x0090bc,
     Green: 0x00a651,
@@ -267,11 +268,6 @@ var CommonSaccharideNames = {
     Sor: ['SOE', 'UEA'],
     Psi: ['PSV', 'SF6', 'SF9', 'TTV'],
 };
-var UnknownSaccharideNames = [
-    'NGZ',
-    'LAT',
-    'PUF', 'GDA', '9WJ', // via updated CCD
-];
 /**
  * From http://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/#CHARMM
  */
@@ -314,8 +310,9 @@ exports.SaccharideCompIdMap = (function () {
             }
         }
     }
-    for (var i = 0, il = UnknownSaccharideNames.length; i < il; ++i) {
-        map.set(UnknownSaccharideNames[i], exports.UnknownSaccharideComponent);
-    }
+    saccharides_1.SaccharideNames.forEach(function (name) {
+        if (!map.has(name))
+            map.set(name, exports.UnknownSaccharideComponent);
+    });
     return map;
 })();

package/lib/commonjs/mol-model/structure/structure/element/element.js

@@ -7,8 +7,8 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./location"), exports);
-(0, tslib_1.__exportStar)(require("./loci"), exports);
-(0, tslib_1.__exportStar)(require("./bundle"), exports);
-(0, tslib_1.__exportStar)(require("./stats"), exports);
-(0, tslib_1.__exportStar)(require("./util"), exports);
+tslib_1.__exportStar(require("./location"), exports);
+tslib_1.__exportStar(require("./loci"), exports);
+tslib_1.__exportStar(require("./bundle"), exports);
+tslib_1.__exportStar(require("./stats"), exports);
+tslib_1.__exportStar(require("./util"), exports);

package/lib/commonjs/mol-model/structure/structure/element.js

@@ -8,5 +8,5 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.StructureElement = void 0;
 var tslib_1 = require("tslib");
-var StructureElement = (0, tslib_1.__importStar)(require("./element/element"));
+var StructureElement = tslib_1.__importStar(require("./element/element"));
 exports.StructureElement = StructureElement;

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

@@ -514,7 +514,7 @@ var Structure = /** @class */ (function () {
         if (this.parent) {
             var p = this.parent.coordinateSystem.isIdentity ? this.parent : Structure.transform(this.parent, this.parent.coordinateSystem.inverse);
             var s = this.coordinateSystem.isIdentity ? p : Structure.transform(p, this.coordinateSystem.matrix);
-            this._proxy = new Structure(s.units, s.unitMap, s.unitIndexMap, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, s.state), { dynamicBonds: this.dynamicBonds }), { child: this, target: this.parent });
+            this._proxy = new Structure(s.units, s.unitMap, s.unitIndexMap, tslib_1.__assign(tslib_1.__assign({}, s.state), { dynamicBonds: this.dynamicBonds }), { child: this, target: this.parent });
         }
         else {
             this._proxy = this;
@@ -822,9 +822,9 @@ function getSerialMapping(structure) {
     }
     Structure.create = create;
     function ofTrajectory(trajectory, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var units, first, count, i, il, frame, structure, j, jl, u, invariantId, chainGroupId, newUnit;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         if (trajectory.frameCount === 0)
@@ -873,7 +873,7 @@ function getSerialMapping(structure) {
         var index = model.atomicHierarchy.index;
         var auth_asym_id = model.atomicHierarchy.chains.auth_asym_id;
         var atomicChainOperatorMappinng = model.atomicChainOperatorMappinng;
-        var builder = new StructureBuilder((0, tslib_1.__assign)({ label: model.label }, props));
+        var builder = new StructureBuilder(tslib_1.__assign({ label: model.label }, props));
         for (var c = 0; c < chains.count; c++) {
             var operator = atomicChainOperatorMappinng.get(c) || symmetry_operator_1.SymmetryOperator.Default;
             var start = chains.offsets[c];
@@ -1362,7 +1362,7 @@ function getSerialMapping(structure) {
     function getSize(structure, thresholds, residueCountFactor) {
         if (thresholds === void 0) { thresholds = {}; }
         if (residueCountFactor === void 0) { residueCountFactor = 1; }
-        var t = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, Structure.DefaultSizeThresholds), thresholds);
+        var t = tslib_1.__assign(tslib_1.__assign({}, Structure.DefaultSizeThresholds), thresholds);
         if (structure.polymerResidueCount >= t.largeResidueCount * residueCountFactor) {
             if (hasHighSymmetry(structure, t)) {
                 return Size.Huge;