molstar 3.2.0 → 3.4.0

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)];
@@ -60,4 +60,3 @@ exports.AccessibleSurfaceAreaProvider = custom_structure_property_1.CustomStruct
         });
     }); }
 });
-//# sourceMappingURL=accessible-surface-area.js.map

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

@@ -204,4 +204,3 @@ function hasAromaticNeighbour(structure, unit, index) {
     return flag;
 }
 exports.hasAromaticNeighbour = hasAromaticNeighbour;
-//# sourceMappingURL=functional-group.js.map

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

@@ -118,4 +118,3 @@ function calcPlaneAngle(structure, unitA, indexA, unitB, indexB) {
     return Math.abs((Math.PI / 2) - linear_algebra_1.Vec3.angle(tmpDir2, tmpDir1));
 }
 exports.calcPlaneAngle = calcPlaneAngle;
-//# sourceMappingURL=geometry.js.map

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

@@ -119,4 +119,3 @@ function eachResidueAtom(unit, index, cb) {
     }
 }
 exports.eachResidueAtom = eachResidueAtom;
-//# sourceMappingURL=util.js.map

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];
@@ -323,4 +323,3 @@ function calcValenceModel(ctx, structure, props) {
     });
 }
 exports.calcValenceModel = calcValenceModel;
-//# sourceMappingURL=valence-model.js.map

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

@@ -108,4 +108,3 @@ function calcHelixOrientation(model) {
     };
 }
 exports.calcHelixOrientation = calcHelixOrientation;
-//# sourceMappingURL=helix-orientation.js.map

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

@@ -20,10 +20,9 @@ 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) }];
         });
     }); }
 });
-//# sourceMappingURL=helix-orientation.js.map

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

@@ -323,4 +323,3 @@ exports.CationPiProvider = {
         };
     }
 };
-//# sourceMappingURL=charged.js.map

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();
@@ -173,4 +173,3 @@ function featureGroupLabel(group) {
     }
 }
 exports.featureGroupLabel = featureGroupLabel;
-//# sourceMappingURL=common.js.map

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

@@ -65,4 +65,3 @@ var InterContactsBuilder;
     InterContactsBuilder.create = create;
 })(InterContactsBuilder || (InterContactsBuilder = {}));
 exports.InterContactsBuilder = InterContactsBuilder;
-//# sourceMappingURL=contacts-builder.js.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);
@@ -179,4 +179,3 @@ function addStructureContacts(structure, unitA, featuresA, unitB, featuresB, bui
     builder.finishUnitPair();
 }
 exports.addStructureContacts = addStructureContacts;
-//# sourceMappingURL=contacts.js.map

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));
@@ -191,4 +191,3 @@ var FeaturesBuilder;
     FeaturesBuilder.create = create;
 })(FeaturesBuilder || (FeaturesBuilder = {}));
 exports.FeaturesBuilder = FeaturesBuilder;
-//# sourceMappingURL=features.js.map

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

@@ -107,4 +107,3 @@ exports.HalogenBondsProvider = {
         };
     }
 };
-//# sourceMappingURL=halogen-bonds.js.map

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) {
@@ -257,4 +257,3 @@ exports.WeakHydrogenBondsProvider = {
         };
     }
 };
-//# sourceMappingURL=hydrogen-bonds.js.map

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

@@ -72,4 +72,3 @@ exports.HydrophobicProvider = {
         };
     }
 };
-//# sourceMappingURL=hydrophobic.js.map

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();
@@ -227,4 +227,3 @@ function findInterUnitContacts(structure, unitsFeatures, contactTesters, props)
     });
     return builder.getContacts(unitsFeatures);
 }
-//# sourceMappingURL=interactions.js.map

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

@@ -146,4 +146,3 @@ exports.MetalCoordinationProvider = {
         };
     }
 };
-//# sourceMappingURL=metal.js.map

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

@@ -248,4 +248,3 @@ function metalCoordinationRefiner(structure, interactions) {
         }
     };
 }
-//# sourceMappingURL=refine.js.map

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)];
@@ -36,4 +36,3 @@ exports.InteractionsProvider = custom_structure_property_1.CustomStructureProper
         });
     }); }
 });
-//# sourceMappingURL=interactions.js.map

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),
@@ -211,4 +217,3 @@ function createInteractionsIterator(structure) {
     };
     return (0, location_iterator_1.LocationIterator)(groupCount, instanceCount, 1, getLocation, true);
 }
-//# sourceMappingURL=interactions-inter-unit-cylinder.js.map

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),
@@ -209,4 +214,3 @@ function createInteractionsIterator(structureGroup) {
     };
     return (0, location_iterator_1.LocationIterator)(groupCount, instanceCount, 1, getLocation);
 }
-//# sourceMappingURL=interactions-intra-unit-cylinder.js.map

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);
 }
@@ -48,4 +48,3 @@ exports.InteractionsRepresentationProvider = (0, representation_2.StructureRepre
         return oldProps.includeParent !== newProps.includeParent;
     }
 });
-//# sourceMappingURL=interactions.js.map

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

@@ -122,4 +122,3 @@ function buildHbondGraph(residueCount, oAtomResidues, nAtomResidues, energies) {
     }
     return builder.createGraph({ energies: energies });
 }
-//# sourceMappingURL=backbone-hbonds.js.map

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

@@ -57,4 +57,3 @@ function assignBends(ctx) {
     }
 }
 exports.assignBends = assignBends;
-//# sourceMappingURL=bends.js.map

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

@@ -71,4 +71,3 @@ function assignBridges(ctx) {
     bridges.sort(function (a, b) { return a.partner1 > b.partner1 ? 1 : a.partner1 < b.partner1 ? -1 : 0; });
 }
 exports.assignBridges = assignBridges;
-//# sourceMappingURL=bridges.js.map

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

@@ -23,4 +23,3 @@ var Bridge = /** @class */ (function () {
     return Bridge;
 }());
 exports.Bridge = Bridge;
-//# sourceMappingURL=common.js.map

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

@@ -48,4 +48,3 @@ function calculateUnitDihedralAngles(unit, proteinInfo) {
     return { phi: phi, psi: psi };
 }
 exports.calculateUnitDihedralAngles = calculateUnitDihedralAngles;
-//# sourceMappingURL=dihedral-angles.js.map

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

@@ -61,4 +61,3 @@ function assignHelices(ctx) {
     }
 }
 exports.assignHelices = assignHelices;
-//# sourceMappingURL=helices.js.map

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

@@ -96,4 +96,3 @@ function assignLadders(ctx) {
     }
 }
 exports.assignLadders = assignLadders;
-//# sourceMappingURL=ladders.js.map

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

@@ -34,4 +34,3 @@ function getUnitProteinInfo(unit) {
     };
 }
 exports.getUnitProteinInfo = getUnitProteinInfo;
-//# sourceMappingURL=protein-info.js.map

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

@@ -55,4 +55,3 @@ function assignSheets(ctx) {
     }
 }
 exports.assignSheets = assignSheets;
-//# sourceMappingURL=sheets.js.map

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

@@ -20,4 +20,3 @@ function calcUnitProteinTraceLookup3D(unit, unitProteinResidues) {
     return (0, geometry_1.GridLookup3D)(position, (0, boundary_1.getBoundary)(position));
 }
 exports.calcUnitProteinTraceLookup3D = calcUnitProteinTraceLookup3D;
-//# sourceMappingURL=trace-lookup.js.map

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

@@ -37,4 +37,3 @@ function assignTurns(ctx) {
     }
 }
 exports.assignTurns = assignTurns;
-//# sourceMappingURL=turns.js.map

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);
@@ -209,4 +209,3 @@ function getDSSPAssignment(flags, getResidueFlag) {
     }
     return type;
 }
-//# sourceMappingURL=dssp.js.map

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

@@ -1,3 +1,2 @@
 "use strict";
 // TODO
-//# sourceMappingURL=zhang-skolnik.js.map

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

@@ -46,13 +46,13 @@ exports.SecondaryStructureProvider = custom_structure_property_1.CustomStructure
     defaultParams: exports.SecondaryStructureParams,
     getParams: getSecondaryStructureParams,
     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, _a;
         var _b, _c;
-        return (0, tslib_1.__generator)(this, function (_d) {
+        return tslib_1.__generator(this, function (_d) {
             switch (_d.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.SecondaryStructureParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.SecondaryStructureParams)), props);
                     _a = p.type.name;
                     switch (_a) {
                         case 'dssp': return [3 /*break*/, 1];
@@ -73,9 +73,9 @@ exports.SecondaryStructureProvider = custom_structure_property_1.CustomStructure
     }); }
 });
 function computeDssp(structure, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var map, i, il, u, secondaryStructure;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     map = new Map();
@@ -99,9 +99,9 @@ function computeDssp(structure, props) {
     });
 }
 function computeModel(structure) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var map, i, il, u, secondaryStructure;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             map = new Map();
             for (i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {
                 u = structure.unitSymmetryGroups[i].units[0];
@@ -116,4 +116,3 @@ function computeModel(structure) {
         });
     });
 }
-//# sourceMappingURL=secondary-structure.js.map

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

@@ -79,4 +79,3 @@ exports.AccessibleSurfaceAreaColorThemeProvider = {
         detach: function (data) { return data.structure && accessible_surface_area_1.AccessibleSurfaceAreaProvider.ref(data.structure, false); }
     }
 };
-//# sourceMappingURL=accessible-surface-area.js.map

package/lib/commonjs/mol-model-props/computed/themes/interaction-type.js

@@ -110,4 +110,3 @@ exports.InteractionTypeColorThemeProvider = {
         detach: function (data) { return data.structure && interactions_1.InteractionsProvider.ref(data.structure, false); }
     }
 };
-//# sourceMappingURL=interaction-type.js.map

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

@@ -11,7 +11,7 @@ var param_definition_1 = require("../../mol-util/param-definition");
 var valence_model_1 = require("./chemistry/valence-model");
 var custom_structure_property_1 = require("../common/custom-structure-property");
 var custom_property_1 = require("../../mol-model/custom-property");
-exports.ValenceModelParams = (0, tslib_1.__assign)({}, valence_model_1.ValenceModelParams);
+exports.ValenceModelParams = tslib_1.__assign({}, valence_model_1.ValenceModelParams);
 exports.ValenceModelProvider = custom_structure_property_1.CustomStructureProperty.createProvider({
     label: 'Valence Model',
     descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
@@ -22,13 +22,13 @@ exports.ValenceModelProvider = custom_structure_property_1.CustomStructureProper
     defaultParams: exports.ValenceModelParams,
     getParams: function (data) { return exports.ValenceModelParams; },
     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.ValenceModelParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ValenceModelParams)), props);
                     _a = {};
                     return [4 /*yield*/, (0, valence_model_1.calcValenceModel)(ctx.runtime, data, p)];
                 case 1: return [2 /*return*/, (_a.value = _b.sent(), _a)];
@@ -36,4 +36,3 @@ exports.ValenceModelProvider = custom_structure_property_1.CustomStructureProper
         });
     }); }
 });
-//# sourceMappingURL=valence-model.js.map

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/color.js

@@ -65,4 +65,3 @@ exports.CrossLinkColorThemeProvider = {
         detach: function (data) { return data.structure && property_1.CrossLinkRestraintProvider.ref(data.structure, false); }
     }
 };
-//# sourceMappingURL=color.js.map

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/format.js

@@ -90,4 +90,3 @@ var ModelCrossLinkRestraint;
     ModelCrossLinkRestraint.fromTable = fromTable;
 })(ModelCrossLinkRestraint || (ModelCrossLinkRestraint = {}));
 exports.ModelCrossLinkRestraint = ModelCrossLinkRestraint;
-//# sourceMappingURL=format.js.map

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/property.js

@@ -27,8 +27,8 @@ exports.CrossLinkRestraintProvider = custom_structure_property_1.CustomStructure
     defaultParams: {},
     getParams: function (data) { return ({}); },
     isApplicable: function (data) { return data.models.some(function (m) { return !!format_1.ModelCrossLinkRestraint.Provider.get(m); }); },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, { value: extractCrossLinkRestraints(data) }];
         });
     }); }
@@ -194,4 +194,3 @@ function extractCrossLinkRestraints(structure) {
     }
     return new pair_restraints_1.PairRestraints(pairs);
 }
-//# sourceMappingURL=property.js.map

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.js

@@ -18,6 +18,7 @@ var link_1 = require("../../../mol-repr/structure/visual/util/link");
 var complex_visual_1 = require("../../../mol-repr/structure/complex-visual");
 var representation_2 = require("../../../mol-repr/structure/representation");
 var property_1 = require("./property");
+var geometry_1 = require("../../../mol-math/geometry");
 function createCrossLinkRestraintCylinderMesh(ctx, structure, theme, props, mesh) {
     var crossLinks = property_1.CrossLinkRestraintProvider.get(structure).value;
     if (!crossLinks.count)
@@ -39,9 +40,17 @@ function createCrossLinkRestraintCylinderMesh(ctx, structure, theme, props, mesh
             return theme.size.size(location) * sizeFactor;
         },
     };
-    return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
+    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 sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+    return m;
 }
-exports.CrossLinkRestraintCylinderParams = (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(0.5, { min: 0, max: 10, step: 0.1 }) });
+exports.CrossLinkRestraintCylinderParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), link_1.LinkCylinderParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 10, step: 0.1 }) });
 function CrossLinkRestraintVisual(materialId) {
     return (0, complex_visual_1.ComplexMeshVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.CrossLinkRestraintCylinderParams),
@@ -100,7 +109,7 @@ function eachCrossLink(loci, structure, apply) {
 var CrossLinkRestraintVisuals = {
     'cross-link-restraint': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Cross-link restraint', ctx, getParams, CrossLinkRestraintVisual); },
 };
-exports.CrossLinkRestraintParams = (0, tslib_1.__assign)({}, exports.CrossLinkRestraintCylinderParams);
+exports.CrossLinkRestraintParams = tslib_1.__assign({}, exports.CrossLinkRestraintCylinderParams);
 function getCrossLinkRestraintParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.CrossLinkRestraintParams);
 }
@@ -124,4 +133,3 @@ exports.CrossLinkRestraintRepresentationProvider = (0, representation_2.Structur
         detach: function (data) { return property_1.CrossLinkRestraintProvider.ref(data, false); }
     }
 });
-//# sourceMappingURL=representation.js.map

package/lib/commonjs/mol-model-props/integrative/pair-restraints.js

@@ -38,4 +38,3 @@ var PairRestraints = /** @class */ (function () {
     return PairRestraints;
 }());
 exports.PairRestraints = PairRestraints;
-//# sourceMappingURL=pair-restraints.js.map

package/lib/commonjs/mol-model-props/sequence/sifts-mapping.js

@@ -22,8 +22,8 @@ var SIFTSMapping;
         defaultParams: {},
         getParams: function () { return ({}); },
         isApplicable: function (data) { return isAvailable(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) {
                 return [2 /*return*/, { value: fromCif(data) }];
             });
         }); }
@@ -88,4 +88,3 @@ var SIFTSMapping;
     }
 })(SIFTSMapping || (SIFTSMapping = {}));
 exports.SIFTSMapping = SIFTSMapping;
-//# sourceMappingURL=sifts-mapping.js.map