molstar 3.0.0 → 3.0.1

package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js

@@ -1,220 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2020 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.AssemblySymmetryProvider = exports.AssemblySymmetryParams = exports.AssemblySymmetryDataProvider = exports.AssemblySymmetryDataParams = exports.getSymmetrySelectParam = exports.AssemblySymmetry = exports.isBiologicalAssembly = void 0;
-var tslib_1 = require("tslib");
-var symmetry_gql_1 = require("../graphql/symmetry.gql");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var structure_1 = require("../../../mol-model/structure");
-var db_1 = require("../../../mol-data/db");
-var graphql_client_1 = require("../../../mol-util/graphql-client");
-var custom_structure_property_1 = require("../../../mol-model-props/common/custom-structure-property");
-var mmcif_1 = require("../../../mol-model-formats/structure/mmcif");
-var set_1 = require("../../../mol-util/set");
-var builder_1 = require("../../../mol-script/language/builder");
-var compiler_1 = require("../../../mol-script/runtime/query/compiler");
-var custom_property_1 = require("../../../mol-model/custom-property");
-var BiologicalAssemblyNames = new Set([
-    'author_and_software_defined_assembly',
-    'author_defined_assembly',
-    'complete icosahedral assembly',
-    'complete point assembly',
-    'representative helical assembly',
-    'software_defined_assembly'
-]);
-function isBiologicalAssembly(structure) {
-    var _a;
-    if (!mmcif_1.MmcifFormat.is(structure.models[0].sourceData))
-        return false;
-    var mmcif = structure.models[0].sourceData.data.db;
-    if (!mmcif.pdbx_struct_assembly.details.isDefined)
-        return false;
-    var id = ((_a = structure.units[0].conformation.operator.assembly) === null || _a === void 0 ? void 0 : _a.id) || '';
-    if (id === '')
-        return true;
-    var indices = db_1.Column.indicesOf(mmcif.pdbx_struct_assembly.id, function (e) { return e === id; });
-    if (indices.length !== 1)
-        return false;
-    var details = mmcif.pdbx_struct_assembly.details.value(indices[0]);
-    return BiologicalAssemblyNames.has(details);
-}
-exports.isBiologicalAssembly = isBiologicalAssembly;
-var AssemblySymmetry;
-(function (AssemblySymmetry) {
-    var Tag;
-    (function (Tag) {
-        Tag["Cluster"] = "rcsb-assembly-symmetry-cluster";
-        Tag["Representation"] = "rcsb-assembly-symmetry-3d";
-    })(Tag = AssemblySymmetry.Tag || (AssemblySymmetry.Tag = {}));
-    AssemblySymmetry.DefaultServerUrl = 'https://data.rcsb.org/graphql';
-    function isApplicable(structure) {
-        return (!!structure && structure.models.length === 1 &&
-            structure_1.Model.hasPdbId(structure.models[0]) &&
-            isBiologicalAssembly(structure));
-    }
-    AssemblySymmetry.isApplicable = isApplicable;
-    function fetch(ctx, structure, props) {
-        var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var client, variables, result, value;
-            return (0, tslib_1.__generator)(this, function (_c) {
-                switch (_c.label) {
-                    case 0:
-                        if (!isApplicable(structure))
-                            return [2 /*return*/, { value: [] }];
-                        client = new graphql_client_1.GraphQLClient(props.serverUrl, ctx.assetManager);
-                        variables = {
-                            assembly_id: ((_a = structure.units[0].conformation.operator.assembly) === null || _a === void 0 ? void 0 : _a.id) || '',
-                            entry_id: structure.units[0].model.entryId
-                        };
-                        return [4 /*yield*/, client.request(ctx.runtime, symmetry_gql_1.symmetry_gql, variables)];
-                    case 1:
-                        result = _c.sent();
-                        value = [];
-                        if (!((_b = result.data.assembly) === null || _b === void 0 ? void 0 : _b.rcsb_struct_symmetry)) {
-                            console.error('expected `rcsb_struct_symmetry` field');
-                        }
-                        else {
-                            value = result.data.assembly.rcsb_struct_symmetry;
-                        }
-                        return [2 /*return*/, { value: value, assets: [result] }];
-                }
-            });
-        });
-    }
-    AssemblySymmetry.fetch = fetch;
-    /** Returns the index of the first non C1 symmetry or -1 */
-    function firstNonC1(assemblySymmetryData) {
-        for (var i = 0, il = assemblySymmetryData.length; i < il; ++i) {
-            if (assemblySymmetryData[i].symbol !== 'C1')
-                return i;
-        }
-        return -1;
-    }
-    AssemblySymmetry.firstNonC1 = firstNonC1;
-    function isRotationAxes(x) {
-        return !!x && x.length > 0;
-    }
-    AssemblySymmetry.isRotationAxes = isRotationAxes;
-    function getAsymIds(assemblySymmetry) {
-        var asymIds = new Set();
-        for (var _i = 0, _a = assemblySymmetry.clusters; _i < _a.length; _i++) {
-            var c = _a[_i];
-            if (!(c === null || c === void 0 ? void 0 : c.members))
-                continue;
-            for (var _b = 0, _c = c.members; _b < _c.length; _b++) {
-                var m = _c[_b];
-                if (m === null || m === void 0 ? void 0 : m.asym_id)
-                    asymIds.add(m.asym_id);
-            }
-        }
-        return set_1.SetUtils.toArray(asymIds);
-    }
-    AssemblySymmetry.getAsymIds = getAsymIds;
-    function getAsymIdsStructure(structure, asymIds) {
-        var query = builder_1.MolScriptBuilder.struct.modifier.union([
-            builder_1.MolScriptBuilder.struct.generator.atomGroups({
-                'chain-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set.apply(builder_1.MolScriptBuilder, asymIds), builder_1.MolScriptBuilder.ammp('label_asym_id')])
-            })
-        ]);
-        var compiled = (0, compiler_1.compile)(query);
-        var result = compiled(new structure_1.QueryContext(structure));
-        return structure_1.StructureSelection.unionStructure(result);
-    }
-    /** Returns structure limited to all cluster member chains */
-    function getStructure(structure, assemblySymmetry) {
-        var asymIds = AssemblySymmetry.getAsymIds(assemblySymmetry);
-        return asymIds.length > 0 ? getAsymIdsStructure(structure, asymIds) : structure;
-    }
-    AssemblySymmetry.getStructure = getStructure;
-})(AssemblySymmetry = exports.AssemblySymmetry || (exports.AssemblySymmetry = {}));
-function getSymmetrySelectParam(structure) {
-    var param = param_definition_1.ParamDefinition.Select(0, [[0, 'First Symmetry']]);
-    if (structure) {
-        var assemblySymmetryData = exports.AssemblySymmetryDataProvider.get(structure).value;
-        if (assemblySymmetryData) {
-            var options = [
-                [-1, 'Off']
-            ];
-            for (var i = 0, il = assemblySymmetryData.length; i < il; ++i) {
-                var _a = assemblySymmetryData[i], symbol = _a.symbol, kind = _a.kind;
-                if (symbol !== 'C1') {
-                    options.push([i, "".concat(i + 1, ": ").concat(symbol, " ").concat(kind)]);
-                }
-            }
-            if (options.length > 1) {
-                param.options = options;
-                param.defaultValue = options[1][0];
-            }
-            else {
-                options.length = 0;
-            }
-        }
-    }
-    return param;
-}
-exports.getSymmetrySelectParam = getSymmetrySelectParam;
-//
-exports.AssemblySymmetryDataParams = {
-    serverUrl: param_definition_1.ParamDefinition.Text(AssemblySymmetry.DefaultServerUrl, { description: 'GraphQL endpoint URL' })
-};
-exports.AssemblySymmetryDataProvider = custom_structure_property_1.CustomStructureProperty.createProvider({
-    label: 'Assembly Symmetry Data',
-    descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
-        name: 'rcsb_struct_symmetry_data',
-        // TODO `cifExport` and `symbol`
-    }),
-    type: 'root',
-    defaultParams: exports.AssemblySymmetryDataParams,
-    getParams: function (data) { return exports.AssemblySymmetryDataParams; },
-    isApplicable: function (data) { return AssemblySymmetry.isApplicable(data); },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        var p;
-        return (0, 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.AssemblySymmetryDataParams)), props);
-                    return [4 /*yield*/, AssemblySymmetry.fetch(ctx, data, p)];
-                case 1: return [2 /*return*/, _a.sent()];
-            }
-        });
-    }); }
-});
-//
-function getAssemblySymmetryParams(data) {
-    return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.AssemblySymmetryDataParams), { symmetryIndex: getSymmetrySelectParam(data) });
-}
-exports.AssemblySymmetryParams = getAssemblySymmetryParams();
-exports.AssemblySymmetryProvider = custom_structure_property_1.CustomStructureProperty.createProvider({
-    label: 'Assembly Symmetry',
-    descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
-        name: 'rcsb_struct_symmetry',
-        // TODO `cifExport` and `symbol`
-    }),
-    type: 'root',
-    defaultParams: exports.AssemblySymmetryParams,
-    getParams: getAssemblySymmetryParams,
-    isApplicable: function (data) { return AssemblySymmetry.isApplicable(data); },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        var p, assemblySymmetryData, assemblySymmetry;
-        return (0, 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(getAssemblySymmetryParams(data))), props);
-                    return [4 /*yield*/, exports.AssemblySymmetryDataProvider.attach(ctx, data, p)];
-                case 1:
-                    _a.sent();
-                    assemblySymmetryData = exports.AssemblySymmetryDataProvider.get(data).value;
-                    assemblySymmetry = assemblySymmetryData === null || assemblySymmetryData === void 0 ? void 0 : assemblySymmetryData[p.symmetryIndex];
-                    if (!assemblySymmetry)
-                        new Error("No assembly symmetry found for index ".concat(p.symmetryIndex));
-                    return [2 /*return*/, { value: assemblySymmetry }];
-            }
-        });
-    }); }
-});
-//# sourceMappingURL=prop.js.map

package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.js

@@ -1,363 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2020 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.AssemblySymmetryRepresentation = exports.AssemblySymmetryParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var prop_1 = require("./prop");
-var mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder");
-var linear_algebra_1 = require("../../../mol-math/linear-algebra");
-var cylinder_1 = require("../../../mol-geo/geometry/mesh/builder/cylinder");
-var mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
-var shape_1 = require("../../../mol-model/shape");
-var names_1 = require("../../../mol-util/color/names");
-var representation_1 = require("../../../mol-repr/shape/representation");
-var marker_action_1 = require("../../../mol-util/marker-action");
-var prism_1 = require("../../../mol-geo/primitive/prism");
-var wedge_1 = require("../../../mol-geo/primitive/wedge");
-var primitive_1 = require("../../../mol-geo/primitive/primitive");
-var memoize_1 = require("../../../mol-util/memoize");
-var polygon_1 = require("../../../mol-geo/primitive/polygon");
-var color_1 = require("../../../mol-util/color");
-var legend_1 = require("../../../mol-util/legend");
-var representation_2 = require("../../../mol-repr/representation");
-var cage_1 = require("../../../mol-geo/primitive/cage");
-var octahedron_1 = require("../../../mol-geo/primitive/octahedron");
-var tetrahedron_1 = require("../../../mol-geo/primitive/tetrahedron");
-var icosahedron_1 = require("../../../mol-geo/primitive/icosahedron");
-var misc_1 = require("../../../mol-math/misc");
-var common_1 = require("../../../mol-math/linear-algebra/3d/common");
-var number_1 = require("../../../mol-util/number");
-var geometry_1 = require("../../../mol-math/geometry");
-var OrderColors = (0, color_1.ColorMap)({
-    '2': names_1.ColorNames.deepskyblue,
-    '3': names_1.ColorNames.lime,
-    'N': names_1.ColorNames.red,
-});
-var OrderColorsLegend = (0, legend_1.TableLegend)(Object.keys(OrderColors).map(function (name) {
-    return [name, OrderColors[name]];
-}));
-function axesColorHelp(value) {
-    return value.name === 'byOrder'
-        ? { description: 'Color axes by their order', legend: OrderColorsLegend }
-        : {};
-}
-var SharedParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), { scale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }) });
-var AxesParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, SharedParams), { axesColor: param_definition_1.ParamDefinition.MappedStatic('byOrder', {
-        byOrder: param_definition_1.ParamDefinition.EmptyGroup(),
-        uniform: param_definition_1.ParamDefinition.Group({
-            colorValue: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange),
-        }, { isFlat: true })
-    }, { help: axesColorHelp }) });
-var CageParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, SharedParams), { cageColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange) });
-var AssemblySymmetryVisuals = {
-    // cage should come before 'axes' so that the representative loci uses the cage shape
-    'cage': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getCageShape, mesh_1.Mesh.Utils, { modifyState: function (s) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
-    'axes': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getAxesShape, mesh_1.Mesh.Utils, { modifyState: function (s) { return ((0, tslib_1.__assign)((0, tslib_1.__assign)({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); } }); },
-};
-exports.AssemblySymmetryParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, AxesParams), CageParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['axes', 'cage'], param_definition_1.ParamDefinition.objectToOptions(AssemblySymmetryVisuals)) });
-//
-function getAssemblyName(s) {
-    var _a;
-    var id = ((_a = s.units[0].conformation.operator.assembly) === null || _a === void 0 ? void 0 : _a.id) || '';
-    return (0, number_1.isInteger)(id) ? "Assembly ".concat(id) : id;
-}
-var t = linear_algebra_1.Mat4.identity();
-var tmpV = (0, linear_algebra_1.Vec3)();
-var tmpCenter = (0, linear_algebra_1.Vec3)();
-var tmpScale = (0, linear_algebra_1.Vec3)();
-var getOrderPrimitive = (0, memoize_1.memoize1)(function (order) {
-    if (order < 2) {
-        return (0, prism_1.Prism)((0, polygon_1.polygon)(48, false));
-    }
-    else if (order === 2) {
-        var lens = (0, prism_1.Prism)((0, polygon_1.polygon)(48, false));
-        var m = linear_algebra_1.Mat4.identity();
-        linear_algebra_1.Mat4.scale(m, m, linear_algebra_1.Vec3.create(1, 0.35, 1));
-        (0, primitive_1.transformPrimitive)(lens, m);
-        return lens;
-    }
-    else if (order === 3) {
-        return (0, wedge_1.Wedge)();
-    }
-    else {
-        return (0, prism_1.Prism)((0, polygon_1.polygon)(order, false));
-    }
-});
-function getAxesMesh(data, props, mesh) {
-    var scale = props.scale;
-    var rotation_axes = data.rotation_axes;
-    if (!prop_1.AssemblySymmetry.isRotationAxes(rotation_axes))
-        return mesh_1.Mesh.createEmpty(mesh);
-    var _a = rotation_axes[0], start = _a.start, end = _a.end;
-    var radius = (linear_algebra_1.Vec3.distance(start, end) / 500) * scale;
-    linear_algebra_1.Vec3.set(tmpScale, radius * 7, radius * 7, radius * 0.4);
-    var cylinderProps = { radiusTop: radius, radiusBottom: radius };
-    var builderState = mesh_builder_1.MeshBuilder.createState(256, 128, mesh);
-    builderState.currentGroup = 0;
-    linear_algebra_1.Vec3.scale(tmpCenter, linear_algebra_1.Vec3.add(tmpCenter, start, end), 0.5);
-    for (var i = 0, il = rotation_axes.length; i < il; ++i) {
-        var _b = rotation_axes[i], order = _b.order, start_1 = _b.start, end_1 = _b.end;
-        builderState.currentGroup = i;
-        (0, cylinder_1.addCylinder)(builderState, start_1, end_1, 1, cylinderProps);
-        var primitive = getOrderPrimitive(order);
-        if (primitive) {
-            linear_algebra_1.Vec3.scale(tmpCenter, linear_algebra_1.Vec3.add(tmpCenter, start_1, end_1), 0.5);
-            if (linear_algebra_1.Vec3.dot(linear_algebra_1.Vec3.unitY, linear_algebra_1.Vec3.sub(tmpV, start_1, tmpCenter)) === 0) {
-                linear_algebra_1.Mat4.targetTo(t, start_1, tmpCenter, linear_algebra_1.Vec3.unitY);
-            }
-            else {
-                linear_algebra_1.Mat4.targetTo(t, start_1, tmpCenter, linear_algebra_1.Vec3.unitX);
-            }
-            linear_algebra_1.Mat4.scale(t, t, tmpScale);
-            linear_algebra_1.Mat4.setTranslation(t, start_1);
-            mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, primitive);
-            linear_algebra_1.Mat4.setTranslation(t, end_1);
-            mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, primitive);
-        }
-    }
-    return mesh_builder_1.MeshBuilder.getMesh(builderState);
-}
-function getAxesShape(ctx, data, props, shape) {
-    var assemblySymmetry = prop_1.AssemblySymmetryProvider.get(data).value;
-    var geo = getAxesMesh(assemblySymmetry, props, shape && shape.geometry);
-    var getColor = function (groupId) {
-        var _a;
-        if (props.axesColor.name === 'byOrder') {
-            var rotation_axes = assemblySymmetry.rotation_axes;
-            var order = (_a = rotation_axes[groupId]) === null || _a === void 0 ? void 0 : _a.order;
-            if (order === 2)
-                return OrderColors[2];
-            else if (order === 3)
-                return OrderColors[3];
-            else
-                return OrderColors.N;
-        }
-        else {
-            return props.axesColor.params.colorValue;
-        }
-    };
-    var getLabel = function (groupId) {
-        var _a;
-        var type = assemblySymmetry.type, symbol = assemblySymmetry.symbol, kind = assemblySymmetry.kind, rotation_axes = assemblySymmetry.rotation_axes;
-        var order = (_a = rotation_axes[groupId]) === null || _a === void 0 ? void 0 : _a.order;
-        return [
-            "<small>".concat(data.model.entryId, "</small>"),
-            "<small>".concat(getAssemblyName(data), "</small>"),
-            "Axis ".concat(groupId + 1, " with Order ").concat(order, " of ").concat(type, " ").concat(kind, " (").concat(symbol, ")")
-        ].join(' | ');
-    };
-    return shape_1.Shape.create('Axes', data, geo, getColor, function () { return 1; }, getLabel);
-}
-//
-var getSymbolCage = (0, memoize_1.memoize1)(function (symbol) {
-    if (symbol.startsWith('D') || symbol.startsWith('C')) {
-        // z axis is prism axis, x/y axes cut through edge midpoints
-        var fold = parseInt(symbol.substr(1));
-        var cage = void 0;
-        if (fold === 2) {
-            cage = (0, prism_1.PrismCage)((0, polygon_1.polygon)(4, false));
-        }
-        else if (fold === 3) {
-            cage = (0, wedge_1.WedgeCage)();
-        }
-        else if (fold > 3) {
-            cage = (0, prism_1.PrismCage)((0, polygon_1.polygon)(fold, false));
-        }
-        else {
-            return;
-        }
-        if (fold % 2 === 0) {
-            return cage;
-        }
-        else {
-            var m = linear_algebra_1.Mat4.identity();
-            linear_algebra_1.Mat4.rotate(m, m, 1 / fold * Math.PI / 2, linear_algebra_1.Vec3.unitZ);
-            return (0, cage_1.transformCage)((0, cage_1.cloneCage)(cage), m);
-        }
-    }
-    else if (symbol === 'O') {
-        // x/y/z axes cut through order 4 vertices
-        return (0, octahedron_1.OctahedronCage)();
-    }
-    else if (symbol === 'I') {
-        // z axis cut through order 5 vertex
-        // x axis cut through edge midpoint
-        var cage = (0, icosahedron_1.IcosahedronCage)();
-        var m = linear_algebra_1.Mat4.identity();
-        linear_algebra_1.Mat4.rotate(m, m, (0, misc_1.degToRad)(31.7), linear_algebra_1.Vec3.unitX);
-        return (0, cage_1.transformCage)((0, cage_1.cloneCage)(cage), m);
-    }
-    else if (symbol === 'T') {
-        // x/y/z axes cut through edge midpoints
-        return (0, tetrahedron_1.TetrahedronCage)();
-    }
-});
-function getSymbolScale(symbol) {
-    if (symbol.startsWith('D') || symbol.startsWith('C')) {
-        return 0.75;
-    }
-    else if (symbol === 'O') {
-        return 1.2;
-    }
-    else if (symbol === 'I') {
-        return 0.25;
-    }
-    else if (symbol === 'T') {
-        return 0.8;
-    }
-    return 1;
-}
-function setSymbolTransform(t, symbol, axes, size, structure) {
-    var eye = (0, linear_algebra_1.Vec3)();
-    var target = (0, linear_algebra_1.Vec3)();
-    var dir = (0, linear_algebra_1.Vec3)();
-    var up = (0, linear_algebra_1.Vec3)();
-    var pair = undefined;
-    if (symbol.startsWith('C')) {
-        pair = [axes[0]];
-    }
-    else if (symbol.startsWith('D')) {
-        var fold_1 = parseInt(symbol.substr(1));
-        if (fold_1 === 2) {
-            pair = axes.filter(function (a) { return a.order === 2; });
-        }
-        else if (fold_1 >= 3) {
-            var aN = axes.filter(function (a) { return a.order === fold_1; })[0];
-            var a2 = axes.filter(function (a) { return a.order === 2; })[1];
-            pair = [aN, a2];
-        }
-    }
-    else if (symbol === 'O') {
-        pair = axes.filter(function (a) { return a.order === 4; });
-    }
-    else if (symbol === 'I') {
-        var a5 = axes.filter(function (a) { return a.order === 5; })[0];
-        var a5dir = linear_algebra_1.Vec3.sub((0, linear_algebra_1.Vec3)(), a5.end, a5.start);
-        pair = [a5];
-        for (var _i = 0, _a = axes.filter(function (a) { return a.order === 3; }); _i < _a.length; _i++) {
-            var a = _a[_i];
-            var d = (0, misc_1.radToDeg)(linear_algebra_1.Vec3.angle(linear_algebra_1.Vec3.sub(up, a.end, a.start), a5dir));
-            if (!pair[1] && ((0, common_1.equalEps)(d, 100.81, 0.1) || (0, common_1.equalEps)(d, 79.19, 0.1))) {
-                pair[1] = a;
-                break;
-            }
-        }
-    }
-    else if (symbol === 'T') {
-        pair = axes.filter(function (a) { return a.order === 2; });
-    }
-    linear_algebra_1.Mat4.setIdentity(t);
-    if (pair) {
-        var aA = pair[0], aB = pair[1];
-        linear_algebra_1.Vec3.scale(eye, linear_algebra_1.Vec3.add(eye, aA.end, aA.start), 0.5);
-        linear_algebra_1.Vec3.copy(target, aA.end);
-        if (aB) {
-            linear_algebra_1.Vec3.sub(up, aB.end, aB.start);
-            linear_algebra_1.Vec3.sub(dir, eye, target);
-            if (linear_algebra_1.Vec3.dot(dir, up) < 0)
-                linear_algebra_1.Vec3.negate(up, up);
-            linear_algebra_1.Mat4.targetTo(t, eye, target, up);
-            if (symbol.startsWith('D')) {
-                var sphere = structure.lookup3d.boundary.sphere;
-                var sizeXY = (sphere.radius * 2) * 0.8; // fallback for missing extrema
-                if (geometry_1.Sphere3D.hasExtrema(sphere)) {
-                    var n_1 = linear_algebra_1.Mat3.directionTransform((0, linear_algebra_1.Mat3)(), t);
-                    var dirs = unitCircleDirections.map(function (d) { return linear_algebra_1.Vec3.transformMat3((0, linear_algebra_1.Vec3)(), d, n_1); });
-                    sizeXY = getMaxProjectedDistance(sphere.extrema, dirs, sphere.center) * 1.6;
-                }
-                linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.create(sizeXY, sizeXY, linear_algebra_1.Vec3.distance(aA.start, aA.end) * 0.9));
-            }
-            else {
-                linear_algebra_1.Mat4.scaleUniformly(t, t, size * getSymbolScale(symbol));
-            }
-        }
-        else {
-            if (linear_algebra_1.Vec3.dot(linear_algebra_1.Vec3.unitY, linear_algebra_1.Vec3.sub(tmpV, aA.end, aA.start)) === 0) {
-                linear_algebra_1.Vec3.copy(up, linear_algebra_1.Vec3.unitY);
-            }
-            else {
-                linear_algebra_1.Vec3.copy(up, linear_algebra_1.Vec3.unitX);
-            }
-            linear_algebra_1.Mat4.targetTo(t, eye, target, up);
-            var sphere = structure.lookup3d.boundary.sphere;
-            var sizeXY = (sphere.radius * 2) * 0.8; // fallback for missing extrema
-            if (geometry_1.Sphere3D.hasExtrema(sphere)) {
-                var n_2 = linear_algebra_1.Mat3.directionTransform((0, linear_algebra_1.Mat3)(), t);
-                var dirs = unitCircleDirections.map(function (d) { return linear_algebra_1.Vec3.transformMat3((0, linear_algebra_1.Vec3)(), d, n_2); });
-                sizeXY = getMaxProjectedDistance(sphere.extrema, dirs, sphere.center);
-            }
-            linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.create(sizeXY, sizeXY, size * 0.9));
-        }
-    }
-}
-var unitCircleDirections = (function () {
-    var dirs = [];
-    var circle = (0, polygon_1.polygon)(12, false, 1);
-    for (var i = 0, il = circle.length; i < il; i += 3) {
-        dirs.push(linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), circle, i));
-    }
-    return dirs;
-})();
-var tmpProj = (0, linear_algebra_1.Vec3)();
-function getMaxProjectedDistance(points, directions, center) {
-    var maxDist = 0;
-    for (var _i = 0, points_1 = points; _i < points_1.length; _i++) {
-        var p = points_1[_i];
-        for (var _a = 0, directions_1 = directions; _a < directions_1.length; _a++) {
-            var d = directions_1[_a];
-            linear_algebra_1.Vec3.projectPointOnVector(tmpProj, p, d, center);
-            var dist = linear_algebra_1.Vec3.distance(tmpProj, center);
-            if (dist > maxDist)
-                maxDist = dist;
-        }
-    }
-    return maxDist;
-}
-function getCageMesh(data, props, mesh) {
-    var assemblySymmetry = prop_1.AssemblySymmetryProvider.get(data).value;
-    var scale = props.scale;
-    var rotation_axes = assemblySymmetry.rotation_axes, symbol = assemblySymmetry.symbol;
-    if (!prop_1.AssemblySymmetry.isRotationAxes(rotation_axes))
-        return mesh_1.Mesh.createEmpty(mesh);
-    var structure = prop_1.AssemblySymmetry.getStructure(data, assemblySymmetry);
-    var cage = getSymbolCage(symbol);
-    if (!cage)
-        return mesh_1.Mesh.createEmpty(mesh);
-    var _a = rotation_axes[0], start = _a.start, end = _a.end;
-    var size = linear_algebra_1.Vec3.distance(start, end);
-    var radius = (size / 500) * scale;
-    var builderState = mesh_builder_1.MeshBuilder.createState(256, 128, mesh);
-    builderState.currentGroup = 0;
-    setSymbolTransform(t, symbol, rotation_axes, size, structure);
-    linear_algebra_1.Vec3.scale(tmpCenter, linear_algebra_1.Vec3.add(tmpCenter, start, end), 0.5);
-    linear_algebra_1.Mat4.setTranslation(t, tmpCenter);
-    mesh_builder_1.MeshBuilder.addCage(builderState, t, cage, radius, 1, 8);
-    return mesh_builder_1.MeshBuilder.getMesh(builderState);
-}
-function getCageShape(ctx, data, props, shape) {
-    var assemblySymmetry = prop_1.AssemblySymmetryProvider.get(data).value;
-    var geo = getCageMesh(data, props, shape && shape.geometry);
-    var getColor = function (groupId) {
-        return props.cageColor;
-    };
-    var getLabel = function (groupId) {
-        var type = assemblySymmetry.type, symbol = assemblySymmetry.symbol, kind = assemblySymmetry.kind;
-        data.model.entryId;
-        return [
-            "<small>".concat(data.model.entryId, "</small>"),
-            "<small>".concat(getAssemblyName(data), "</small>"),
-            "Cage of ".concat(type, " ").concat(kind, " (").concat(symbol, ")")
-        ].join(' | ');
-    };
-    return shape_1.Shape.create('Cage', data, geo, getColor, function () { return 1; }, getLabel);
-}
-function AssemblySymmetryRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Assembly Symmetry', ctx, getParams, representation_2.Representation.StateBuilder, AssemblySymmetryVisuals);
-}
-exports.AssemblySymmetryRepresentation = AssemblySymmetryRepresentation;
-//# sourceMappingURL=representation.js.map