molstar 3.3.0 → 3.5.0

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

@@ -0,0 +1,46 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.coordinatesFromTrr = void 0;
+var tslib_1 = require("tslib");
+var mol_task_1 = require("../../mol-task");
+var coordinates_1 = require("../../mol-model/structure/coordinates");
+var cell_1 = require("../../mol-math/geometry/spacegroup/cell");
+var linear_algebra_1 = require("../../mol-math/linear-algebra");
+function coordinatesFromTrr(file) {
+    var _this = this;
+    return mol_task_1.Task.create('Parse TRR', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var deltaTime, offsetTime, frames, i, il, box, x, y, z;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
+                case 1:
+                    _a.sent();
+                    deltaTime = (0, coordinates_1.Time)(file.deltaTime, 'step');
+                    offsetTime = (0, coordinates_1.Time)(file.timeOffset, deltaTime.unit);
+                    frames = [];
+                    for (i = 0, il = file.frames.length; i < il; ++i) {
+                        box = file.boxes[i];
+                        x = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 0);
+                        y = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 3);
+                        z = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 6);
+                        frames.push({
+                            elementCount: file.frames[i].count,
+                            cell: cell_1.Cell.fromBasis(x, y, z),
+                            x: file.frames[i].x,
+                            y: file.frames[i].y,
+                            z: file.frames[i].z,
+                            xyzOrdering: { isIdentity: true },
+                            time: (0, coordinates_1.Time)(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+                        });
+                    }
+                    return [2 /*return*/, coordinates_1.Coordinates.create(frames, deltaTime, offsetTime)];
+            }
+        });
+    }); });
+}
+exports.coordinatesFromTrr = coordinatesFromTrr;

package/lib/commonjs/mol-model-formats/structure/util.d.ts

@@ -1,8 +1,8 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Tokens } from '../../mol-io/reader/common/text/tokenizer';
 export declare function guessElementSymbolTokens(tokens: Tokens, str: string, start: number, end: number): void;
-export declare function guessElementSymbolString(str: string): string;
+export declare function guessElementSymbolString(atomId: string, compId: string): string;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -44,35 +44,34 @@ function guessElementSymbolTokens(tokens, str, start, end) {
     tokenizer_1.TokenBuilder.add(tokens, s, s); // no reasonable guess, add empty token
 }
 exports.guessElementSymbolTokens = guessElementSymbolTokens;
+var TwoCharElementNames = new Set(['NA', 'CL', 'FE', 'SI', 'BR', 'AS']);
+var OneCharElementNames = new Set(['C', 'H', 'N', 'O', 'P', 'S']);
 var reTrimSpacesAndNumbers = /^[\s\d]+|[\s\d]+$/g;
-function guessElementSymbolString(str) {
+function guessElementSymbolString(atomId, compId) {
     // trim spaces and numbers, convert to upper case
-    str = str.replace(reTrimSpacesAndNumbers, '').toUpperCase();
-    var l = str.length;
+    atomId = atomId.replace(reTrimSpacesAndNumbers, '').toUpperCase();
+    var l = atomId.length;
     if (l === 0)
-        return str; // empty
+        return atomId; // empty
     if (l === 1)
-        return str; // one char
-    if (l === 2) { // two chars
-        if (str === 'NA' || str === 'CL' || str === 'FE' || str === 'SI' ||
-            str === 'BR' || str === 'AS')
-            return str;
-    }
-    if (l === 3) { // three chars
-        if (str === 'SOD')
+        return atomId; // one char
+    if (TwoCharElementNames.has(atomId))
+        return atomId; // two chars
+    // check for Charmm ion names where component and atom id are the same
+    if (l === 3 && compId === atomId) {
+        if (atomId === 'SOD')
             return 'NA';
-        if (str === 'POT')
+        if (atomId === 'POT')
             return 'K';
-        if (str === 'CES')
+        if (atomId === 'CES')
             return 'CS';
-        if (str === 'CAL')
+        if (atomId === 'CAL')
             return 'CA';
-        if (str === 'CLA')
+        if (atomId === 'CLA')
             return 'CL';
     }
-    var c = str[0];
-    if (c === 'C' || c === 'H' || c === 'N' || c === 'O' || c === 'P' || c === 'S')
-        return c;
+    if (OneCharElementNames.has(atomId[0]))
+        return atomId[0];
     return ''; // no reasonable guess, return empty string
 }
 exports.guessElementSymbolString = guessElementSymbolString;

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

@@ -14,9 +14,9 @@ var cell_1 = require("../../mol-math/geometry/spacegroup/cell");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 function coordinatesFromXtc(file) {
     var _this = this;
-    return mol_task_1.Task.create('Parse XTC', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse XTC', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var deltaTime, offsetTime, frames, i, il, box, x, y, z;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
                 case 1:

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

@@ -66,12 +66,12 @@ function getModels(mol, ctx) {
     var componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
     componentBuilder.add('MOL', 0);
-    var basics = (0, schema_1.createBasic)({
+    var basic = (0, schema_1.createBasic)({
         entity: entityBuilder.getEntityTable(),
         chem_comp: componentBuilder.getChemCompTable(),
         atom_site: atom_site
     });
-    return (0, parser_1.createModels)(basics, XyzFormat.create(mol), ctx);
+    return (0, parser_1.createModels)(basic, XyzFormat.create(mol), ctx);
 }
 var XyzFormat;
 (function (XyzFormat) {

package/lib/commonjs/mol-model-formats/volume/ccp4.js

@@ -37,9 +37,9 @@ function getTypedArrayCtor(header) {
 }
 function volumeFromCcp4(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, values, size, angles, spacegroup, cell, axis_order_fast_to_slow, normalizeOrder, grid, extent, origin, gridOrigin, origin_frac, dimensions_frac, space, data, calcStats;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             header = source.header, values = source.values;
             size = linear_algebra_1.Vec3.create(header.xLength, header.yLength, header.zLength);
             if (params && params.voxelSize)

package/lib/commonjs/mol-model-formats/volume/cube.js

@@ -13,9 +13,9 @@ var array_1 = require("../../mol-util/array");
 var custom_property_1 = require("../../mol-model/custom-property");
 function volumeFromCube(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, sourceValues, space, values, _a, h, k, l, nth, o, s, u, v, w, data, matrix, basis;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             header = source.header, sourceValues = source.values;
             space = linear_algebra_1.Tensor.Space(header.dim, [0, 1, 2], Float64Array);
             if (header.dataSetIds.length === 0) {

package/lib/commonjs/mol-model-formats/volume/density-server.js

@@ -13,9 +13,9 @@ var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var custom_property_1 = require("../../mol-model/custom-property");
 function volumeFromDensityServerData(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var info, values, cell, axis_order_fast_to_slow, normalizeOrder, sample_count, tensorSpace, data, origin, dimensions;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             info = source.volume_data_3d_info, values = source.volume_data_3d;
             cell = geometry_1.SpacegroupCell.create(info.spacegroup_number.value(0), linear_algebra_1.Vec3.ofArray(info.spacegroup_cell_size.value(0)), linear_algebra_1.Vec3.scale(linear_algebra_1.Vec3.zero(), linear_algebra_1.Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180));
             axis_order_fast_to_slow = info.axis_order.value(0);

package/lib/commonjs/mol-model-formats/volume/dsn6.js

@@ -15,9 +15,9 @@ var array_1 = require("../../mol-util/array");
 var custom_property_1 = require("../../mol-model/custom-property");
 function volumeFromDsn6(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, values, size, angles, cell, grid, extent, gridOrigin, origin_frac, dimensions_frac, space, data;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             header = source.header, values = source.values;
             size = linear_algebra_1.Vec3.create(header.xlen, header.ylen, header.zlen);
             if (params && params.voxelSize)

package/lib/commonjs/mol-model-formats/volume/dx.js

@@ -13,9 +13,9 @@ var array_1 = require("../../mol-util/array");
 var custom_property_1 = require("../../mol-model/custom-property");
 function volumeFromDx(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, values, space, data, matrix, basis;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             header = source.header, values = source.values;
             space = linear_algebra_1.Tensor.Space(header.dim, [0, 1, 2], Float64Array);
             data = linear_algebra_1.Tensor.create(space, linear_algebra_1.Tensor.Data1(values));

package/lib/commonjs/mol-model-props/common/custom-element-property.js

@@ -35,8 +35,8 @@ var CustomElementProperty;
             defaultParams: {},
             getParams: function (data) { return ({}); },
             isApplicable: function (data) { return !builder.isApplicable || !!builder.isApplicable(data); },
-            obtain: function (ctx, data) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                return (0, tslib_1.__generator)(this, function (_a) {
+            obtain: function (ctx, data) { 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*/, builder.getData(data, ctx)];
                         case 1: return [2 /*return*/, _a.sent()];

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

@@ -20,7 +20,7 @@ var CustomModelProperty;
         var get = function (data) {
             if (!(descriptorName in data[propertyDataName])) {
                 data[propertyDataName][descriptorName] = {
-                    props: (0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(builder.getParams(data))),
+                    props: tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(builder.getParams(data))),
                     data: mol_util_1.ValueBox.create(undefined)
                 };
             }
@@ -46,9 +46,9 @@ var CustomModelProperty;
             isApplicable: builder.isApplicable,
             attach: function (ctx, data, props, addRef) {
                 if (props === void 0) { props = {}; }
-                return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return tslib_1.__awaiter(_this, void 0, void 0, function () {
                     var property, p, _a, value, assets;
-                    return (0, tslib_1.__generator)(this, function (_b) {
+                    return tslib_1.__generator(this, function (_b) {
                         switch (_b.label) {
                             case 0:
                                 if (addRef)
@@ -96,9 +96,9 @@ var CustomModelProperty;
             defaultParams: defaultParams,
             getParams: function () { return ({ value: param_definition_1.ParamDefinition.Value(defaultValue, { isHidden: true }) }); },
             isApplicable: function () { return true; },
-            obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            obtain: function (ctx, data, props) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var _a;
-                return (0, tslib_1.__generator)(this, function (_b) {
+                return tslib_1.__generator(this, function (_b) {
                     return [2 /*return*/, { value: (_a = props.value) !== null && _a !== void 0 ? _a : defaultValue }];
                 });
             }); }

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

@@ -36,7 +36,7 @@ var CustomProperty;
                             autoAttachDefault.push(provider.descriptor.name);
                         }
                     }
-                    propertiesParams[provider.descriptor.name] = param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({}, provider.getParams(data)), { label: provider.label, isHidden: provider.isHidden });
+                    propertiesParams[provider.descriptor.name] = param_definition_1.ParamDefinition.Group(tslib_1.__assign({}, provider.getParams(data)), { label: provider.label, isHidden: provider.isHidden });
                 }
             }
             return {

package/lib/commonjs/mol-model-props/common/custom-structure-property.js

@@ -20,7 +20,7 @@ var CustomStructureProperty;
         var get = function (data) {
             if (!(descriptorName in data[propertyDataName])) {
                 data[propertyDataName][descriptorName] = {
-                    props: (0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(builder.getParams(data))),
+                    props: tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(builder.getParams(data))),
                     data: mol_util_1.ValueBox.create(undefined)
                 };
             }
@@ -46,9 +46,9 @@ var CustomStructureProperty;
             isApplicable: builder.isApplicable,
             attach: function (ctx, data, props, addRef) {
                 if (props === void 0) { props = {}; }
-                return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return tslib_1.__awaiter(_this, void 0, void 0, function () {
                     var rootProps, property, p, _a, value, assets;
-                    return (0, tslib_1.__generator)(this, function (_b) {
+                    return tslib_1.__generator(this, function (_b) {
                         switch (_b.label) {
                             case 0:
                                 if (addRef)
@@ -101,9 +101,9 @@ var CustomStructureProperty;
             defaultParams: defaultParams,
             getParams: function () { return ({ value: param_definition_1.ParamDefinition.Value(defaultValue, { isHidden: true }) }); },
             isApplicable: function () { return true; },
-            obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                return (0, tslib_1.__generator)(this, function (_a) {
-                    return [2 /*return*/, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(defaultParams)), props)];
+            obtain: function (ctx, data, props) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                return tslib_1.__generator(this, function (_a) {
+                    return [2 /*return*/, tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(defaultParams)), props)];
                 });
             }); }
         });

package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js

@@ -16,9 +16,9 @@ var common_1 = require("./common");
 // - factor serialResidueIndex out
 var updateChunk = 5000;
 function computeArea(runtime, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var atomRadius, i;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     atomRadius = ctx.atomRadiusType;

package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js

@@ -33,9 +33,9 @@ var AccessibleSurfaceArea;
     function compute(structure, props) {
         var _this = this;
         if (props === void 0) { props = {}; }
-        var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ShrakeRupleyComputationParams)), props);
-        return mol_task_1.Task.create('Compute Accessible Surface Area', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        var p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ShrakeRupleyComputationParams)), props);
+        return mol_task_1.Task.create('Compute Accessible Surface Area', function (runtime) { 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*/, calculate(runtime, structure, p)];
                     case 1: return [2 /*return*/, _a.sent()];
@@ -45,9 +45,9 @@ var AccessibleSurfaceArea;
     }
     AccessibleSurfaceArea.compute = compute;
     function calculate(runtime, structure, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var ctx, area, serialResidueIndex;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         ctx = initialize(structure, props);

package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js

@@ -16,7 +16,7 @@ var compiler_1 = require("../../mol-script/runtime/query/compiler");
 var symbol_1 = require("../../mol-script/language/symbol");
 var type_1 = require("../../mol-script/language/type");
 var custom_property_1 = require("../../mol-model/custom-property");
-exports.AccessibleSurfaceAreaParams = (0, tslib_1.__assign)({}, shrake_rupley_1.ShrakeRupleyComputationParams);
+exports.AccessibleSurfaceAreaParams = tslib_1.__assign({}, shrake_rupley_1.ShrakeRupleyComputationParams);
 exports.AccessibleSurfaceAreaSymbols = {
     isBuried: compiler_1.QuerySymbolRuntime.Dynamic((0, symbol_1.CustomPropSymbol)('computed', 'accessible-surface-area.is-buried', type_1.Type.Bool), function (ctx) {
         if (!structure_1.Unit.isAtomic(ctx.element.unit))
@@ -46,13 +46,13 @@ exports.AccessibleSurfaceAreaProvider = custom_structure_property_1.CustomStruct
     defaultParams: exports.AccessibleSurfaceAreaParams,
     getParams: function (data) { return exports.AccessibleSurfaceAreaParams; },
     isApplicable: function (data) { return true; },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var p;
         var _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.AccessibleSurfaceAreaParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.AccessibleSurfaceAreaParams)), props);
                     _a = {};
                     return [4 /*yield*/, shrake_rupley_1.AccessibleSurfaceArea.compute(data, p).runInContext(ctx.runtime)];
                 case 1: return [2 /*return*/, (_a.value = _b.sent(), _a)];

package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js

@@ -306,10 +306,10 @@ exports.ValenceModelParams = {
     assignH: param_definition_1.ParamDefinition.Select('auto', [['always', 'always'], ['auto', 'auto'], ['never', 'never']]),
 };
 function calcValenceModel(ctx, structure, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var p, map, i, il, u, valenceModel;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ValenceModelParams)), props);
+        return tslib_1.__generator(this, function (_a) {
+            p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ValenceModelParams)), props);
             map = new Map();
             for (i = 0, il = structure.units.length; i < il; ++i) {
                 u = structure.units[i];

package/lib/commonjs/mol-model-props/computed/helix-orientation.js

@@ -20,8 +20,8 @@ exports.HelixOrientationProvider = custom_model_property_1.CustomModelProperty.c
     defaultParams: {},
     getParams: function () { return ({}); },
     isApplicable: function (data) { return true; },
-    obtain: function (ctx, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    obtain: function (ctx, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, { value: (0, helix_orientation_1.calcHelixOrientation)(data) }];
         });
     }); }

package/lib/commonjs/mol-model-props/computed/interactions/common.js

@@ -61,7 +61,7 @@ var InteractionsIntraContacts;
 })(InteractionsIntraContacts || (InteractionsIntraContacts = {}));
 exports.InteractionsIntraContacts = InteractionsIntraContacts;
 var InteractionsInterContacts = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(InteractionsInterContacts, _super);
+    tslib_1.__extends(InteractionsInterContacts, _super);
     function InteractionsInterContacts(map, unitsFeatures) {
         var _this = _super.call(this, map) || this;
         _this.elementKeyIndex = new Map();

package/lib/commonjs/mol-model-props/computed/interactions/contacts.js

@@ -107,7 +107,7 @@ function _addUnitContacts(structure, unit, features, builder, tester, props) {
     var x = features.x, y = features.y, z = features.z;
     var _a = features.subset(tester.requiredFeatures), lookup3d = _a.lookup3d, subsetIndices = _a.indices;
     var infoA = features_1.Features.Info(structure, unit, features);
-    var infoB = (0, tslib_1.__assign)({}, infoA);
+    var infoB = tslib_1.__assign({}, infoA);
     var distFactor = props.lineOfSightDistFactor;
     for (var t = 0, tl = int_1.OrderedSet.size(subsetIndices); t < tl; ++t) {
         var i = int_1.OrderedSet.getAt(subsetIndices, t);

package/lib/commonjs/mol-model-props/computed/interactions/features.js

@@ -49,7 +49,7 @@ var Features;
     function create(elementsCount, data) {
         var lookup3d;
         var elementsIndex;
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, data), { get lookup3d() {
+        return tslib_1.__assign(tslib_1.__assign({}, data), { get lookup3d() {
                 if (!lookup3d) {
                     var position_1 = { x: data.x, y: data.y, z: data.z, indices: int_1.OrderedSet.ofBounds(0, data.count) };
                     lookup3d = (0, geometry_1.GridLookup3D)(position_1, (0, boundary_1.getBoundary)(position_1));

package/lib/commonjs/mol-model-props/computed/interactions/hydrogen-bonds.js

@@ -25,8 +25,8 @@ var GeometryParams = {
     accOutOfPlaneAngleMax: param_definition_1.ParamDefinition.Numeric(90, { min: 0, max: 180, step: 1 }),
     donOutOfPlaneAngleMax: param_definition_1.ParamDefinition.Numeric(45, { min: 0, max: 180, step: 1 }),
 };
-var HydrogenBondsParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, GeometryParams), { water: param_definition_1.ParamDefinition.Boolean(false, { description: 'Include water-to-water hydrogen bonds' }), sulfurDistanceMax: param_definition_1.ParamDefinition.Numeric(4.1, { min: 1, max: 5, step: 0.1 }) });
-var WeakHydrogenBondsParams = (0, tslib_1.__assign)({}, GeometryParams);
+var HydrogenBondsParams = tslib_1.__assign(tslib_1.__assign({}, GeometryParams), { water: param_definition_1.ParamDefinition.Boolean(false, { description: 'Include water-to-water hydrogen bonds' }), sulfurDistanceMax: param_definition_1.ParamDefinition.Numeric(4.1, { min: 1, max: 5, step: 0.1 }) });
+var WeakHydrogenBondsParams = tslib_1.__assign({}, GeometryParams);
 //
 // Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins
 // https://doi.org/10.1002/prot.22327
@@ -171,7 +171,7 @@ function getGeometryOptions(props) {
     };
 }
 function getHydrogenBondsOptions(props) {
-    return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, getGeometryOptions(props)), { includeWater: props.water, maxSulfurDistSq: props.sulfurDistanceMax * props.sulfurDistanceMax, maxDistSq: props.distanceMax * props.distanceMax });
+    return tslib_1.__assign(tslib_1.__assign({}, getGeometryOptions(props)), { includeWater: props.water, maxSulfurDistSq: props.sulfurDistanceMax * props.sulfurDistanceMax, maxDistSq: props.distanceMax * props.distanceMax });
 }
 var deg120InRad = (0, misc_1.degToRad)(120);
 function checkGeometry(structure, don, acc, opts) {

package/lib/commonjs/mol-model-props/computed/interactions/interactions.js

@@ -143,12 +143,12 @@ exports.InteractionsParams = {
     contacts: param_definition_1.ParamDefinition.Group(contacts_1.ContactsParams, { label: 'Advanced Options' }),
 };
 function computeInteractions(ctx, structure, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var p, contactTesters, requiredFeatures, featureProviders, unitsFeatures, unitsContacts, i, il, group, features, intraUnitContacts, j, jl, u, contacts, interactions;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.InteractionsParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.InteractionsParams)), props);
                     return [4 /*yield*/, valence_model_1.ValenceModelProvider.attach(ctx, structure)];
                 case 1:
                     _a.sent();

package/lib/commonjs/mol-model-props/computed/interactions.js

@@ -11,7 +11,7 @@ var param_definition_1 = require("../../mol-util/param-definition");
 var interactions_1 = require("./interactions/interactions");
 var custom_structure_property_1 = require("../common/custom-structure-property");
 var custom_property_1 = require("../../mol-model/custom-property");
-exports.InteractionsParams = (0, tslib_1.__assign)({}, interactions_1.InteractionsParams);
+exports.InteractionsParams = tslib_1.__assign({}, interactions_1.InteractionsParams);
 exports.InteractionsProvider = custom_structure_property_1.CustomStructureProperty.createProvider({
     label: 'Interactions',
     descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
@@ -22,13 +22,13 @@ exports.InteractionsProvider = custom_structure_property_1.CustomStructureProper
     defaultParams: exports.InteractionsParams,
     getParams: function (data) { return exports.InteractionsParams; },
     isApplicable: function (data) { return !data.isCoarseGrained; },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var p;
         var _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.InteractionsParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.InteractionsParams)), props);
                     _a = {};
                     return [4 /*yield*/, (0, interactions_1.computeInteractions)(ctx, data, p)];
                 case 1: return [2 /*return*/, (_a.value = _b.sent(), _a)];

package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js

@@ -76,12 +76,18 @@ function createInterUnitInteractionCylinderMesh(ctx, structure, theme, props, me
             return false;
         }
     };
-    var m = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
-    var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * sizeFactor);
-    m.setBoundingSphere(sphere);
+    var _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    }
+    else if (m.triangleCount > 0) {
+        var child_1 = structure.child;
+        var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child_1 !== null && child_1 !== void 0 ? child_1 : structure).boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
     return m;
 }
-exports.InteractionsInterUnitParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), dashCount: param_definition_1.ParamDefinition.Numeric(6, { min: 2, max: 10, step: 2 }), dashScale: param_definition_1.ParamDefinition.Numeric(0.4, { min: 0, max: 2, step: 0.1 }), includeParent: param_definition_1.ParamDefinition.Boolean(false) });
+exports.InteractionsInterUnitParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), dashCount: param_definition_1.ParamDefinition.Numeric(6, { min: 2, max: 10, step: 2 }), dashScale: param_definition_1.ParamDefinition.Numeric(0.4, { min: 0, max: 2, step: 0.1 }), includeParent: param_definition_1.ParamDefinition.Boolean(false) });
 function InteractionsInterUnitVisual(materialId) {
     return (0, complex_visual_1.ComplexMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InteractionsInterUnitParams),

package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js

@@ -20,9 +20,9 @@ var location_iterator_1 = require("../../../mol-geo/util/location-iterator");
 var interactions_2 = require("../interactions/interactions");
 var geometry_1 = require("../../../mol-math/geometry");
 function createIntraUnitInteractionsCylinderMesh(ctx, unit, structure, theme, props, mesh) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var child, childUnit, location, interactions, features, contacts, x, y, z, members, offsets, edgeCount, a, b, flag, sizeFactor, builderProps, m, sphere;
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var child, childUnit, location, interactions, features, contacts, x, y, z, members, offsets, edgeCount, a, b, flag, sizeFactor, builderProps, _a, m, boundingSphere, sphere;
+        return tslib_1.__generator(this, function (_b) {
             if (!structure_1.Unit.isAtomic(unit))
                 return [2 /*return*/, mesh_1.Mesh.createEmpty(mesh)];
             child = structure.child;
@@ -66,14 +66,19 @@ function createIntraUnitInteractionsCylinderMesh(ctx, unit, structure, theme, pr
                     return false;
                 }
             };
-            m = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
-            sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
-            m.setBoundingSphere(sphere);
+            _a = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _a.mesh, boundingSphere = _a.boundingSphere;
+            if (boundingSphere) {
+                m.setBoundingSphere(boundingSphere);
+            }
+            else if (m.triangleCount > 0) {
+                sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
+                m.setBoundingSphere(sphere);
+            }
             return [2 /*return*/, m];
         });
     });
 }
-exports.InteractionsIntraUnitParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), dashCount: param_definition_1.ParamDefinition.Numeric(6, { min: 2, max: 10, step: 2 }), dashScale: param_definition_1.ParamDefinition.Numeric(0.4, { min: 0, max: 2, step: 0.1 }), includeParent: param_definition_1.ParamDefinition.Boolean(false) });
+exports.InteractionsIntraUnitParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), link_1.LinkCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 10, step: 0.01 }), dashCount: param_definition_1.ParamDefinition.Numeric(6, { min: 2, max: 10, step: 2 }), dashScale: param_definition_1.ParamDefinition.Numeric(0.4, { min: 0, max: 2, step: 0.1 }), includeParent: param_definition_1.ParamDefinition.Boolean(false) });
 function InteractionsIntraUnitVisual(materialId) {
     return (0, units_visual_1.UnitsMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.InteractionsIntraUnitParams),

package/lib/commonjs/mol-model-props/computed/representations/interactions.js

@@ -18,7 +18,7 @@ var InteractionsVisuals = {
     'intra-unit': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Intra-unit interactions cylinder', ctx, getParams, interactions_intra_unit_cylinder_1.InteractionsIntraUnitVisual); },
     'inter-unit': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Inter-unit interactions cylinder', ctx, getParams, interactions_inter_unit_cylinder_1.InteractionsInterUnitVisual); },
 };
-exports.InteractionsParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, interactions_intra_unit_cylinder_1.InteractionsIntraUnitParams), interactions_inter_unit_cylinder_1.InteractionsInterUnitParams), { unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0.01, max: 1, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-unit', 'inter-unit'], param_definition_1.ParamDefinition.objectToOptions(InteractionsVisuals)) });
+exports.InteractionsParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, interactions_intra_unit_cylinder_1.InteractionsIntraUnitParams), interactions_inter_unit_cylinder_1.InteractionsInterUnitParams), { unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0.01, max: 1, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-unit', 'inter-unit'], param_definition_1.ParamDefinition.objectToOptions(InteractionsVisuals)) });
 function getInteractionParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.InteractionsParams);
 }

package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js

@@ -35,9 +35,9 @@ exports.DSSPComputationParams = {
     oldOrdering: param_definition_1.ParamDefinition.Boolean(true, { description: 'Alpha-helices are preferred over 3-10 helices' })
 };
 function computeUnitDSSP(unit, params) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var proteinInfo, residueIndices, lookup3d, hbonds, residueCount, flags, torsionAngles, ladders, bridges, getResidueFlag, getFlagName, ctx, assignment, type, keys, elements, getIndex, i, il, assign, flag;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             proteinInfo = (0, protein_info_1.getUnitProteinInfo)(unit);
             residueIndices = proteinInfo.residueIndices;
             lookup3d = (0, trace_lookup_1.calcUnitProteinTraceLookup3D)(unit, residueIndices);