molstar 3.0.0 → 3.0.1

package/lib/commonjs/extensions/cellpack/model.js

@@ -1,903 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Ludovic Autin <ludovic.autin@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.LoadCellPackModel = exports.createStructureFromCellPack = void 0;
-var tslib_1 = require("tslib");
-var mol_state_1 = require("../../mol-state");
-var objects_1 = require("../../mol-plugin-state/objects");
-var param_definition_1 = require("../../mol-util/param-definition");
-var util_1 = require("./util");
-var structure_1 = require("../../mol-model/structure");
-var mmcif_1 = require("../../mol-model-formats/structure/mmcif");
-var pdb_1 = require("../../mol-model-formats/structure/pdb");
-var linear_algebra_1 = require("../../mol-math/linear-algebra");
-var geometry_1 = require("../../mol-math/geometry");
-var mol_task_1 = require("../../mol-task");
-var transforms_1 = require("../../mol-plugin-state/transforms");
-var state_1 = require("./state");
-var builder_1 = require("../../mol-script/language/builder");
-var curve_1 = require("./curve");
-var compiler_1 = require("../../mol-script/runtime/query/compiler");
-var cif_1 = require("../../mol-io/reader/cif");
-var db_1 = require("../../mol-data/db");
-var parser_1 = require("../../mol-model-formats/structure/basic/parser");
-var preset_1 = require("./preset");
-var assets_1 = require("../../mol-util/assets");
-var color_1 = require("../../mol-util/color");
-var object_1 = require("../../mol-util/object");
-var data_source_1 = require("../../mol-util/data-source");
-var names_1 = require("../../mol-util/color/names");
-function getCellPackModelUrl(fileName, baseUrl) {
-    return "".concat(baseUrl, "/results/").concat(fileName);
-}
-var TrajectoryCache = /** @class */ (function () {
-    function TrajectoryCache() {
-        this.map = new Map();
-    }
-    TrajectoryCache.prototype.set = function (id, trajectory) { this.map.set(id, trajectory); };
-    TrajectoryCache.prototype.get = function (id) { return this.map.get(id); };
-    return TrajectoryCache;
-}());
-function getModel(plugin, id, ingredient, baseUrl, trajCache, location, file) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var assetManager, modelIndex, surface, trajectory, assets, text, cif, binary, cif, text, pdb, data, e_1, _a, mmcif, asset, _b, mmcif, asset, data, model;
-        return (0, tslib_1.__generator)(this, function (_c) {
-            switch (_c.label) {
-                case 0:
-                    assetManager = plugin.managers.asset;
-                    modelIndex = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
-                    surface = (ingredient.ingtype) ? (ingredient.ingtype === 'transmembrane') : false;
-                    if (location === 'surface')
-                        surface = true;
-                    trajectory = trajCache.get(id);
-                    assets = [];
-                    if (!!trajectory) return [3 /*break*/, 32];
-                    if (!file) return [3 /*break*/, 14];
-                    if (!file.name.endsWith('.cif')) return [3 /*break*/, 4];
-                    return [4 /*yield*/, plugin.runTask(assetManager.resolve(file, 'string'))];
-                case 1:
-                    text = _c.sent();
-                    assets.push(text);
-                    return [4 /*yield*/, (0, util_1.parseCif)(plugin, text.data)];
-                case 2:
-                    cif = (_c.sent()).blocks[0];
-                    return [4 /*yield*/, plugin.runTask((0, mmcif_1.trajectoryFromMmCIF)(cif))];
-                case 3:
-                    trajectory = _c.sent();
-                    return [3 /*break*/, 13];
-                case 4:
-                    if (!file.name.endsWith('.bcif')) return [3 /*break*/, 8];
-                    return [4 /*yield*/, plugin.runTask(assetManager.resolve(file, 'binary'))];
-                case 5:
-                    binary = _c.sent();
-                    assets.push(binary);
-                    return [4 /*yield*/, (0, util_1.parseCif)(plugin, binary.data)];
-                case 6:
-                    cif = (_c.sent()).blocks[0];
-                    return [4 /*yield*/, plugin.runTask((0, mmcif_1.trajectoryFromMmCIF)(cif))];
-                case 7:
-                    trajectory = _c.sent();
-                    return [3 /*break*/, 13];
-                case 8:
-                    if (!file.name.endsWith('.pdb')) return [3 /*break*/, 12];
-                    return [4 /*yield*/, plugin.runTask(assetManager.resolve(file, 'string'))];
-                case 9:
-                    text = _c.sent();
-                    assets.push(text);
-                    return [4 /*yield*/, (0, util_1.parsePDBfile)(plugin, text.data, id)];
-                case 10:
-                    pdb = _c.sent();
-                    return [4 /*yield*/, plugin.runTask((0, pdb_1.trajectoryFromPDB)(pdb))];
-                case 11:
-                    trajectory = _c.sent();
-                    return [3 /*break*/, 13];
-                case 12: throw new Error("unsupported file type '".concat(file.name, "'"));
-                case 13: return [3 /*break*/, 31];
-                case 14:
-                    if (!id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) return [3 /*break*/, 26];
-                    if (!surface) return [3 /*break*/, 22];
-                    _c.label = 15;
-                case 15:
-                    _c.trys.push([15, 18, , 21]);
-                    return [4 /*yield*/, (0, util_1.getFromOPM)(plugin, id, assetManager)];
-                case 16:
-                    data = _c.sent();
-                    assets.push(data.asset);
-                    data.pdb.id = id.toUpperCase();
-                    return [4 /*yield*/, plugin.runTask((0, pdb_1.trajectoryFromPDB)(data.pdb))];
-                case 17:
-                    trajectory = _c.sent();
-                    return [3 /*break*/, 21];
-                case 18:
-                    e_1 = _c.sent();
-                    return [4 /*yield*/, (0, util_1.getFromPdb)(plugin, id, assetManager)];
-                case 19:
-                    _a = _c.sent(), mmcif = _a.mmcif, asset = _a.asset;
-                    assets.push(asset);
-                    return [4 /*yield*/, plugin.runTask((0, mmcif_1.trajectoryFromMmCIF)(mmcif))];
-                case 20:
-                    trajectory = _c.sent();
-                    return [3 /*break*/, 21];
-                case 21: return [3 /*break*/, 25];
-                case 22: return [4 /*yield*/, (0, util_1.getFromPdb)(plugin, id, assetManager)];
-                case 23:
-                    _b = _c.sent(), mmcif = _b.mmcif, asset = _b.asset;
-                    assets.push(asset);
-                    return [4 /*yield*/, plugin.runTask((0, mmcif_1.trajectoryFromMmCIF)(mmcif))];
-                case 24:
-                    trajectory = _c.sent();
-                    _c.label = 25;
-                case 25: return [3 /*break*/, 31];
-                case 26: return [4 /*yield*/, (0, util_1.getFromCellPackDB)(plugin, id, baseUrl, assetManager)];
-                case 27:
-                    data = _c.sent();
-                    assets.push(data.asset);
-                    if (!('pdb' in data)) return [3 /*break*/, 29];
-                    return [4 /*yield*/, plugin.runTask((0, pdb_1.trajectoryFromPDB)(data.pdb))];
-                case 28:
-                    trajectory = _c.sent();
-                    return [3 /*break*/, 31];
-                case 29: return [4 /*yield*/, plugin.runTask((0, mmcif_1.trajectoryFromMmCIF)(data.mmcif))];
-                case 30:
-                    trajectory = _c.sent();
-                    _c.label = 31;
-                case 31:
-                    trajCache.set(id, trajectory);
-                    _c.label = 32;
-                case 32: return [4 /*yield*/, plugin.resolveTask(trajectory === null || trajectory === void 0 ? void 0 : trajectory.getFrameAtIndex(modelIndex))];
-                case 33:
-                    model = _c.sent();
-                    return [2 /*return*/, { model: model, assets: assets }];
-            }
-        });
-    });
-}
-function getStructure(plugin, model, source, props) {
-    if (props === void 0) { props = {}; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var structure, assembly, query, sel, asymIds, compiled, result;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    structure = structure_1.Structure.ofModel(model);
-                    assembly = props.assembly;
-                    if (!assembly) return [3 /*break*/, 2];
-                    return [4 /*yield*/, plugin.runTask(structure_1.StructureSymmetry.buildAssembly(structure, assembly))];
-                case 1:
-                    structure = _a.sent();
-                    _a.label = 2;
-                case 2:
-                    if (source.source.selection) {
-                        sel = source.source.selection;
-                        asymIds = sel.replace(/ /g, '').replace(/:/g, '').split('or').slice(1);
-                        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('auth_asym_id')])
-                            })
-                        ]);
-                    }
-                    else {
-                        query = builder_1.MolScriptBuilder.struct.modifier.union([
-                            builder_1.MolScriptBuilder.struct.generator.atomGroups({
-                                'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer'])
-                            })
-                        ]);
-                    }
-                    compiled = (0, compiler_1.compile)(query);
-                    result = compiled(new structure_1.QueryContext(structure));
-                    structure = structure_1.StructureSelection.unionStructure(result);
-                    // change here if possible the label ?
-                    // structure.label =  source.name;
-                    return [2 /*return*/, structure];
-            }
-        });
-    });
-}
-function getTransformLegacy(trans, rot) {
-    var q = linear_algebra_1.Quat.create(-rot[3], rot[0], rot[1], rot[2]);
-    var m = linear_algebra_1.Mat4.fromQuat(linear_algebra_1.Mat4.zero(), q);
-    linear_algebra_1.Mat4.transpose(m, m);
-    linear_algebra_1.Mat4.scale(m, m, linear_algebra_1.Vec3.create(-1.0, 1.0, -1.0));
-    linear_algebra_1.Mat4.setTranslation(m, trans);
-    return m;
-}
-function getTransform(trans, rot) {
-    var q = linear_algebra_1.Quat.create(-rot[0], rot[1], rot[2], -rot[3]);
-    var m = linear_algebra_1.Mat4.fromQuat(linear_algebra_1.Mat4.zero(), q);
-    var p = linear_algebra_1.Vec3.create(-trans[0], trans[1], trans[2]);
-    linear_algebra_1.Mat4.setTranslation(m, p);
-    return m;
-}
-function getResultTransforms(results, legacy) {
-    if (legacy)
-        return results.map(function (r) { return getTransformLegacy(r[0], r[1]); });
-    else
-        return results.map(function (r) { return getTransform(r[0], r[1]); });
-}
-function getCurveTransforms(ingredient) {
-    var n = ingredient.nbCurve || 0;
-    var instances = [];
-    var segmentLength = 3.4;
-    if (ingredient.uLength) {
-        segmentLength = ingredient.uLength;
-    }
-    else if (ingredient.radii) {
-        segmentLength = ingredient.radii[0].radii
-            ? ingredient.radii[0].radii[0] * 2.0
-            : 3.4;
-    }
-    var resampling = false;
-    for (var i = 0; i < n; ++i) {
-        var cname = "curve".concat(i);
-        if (!(cname in ingredient)) {
-            console.warn("Expected '".concat(cname, "' in ingredient"));
-            continue;
-        }
-        var _points = ingredient[cname];
-        if (_points.length <= 2) {
-            // TODO handle curve with 2 or less points
-            continue;
-        }
-        // test for resampling
-        var distance = linear_algebra_1.Vec3.distance(_points[0], _points[1]);
-        if (distance >= segmentLength + 2.0) {
-            // console.info(distance);
-            resampling = true;
-        }
-        var points = new Float32Array(_points.length * 3);
-        for (var i_1 = 0, il = _points.length; i_1 < il; ++i_1)
-            linear_algebra_1.Vec3.toArray(_points[i_1], points, i_1 * 3);
-        var newInstances = (0, curve_1.getMatFromResamplePoints)(points, segmentLength, resampling);
-        instances.push.apply(instances, newInstances);
-    }
-    return instances;
-}
-function getAssembly(name, transforms, structure) {
-    var builder = structure_1.Structure.Builder({ label: name });
-    var units = structure.units;
-    for (var i = 0, il = transforms.length; i < il; ++i) {
-        var id = "".concat(i + 1);
-        var op = geometry_1.SymmetryOperator.create(id, transforms[i], { assembly: { id: id, operId: i, operList: [id] } });
-        for (var _i = 0, units_1 = units; _i < units_1.length; _i++) {
-            var unit = units_1[_i];
-            builder.addWithOperator(unit, op);
-        }
-    }
-    return builder.getStructure();
-}
-function getCifCurve(name, transforms, model) {
-    if (!mmcif_1.MmcifFormat.is(model.sourceData))
-        throw new Error('mmcif source data needed');
-    var db = model.sourceData.data.db;
-    var d = db.atom_site;
-    var n = d._rowCount;
-    var rowCount = n * transforms.length;
-    var _a = model.atomicHierarchy.chainAtomSegments, offsets = _a.offsets, count = _a.count;
-    var x = d.Cartn_x.toArray();
-    var y = d.Cartn_y.toArray();
-    var z = d.Cartn_z.toArray();
-    var Cartn_x = new Float32Array(rowCount);
-    var Cartn_y = new Float32Array(rowCount);
-    var Cartn_z = new Float32Array(rowCount);
-    var map = new Uint32Array(rowCount);
-    var seq = new Int32Array(rowCount);
-    var offset = 0;
-    for (var c = 0; c < count; ++c) {
-        var cStart = offsets[c];
-        var cEnd = offsets[c + 1];
-        var cLength = cEnd - cStart;
-        for (var t = 0, tl = transforms.length; t < tl; ++t) {
-            var m = transforms[t];
-            for (var j = cStart; j < cEnd; ++j) {
-                var i = offset + j - cStart;
-                var xj = x[j], yj = y[j], zj = z[j];
-                Cartn_x[i] = m[0] * xj + m[4] * yj + m[8] * zj + m[12];
-                Cartn_y[i] = m[1] * xj + m[5] * yj + m[9] * zj + m[13];
-                Cartn_z[i] = m[2] * xj + m[6] * yj + m[10] * zj + m[14];
-                map[i] = j;
-                seq[i] = t + 1;
-            }
-            offset += cLength;
-        }
-    }
-    function multColumn(column) {
-        var array = column.toArray();
-        return db_1.Column.ofLambda({
-            value: function (row) { return array[map[row]]; },
-            areValuesEqual: function (rowA, rowB) { return map[rowA] === map[rowB] || array[map[rowA]] === array[map[rowB]]; },
-            rowCount: rowCount,
-            schema: column.schema
-        });
-    }
-    var _atom_site = {
-        auth_asym_id: cif_1.CifField.ofColumn(multColumn(d.auth_asym_id)),
-        auth_atom_id: cif_1.CifField.ofColumn(multColumn(d.auth_atom_id)),
-        auth_comp_id: cif_1.CifField.ofColumn(multColumn(d.auth_comp_id)),
-        auth_seq_id: cif_1.CifField.ofNumbers(seq),
-        B_iso_or_equiv: cif_1.CifField.ofColumn(db_1.Column.ofConst(0, rowCount, db_1.Column.Schema.float)),
-        Cartn_x: cif_1.CifField.ofNumbers(Cartn_x),
-        Cartn_y: cif_1.CifField.ofNumbers(Cartn_y),
-        Cartn_z: cif_1.CifField.ofNumbers(Cartn_z),
-        group_PDB: cif_1.CifField.ofColumn(db_1.Column.ofConst('ATOM', rowCount, db_1.Column.Schema.str)),
-        id: cif_1.CifField.ofColumn(db_1.Column.ofLambda({
-            value: function (row) { return row; },
-            areValuesEqual: function (rowA, rowB) { return rowA === rowB; },
-            rowCount: rowCount,
-            schema: d.id.schema,
-        })),
-        label_alt_id: cif_1.CifField.ofColumn(multColumn(d.label_alt_id)),
-        label_asym_id: cif_1.CifField.ofColumn(multColumn(d.label_asym_id)),
-        label_atom_id: cif_1.CifField.ofColumn(multColumn(d.label_atom_id)),
-        label_comp_id: cif_1.CifField.ofColumn(multColumn(d.label_comp_id)),
-        label_seq_id: cif_1.CifField.ofNumbers(seq),
-        label_entity_id: cif_1.CifField.ofColumn(db_1.Column.ofConst('1', rowCount, db_1.Column.Schema.str)),
-        occupancy: cif_1.CifField.ofColumn(db_1.Column.ofConst(1, rowCount, db_1.Column.Schema.float)),
-        type_symbol: cif_1.CifField.ofColumn(multColumn(d.type_symbol)),
-        pdbx_PDB_ins_code: cif_1.CifField.ofColumn(db_1.Column.ofConst('', rowCount, db_1.Column.Schema.str)),
-        pdbx_PDB_model_num: cif_1.CifField.ofColumn(db_1.Column.ofConst(1, rowCount, db_1.Column.Schema.int)),
-    };
-    var categories = {
-        entity: cif_1.CifCategory.ofTable('entity', db.entity),
-        chem_comp: cif_1.CifCategory.ofTable('chem_comp', db.chem_comp),
-        atom_site: cif_1.CifCategory.ofFields('atom_site', _atom_site)
-    };
-    return {
-        header: name,
-        categoryNames: Object.keys(categories),
-        categories: categories
-    };
-}
-function getCurve(plugin, name, ingredient, transforms, model) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var cif, curveModelTask, curveModel;
-        var _this = this;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    cif = getCifCurve(name, transforms, model);
-                    curveModelTask = mol_task_1.Task.create('Curve Model', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                        var format, models;
-                        return (0, tslib_1.__generator)(this, function (_a) {
-                            switch (_a.label) {
-                                case 0:
-                                    format = mmcif_1.MmcifFormat.fromFrame(cif);
-                                    return [4 /*yield*/, (0, parser_1.createModels)(format.data.db, format, ctx)];
-                                case 1:
-                                    models = _a.sent();
-                                    return [2 /*return*/, models.representative];
-                            }
-                        });
-                    }); });
-                    return [4 /*yield*/, plugin.runTask(curveModelTask)];
-                case 1:
-                    curveModel = _a.sent();
-                    // ingredient.source.selection = undefined;
-                    return [2 /*return*/, getStructure(plugin, curveModel, ingredient)];
-            }
-        });
-    });
-}
-function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, trajCache, location) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var name, source, results, nbCurve, file, _a, model, assets, structure, bu, legacy, pcp, structureMean, m1, o, m, p, q, m;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0:
-                    name = ingredient.name, source = ingredient.source, results = ingredient.results, nbCurve = ingredient.nbCurve;
-                    if (source.pdb === 'None')
-                        return [2 /*return*/];
-                    file = ingredientFiles[source.pdb];
-                    if (!file) {
-                        // TODO can these be added to the library?
-                        if (name === 'HIV1_CAhex_0_1_0')
-                            return [2 /*return*/]; // 1VU4CtoH_hex.pdb
-                        if (name === 'HIV1_CAhexCyclophilA_0_1_0')
-                            return [2 /*return*/]; // 1AK4fitTo1VU4hex.pdb
-                        if (name === 'iLDL')
-                            return [2 /*return*/]; // EMD-5239
-                        if (name === 'peptides')
-                            return [2 /*return*/]; // peptide.pdb
-                        if (name === 'lypoglycane')
-                            return [2 /*return*/];
-                    }
-                    return [4 /*yield*/, getModel(plugin, source.pdb || name, ingredient, baseUrl, trajCache, location, file)];
-                case 1:
-                    _a = _b.sent(), model = _a.model, assets = _a.assets;
-                    if (!model)
-                        return [2 /*return*/];
-                    if (!nbCurve) return [3 /*break*/, 3];
-                    return [4 /*yield*/, getCurve(plugin, name, ingredient, getCurveTransforms(ingredient), model)];
-                case 2:
-                    structure = _b.sent();
-                    return [3 /*break*/, 5];
-                case 3:
-                    if ((!results || results.length === 0))
-                        return [2 /*return*/];
-                    bu = source.bu ? source.bu : undefined;
-                    if (bu) {
-                        if (bu === 'AU') {
-                            bu = undefined;
-                        }
-                        else {
-                            bu = bu.slice(2);
-                        }
-                    }
-                    return [4 /*yield*/, getStructure(plugin, model, ingredient, { assembly: bu })];
-                case 4:
-                    structure = _b.sent();
-                    legacy = true;
-                    pcp = ingredient.principalVector ? ingredient.principalVector : ingredient.principalAxis;
-                    if (pcp) {
-                        legacy = false;
-                        structureMean = (0, util_1.getStructureMean)(structure);
-                        linear_algebra_1.Vec3.negate(structureMean, structureMean);
-                        m1 = linear_algebra_1.Mat4.identity();
-                        linear_algebra_1.Mat4.setTranslation(m1, structureMean);
-                        structure = structure_1.Structure.transform(structure, m1);
-                        if (ingredient.offset) {
-                            o = linear_algebra_1.Vec3.create(ingredient.offset[0], ingredient.offset[1], ingredient.offset[2]);
-                            if (!linear_algebra_1.Vec3.exactEquals(o, linear_algebra_1.Vec3.zero())) { // -1, 1, 4e-16 ??
-                                if (location !== 'surface') {
-                                    linear_algebra_1.Vec3.negate(o, o);
-                                }
-                                m = linear_algebra_1.Mat4.identity();
-                                linear_algebra_1.Mat4.setTranslation(m, o);
-                                structure = structure_1.Structure.transform(structure, m);
-                            }
-                        }
-                        if (pcp) {
-                            p = linear_algebra_1.Vec3.create(pcp[0], pcp[1], pcp[2]);
-                            if (!linear_algebra_1.Vec3.exactEquals(p, linear_algebra_1.Vec3.unitZ)) {
-                                q = linear_algebra_1.Quat.identity();
-                                linear_algebra_1.Quat.rotationTo(q, p, linear_algebra_1.Vec3.unitZ);
-                                m = linear_algebra_1.Mat4.fromQuat(linear_algebra_1.Mat4.zero(), q);
-                                structure = structure_1.Structure.transform(structure, m);
-                            }
-                        }
-                    }
-                    structure = getAssembly(name, getResultTransforms(results, legacy), structure);
-                    _b.label = 5;
-                case 5: return [2 /*return*/, { structure: structure, assets: assets }];
-            }
-        });
-    });
-}
-function createStructureFromCellPack(plugin, packing, baseUrl, ingredientFiles) {
-    var _this = this;
-    return mol_task_1.Task.create('Create Packing Structure', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        var ingredients, location, name, assets, trajCache, structures, colors, _a, _b, _i, iName, ingredientStructure, c, units, offsetInvariantId, offsetChainGroupId, _c, structures_1, s, maxInvariantId, maxChainGroupId, _d, _e, u, invariantId, chainGroupId, structure, i, il;
-        return (0, tslib_1.__generator)(this, function (_f) {
-            switch (_f.label) {
-                case 0:
-                    ingredients = packing.ingredients, location = packing.location, name = packing.name;
-                    assets = [];
-                    trajCache = new TrajectoryCache();
-                    structures = [];
-                    colors = [];
-                    _a = [];
-                    for (_b in ingredients)
-                        _a.push(_b);
-                    _i = 0;
-                    _f.label = 1;
-                case 1:
-                    if (!(_i < _a.length)) return [3 /*break*/, 6];
-                    iName = _a[_i];
-                    if (!ctx.shouldUpdate) return [3 /*break*/, 3];
-                    return [4 /*yield*/, ctx.update(iName)];
-                case 2:
-                    _f.sent();
-                    _f.label = 3;
-                case 3: return [4 /*yield*/, getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache, location)];
-                case 4:
-                    ingredientStructure = _f.sent();
-                    if (ingredientStructure) {
-                        structures.push(ingredientStructure.structure);
-                        assets.push.apply(assets, ingredientStructure.assets);
-                        c = ingredients[iName].color;
-                        if (c) {
-                            colors.push(color_1.Color.fromNormalizedRgb(c[0], c[1], c[2]));
-                        }
-                        else {
-                            colors.push(color_1.Color.fromNormalizedRgb(1, 0, 0));
-                        }
-                    }
-                    _f.label = 5;
-                case 5:
-                    _i++;
-                    return [3 /*break*/, 1];
-                case 6:
-                    if (!ctx.shouldUpdate) return [3 /*break*/, 8];
-                    return [4 /*yield*/, ctx.update("".concat(name, " - units"))];
-                case 7:
-                    _f.sent();
-                    _f.label = 8;
-                case 8:
-                    units = [];
-                    offsetInvariantId = 0;
-                    offsetChainGroupId = 0;
-                    _c = 0, structures_1 = structures;
-                    _f.label = 9;
-                case 9:
-                    if (!(_c < structures_1.length)) return [3 /*break*/, 13];
-                    s = structures_1[_c];
-                    if (!ctx.shouldUpdate) return [3 /*break*/, 11];
-                    return [4 /*yield*/, ctx.update("".concat(s.label))];
-                case 10:
-                    _f.sent();
-                    _f.label = 11;
-                case 11:
-                    maxInvariantId = 0;
-                    maxChainGroupId = 0;
-                    for (_d = 0, _e = s.units; _d < _e.length; _d++) {
-                        u = _e[_d];
-                        invariantId = u.invariantId + offsetInvariantId;
-                        chainGroupId = u.chainGroupId + offsetChainGroupId;
-                        if (u.invariantId > maxInvariantId)
-                            maxInvariantId = u.invariantId;
-                        units.push(structure_1.Unit.create(units.length, invariantId, chainGroupId, u.traits, u.kind, u.model, u.conformation.operator, u.elements, u.props));
-                    }
-                    offsetInvariantId += maxInvariantId + 1;
-                    offsetChainGroupId += maxChainGroupId + 1;
-                    _f.label = 12;
-                case 12:
-                    _c++;
-                    return [3 /*break*/, 9];
-                case 13:
-                    if (!ctx.shouldUpdate) return [3 /*break*/, 15];
-                    return [4 /*yield*/, ctx.update("".concat(name, " - structure"))];
-                case 14:
-                    _f.sent();
-                    _f.label = 15;
-                case 15:
-                    structure = structure_1.Structure.create(units, { label: name + '.' + location });
-                    for (i = 0, il = structure.models.length; i < il; ++i) {
-                        structure_1.Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
-                    }
-                    return [2 /*return*/, { structure: structure, assets: assets, colors: colors }];
-            }
-        });
-    }); });
-}
-exports.createStructureFromCellPack = createStructureFromCellPack;
-function handleHivRna(plugin, packings, baseUrl) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var i, il, url, json, points, curve0, j, jl;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    i = 0, il = packings.length;
-                    _a.label = 1;
-                case 1:
-                    if (!(i < il)) return [3 /*break*/, 4];
-                    if (!(packings[i].name === 'HIV1_capsid_3j3q_PackInner_0_1_0' || packings[i].name === 'HIV_capsid')) return [3 /*break*/, 3];
-                    url = assets_1.Asset.getUrlAsset(plugin.managers.asset, "".concat(baseUrl, "/extras/rna_allpoints.json"));
-                    return [4 /*yield*/, plugin.runTask(plugin.managers.asset.resolve(url, 'json', false))];
-                case 2:
-                    json = _a.sent();
-                    points = json.data.points;
-                    curve0 = [];
-                    for (j = 0, jl = points.length; j < jl; j += 3) {
-                        curve0.push(linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), points, j));
-                    }
-                    packings[i].ingredients['RNA'] = {
-                        source: { pdb: 'RNA_U_Base.pdb', transform: { center: false } },
-                        results: [],
-                        name: 'RNA',
-                        nbCurve: 1,
-                        curve0: curve0
-                    };
-                    _a.label = 3;
-                case 3:
-                    ++i;
-                    return [3 /*break*/, 1];
-                case 4: return [2 /*return*/];
-            }
-        });
-    });
-}
-function loadMembrane(plugin, name, state, params) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var file, fileName, _i, _a, f, cifileName, _b, _c, f, legacy_membrane, geometry_membrane, b, url, url, url, url, props, membrane, membraneParams, membrane, membraneParams;
-        return (0, tslib_1.__generator)(this, function (_d) {
-            switch (_d.label) {
-                case 0:
-                    file = undefined;
-                    if (params.ingredients !== null) {
-                        fileName = "".concat(name, ".bcif");
-                        for (_i = 0, _a = params.ingredients; _i < _a.length; _i++) {
-                            f = _a[_i];
-                            if (fileName === f.name) {
-                                file = f;
-                                break;
-                            }
-                        }
-                        if (!file) {
-                            cifileName = "".concat(name, ".cif");
-                            for (_b = 0, _c = params.ingredients; _b < _c.length; _b++) {
-                                f = _c[_b];
-                                if (cifileName === f.name) {
-                                    file = f;
-                                    break;
-                                }
-                            }
-                        }
-                    }
-                    legacy_membrane = false;
-                    geometry_membrane = false;
-                    b = state.build().toRoot();
-                    if (file) {
-                        if (file.name.endsWith('.cif')) {
-                            b = b.apply(transforms_1.StateTransforms.Data.ReadFile, { file: file, isBinary: false, label: file.name }, { state: { isGhost: true } });
-                        }
-                        else if (file.name.endsWith('.bcif')) {
-                            b = b.apply(transforms_1.StateTransforms.Data.ReadFile, { file: file, isBinary: true, label: file.name }, { state: { isGhost: true } });
-                        }
-                    }
-                    else {
-                        if (name.toLowerCase().endsWith('.bcif')) {
-                            url = assets_1.Asset.getUrlAsset(plugin.managers.asset, "".concat(params.baseUrl, "/membranes/").concat(name));
-                            b = b.apply(transforms_1.StateTransforms.Data.Download, { url: url, isBinary: true, label: name }, { state: { isGhost: true } });
-                        }
-                        else if (name.toLowerCase().endsWith('.cif')) {
-                            url = assets_1.Asset.getUrlAsset(plugin.managers.asset, "".concat(params.baseUrl, "/membranes/").concat(name));
-                            b = b.apply(transforms_1.StateTransforms.Data.Download, { url: url, isBinary: false, label: name }, { state: { isGhost: true } });
-                        }
-                        else if (name.toLowerCase().endsWith('.ply')) {
-                            url = assets_1.Asset.getUrlAsset(plugin.managers.asset, "".concat(params.baseUrl, "/geometries/").concat(name));
-                            b = b.apply(transforms_1.StateTransforms.Data.Download, { url: url, isBinary: false, label: name }, { state: { isGhost: true } });
-                            geometry_membrane = true;
-                        }
-                        else {
-                            url = assets_1.Asset.getUrlAsset(plugin.managers.asset, "".concat(params.baseUrl, "/membranes/").concat(name, ".bcif"));
-                            b = b.apply(transforms_1.StateTransforms.Data.Download, { url: url, isBinary: true, label: name }, { state: { isGhost: true } });
-                            legacy_membrane = true;
-                        }
-                    }
-                    props = {
-                        type: {
-                            name: 'assembly',
-                            params: { id: '1' }
-                        }
-                    };
-                    if (!legacy_membrane) return [3 /*break*/, 3];
-                    return [4 /*yield*/, b.apply(transforms_1.StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
-                            .apply(transforms_1.StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
-                            .apply(transforms_1.StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
-                            .apply(state_1.StructureFromAssemblies, undefined, { state: { isGhost: true } })
-                            .commit({ revertOnError: true })];
-                case 1:
-                    membrane = _d.sent();
-                    membraneParams = {
-                        representation: params.preset.representation,
-                    };
-                    return [4 /*yield*/, preset_1.CellpackMembranePreset.apply(membrane, membraneParams, plugin)];
-                case 2:
-                    _d.sent();
-                    return [3 /*break*/, 8];
-                case 3:
-                    if (!geometry_membrane) return [3 /*break*/, 5];
-                    return [4 /*yield*/, b.apply(transforms_1.StateTransforms.Data.ParsePly, undefined, { state: { isGhost: true } })
-                            .apply(transforms_1.StateTransforms.Model.ShapeFromPly)
-                            .apply(transforms_1.StateTransforms.Representation.ShapeRepresentation3D, { xrayShaded: true,
-                            doubleSided: true, coloring: { name: 'uniform', params: { color: names_1.ColorNames.orange } } })
-                            .commit({ revertOnError: true })];
-                case 4:
-                    _d.sent();
-                    return [3 /*break*/, 8];
-                case 5: return [4 /*yield*/, b.apply(transforms_1.StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
-                        .apply(transforms_1.StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
-                        .apply(transforms_1.StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
-                        .apply(transforms_1.StateTransforms.Model.StructureFromModel, props, { state: { isGhost: true } })
-                        .commit({ revertOnError: true })];
-                case 6:
-                    membrane = _d.sent();
-                    membraneParams = {
-                        representation: params.preset.representation,
-                    };
-                    return [4 /*yield*/, preset_1.CellpackMembranePreset.apply(membrane, membraneParams, plugin)];
-                case 7:
-                    _d.sent();
-                    _d.label = 8;
-                case 8: return [2 /*return*/];
-            }
-        });
-    });
-}
-function handleMembraneSpheres(state, primitives) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var nSpheres, j;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    nSpheres = primitives.positions.length / 3;
-                    j = 0;
-                    _a.label = 1;
-                case 1:
-                    if (!(j < nSpheres)) return [3 /*break*/, 4];
-                    return [4 /*yield*/, state.build()
-                            .toRoot()
-                            .apply(state_1.CreateCompartmentSphere, {
-                            center: linear_algebra_1.Vec3.create(primitives.positions[j * 3 + 0], primitives.positions[j * 3 + 1], primitives.positions[j * 3 + 2]),
-                            radius: primitives.radii[j]
-                        })
-                            .commit()];
-                case 2:
-                    _a.sent();
-                    _a.label = 3;
-                case 3:
-                    j++;
-                    return [3 /*break*/, 1];
-                case 4: return [2 /*return*/];
-            }
-        });
-    });
-}
-function loadPackings(plugin, runtime, state, params) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var ingredientFiles, cellPackJson, resultsFile, url, file, modelFile, data, cellPackBuilder, cellPackObject, packings, i, il, p, packing, packingParams;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    ingredientFiles = params.ingredients || [];
-                    resultsFile = params.results;
-                    if (!(params.source.name === 'id')) return [3 /*break*/, 1];
-                    url = assets_1.Asset.getUrlAsset(plugin.managers.asset, getCellPackModelUrl(params.source.params, params.baseUrl));
-                    cellPackJson = state.build().toRoot()
-                        .apply(transforms_1.StateTransforms.Data.Download, { url: url, isBinary: false, label: params.source.params }, { state: { isGhost: true } });
-                    return [3 /*break*/, 5];
-                case 1:
-                    file = params.source.params;
-                    if (!(file === null || file === void 0 ? void 0 : file.file)) {
-                        plugin.log.error('No file selected');
-                        return [2 /*return*/];
-                    }
-                    modelFile = void 0;
-                    if (!file.name.toLowerCase().endsWith('.zip')) return [3 /*break*/, 3];
-                    return [4 /*yield*/, (0, data_source_1.readFromFile)(file.file, 'zip').runInContext(runtime)];
-                case 2:
-                    data = _a.sent();
-                    if (data['model.json']) {
-                        modelFile = assets_1.Asset.File(new File([data['model.json']], 'model.json'));
-                    }
-                    else {
-                        throw new Error('model.json missing from zip file');
-                    }
-                    if (data['results.bin']) {
-                        resultsFile = assets_1.Asset.File(new File([data['results.bin']], 'results.bin'));
-                    }
-                    (0, object_1.objectForEach)(data, function (v, k) {
-                        if (k === 'model.json')
-                            return;
-                        if (k === 'results.bin')
-                            return;
-                        ingredientFiles.push(assets_1.Asset.File(new File([v], k)));
-                    });
-                    return [3 /*break*/, 4];
-                case 3:
-                    modelFile = file;
-                    _a.label = 4;
-                case 4:
-                    cellPackJson = state.build().toRoot()
-                        .apply(transforms_1.StateTransforms.Data.ReadFile, { file: modelFile, isBinary: false, label: modelFile.name }, { state: { isGhost: true } });
-                    _a.label = 5;
-                case 5:
-                    cellPackBuilder = cellPackJson
-                        .apply(transforms_1.StateTransforms.Data.ParseJson, undefined, { state: { isGhost: true } })
-                        .apply(state_1.ParseCellPack, { resultsFile: resultsFile, baseUrl: params.baseUrl });
-                    return [4 /*yield*/, state.updateTree(cellPackBuilder).runInContext(runtime)];
-                case 6:
-                    cellPackObject = _a.sent();
-                    packings = cellPackObject.obj.data.packings;
-                    return [4 /*yield*/, handleHivRna(plugin, packings, params.baseUrl)];
-                case 7:
-                    _a.sent();
-                    i = 0, il = packings.length;
-                    _a.label = 8;
-                case 8:
-                    if (!(i < il)) return [3 /*break*/, 23];
-                    p = { packing: i, baseUrl: params.baseUrl, ingredientFiles: ingredientFiles };
-                    return [4 /*yield*/, state.build()
-                            .to(cellPackBuilder.ref)
-                            .apply(state_1.StructureFromCellpack, p)
-                            .commit({ revertOnError: true })];
-                case 9:
-                    packing = _a.sent();
-                    packingParams = {
-                        traceOnly: params.preset.traceOnly,
-                        representation: params.preset.representation,
-                    };
-                    return [4 /*yield*/, preset_1.CellpackPackingPreset.apply(packing, packingParams, plugin)];
-                case 10:
-                    _a.sent();
-                    if (!packings[i].compartment) return [3 /*break*/, 22];
-                    if (!(params.membrane === 'lipids')) return [3 /*break*/, 18];
-                    if (!packings[i].compartment.geom_type) return [3 /*break*/, 15];
-                    if (!(packings[i].compartment.geom_type === 'file')) return [3 /*break*/, 12];
-                    // TODO: load mesh files or vertex,faces data
-                    return [4 /*yield*/, loadMembrane(plugin, packings[i].compartment.filename, state, params)];
-                case 11:
-                    // TODO: load mesh files or vertex,faces data
-                    _a.sent();
-                    return [3 /*break*/, 14];
-                case 12:
-                    if (!packings[i].compartment.compartment_primitives) return [3 /*break*/, 14];
-                    return [4 /*yield*/, handleMembraneSpheres(state, packings[i].compartment.compartment_primitives)];
-                case 13:
-                    _a.sent();
-                    _a.label = 14;
-                case 14: return [3 /*break*/, 17];
-                case 15:
-                    if (!(params.membrane === 'lipids')) return [3 /*break*/, 17];
-                    return [4 /*yield*/, loadMembrane(plugin, packings[i].name, state, params)];
-                case 16:
-                    _a.sent();
-                    _a.label = 17;
-                case 17: return [3 /*break*/, 22];
-                case 18:
-                    if (!(params.membrane === 'geometry')) return [3 /*break*/, 22];
-                    if (!packings[i].compartment.compartment_primitives) return [3 /*break*/, 20];
-                    return [4 /*yield*/, handleMembraneSpheres(state, packings[i].compartment.compartment_primitives)];
-                case 19:
-                    _a.sent();
-                    return [3 /*break*/, 22];
-                case 20:
-                    if (!(packings[i].compartment.geom_type === 'file')) return [3 /*break*/, 22];
-                    if (!packings[i].compartment.filename.toLowerCase().endsWith('.ply')) return [3 /*break*/, 22];
-                    return [4 /*yield*/, loadMembrane(plugin, packings[i].compartment.filename, state, params)];
-                case 21:
-                    _a.sent();
-                    _a.label = 22;
-                case 22:
-                    ++i;
-                    return [3 /*break*/, 8];
-                case 23: return [2 /*return*/];
-            }
-        });
-    });
-}
-var LoadCellPackModelParams = {
-    source: param_definition_1.ParamDefinition.MappedStatic('id', {
-        'id': param_definition_1.ParamDefinition.Select('InfluenzaModel2.json', [
-            ['blood_hiv_immature_inside.json', 'Blood HIV immature'],
-            ['HIV_immature_model.json', 'HIV immature'],
-            ['Blood_HIV.json', 'Blood HIV'],
-            ['HIV-1_0.1.6-8_mixed_radii_pdb.json', 'HIV'],
-            ['influenza_model1.json', 'Influenza envelope'],
-            ['InfluenzaModel2.json', 'Influenza complete'],
-            ['ExosomeModel.json', 'Exosome Model'],
-            ['MycoplasmaGenitalium.json', 'Mycoplasma Genitalium curated model'],
-        ], { description: 'Download the model definition with `id` from the server at `baseUrl.`' }),
-        'file': param_definition_1.ParamDefinition.File({ accept: '.json,.cpr,.zip', description: 'Open model definition from .json/.cpr file or open .zip file containing model definition plus ingredients.', label: 'Recipe file' }),
-    }, { options: [['id', 'Id'], ['file', 'File']] }),
-    baseUrl: param_definition_1.ParamDefinition.Text(state_1.DefaultCellPackBaseUrl),
-    results: param_definition_1.ParamDefinition.File({ accept: '.bin', description: 'open results file in binary format from cellpackgpu for the specified recipe', label: 'Results file' }),
-    membrane: param_definition_1.ParamDefinition.Select('lipids', param_definition_1.ParamDefinition.arrayToOptions(['lipids', 'geometry', 'none'])),
-    ingredients: param_definition_1.ParamDefinition.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredient files' }),
-    preset: param_definition_1.ParamDefinition.Group({
-        traceOnly: param_definition_1.ParamDefinition.Boolean(false),
-        representation: param_definition_1.ParamDefinition.Select('gaussian-surface', param_definition_1.ParamDefinition.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation']))
-    }, { isExpanded: true })
-};
-exports.LoadCellPackModel = mol_state_1.StateAction.build({
-    display: { name: 'Load CellPack', description: 'Open or download a model' },
-    params: LoadCellPackModelParams,
-    from: objects_1.PluginStateObject.Root
-})(function (_a, ctx) {
-    var state = _a.state, params = _a.params;
-    return mol_task_1.Task.create('CellPack Loader', function (taskCtx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, loadPackings(ctx, taskCtx, state, params)];
-                case 1:
-                    _a.sent();
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=model.js.map