molstar 2.3.3 → 2.3.8

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

@@ -3,6 +3,7 @@
  * 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;
@@ -28,10 +29,11 @@ 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 data_source_1 = require("../../mol-util/data-source");
 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 baseUrl + "/results/" + fileName;
+    return "".concat(baseUrl, "/results/").concat(fileName);
 }
 var TrajectoryCache = /** @class */ (function () {
     function TrajectoryCache() {
@@ -41,7 +43,7 @@ var TrajectoryCache = /** @class */ (function () {
     TrajectoryCache.prototype.get = function (id) { return this.map.get(id); };
     return TrajectoryCache;
 }());
-function getModel(plugin, id, ingredient, baseUrl, trajCache, file) {
+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) {
@@ -50,6 +52,8 @@ function getModel(plugin, id, ingredient, baseUrl, trajCache, file) {
                     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];
@@ -92,7 +96,7 @@ function getModel(plugin, id, ingredient, baseUrl, trajCache, file) {
                 case 11:
                     trajectory = _c.sent();
                     return [3 /*break*/, 13];
-                case 12: throw new Error("unsupported file type '" + file.name + "'");
+                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];
@@ -104,6 +108,7 @@ function getModel(plugin, id, ingredient, baseUrl, trajCache, file) {
                 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();
@@ -155,7 +160,7 @@ function getModel(plugin, id, ingredient, baseUrl, trajCache, file) {
 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, asymIds, compiled, result;
+        var structure, assembly, query, sel, asymIds, compiled, result;
         return (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -167,11 +172,11 @@ function getStructure(plugin, model, source, props) {
                     structure = _a.sent();
                     _a.label = 2;
                 case 2:
-                    if (source.selection) {
-                        asymIds = source.selection.replace(' ', '').replace(':', '').split('or');
+                    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({
-                                'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
                                 'chain-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set.apply(builder_1.MolScriptBuilder, asymIds), builder_1.MolScriptBuilder.ammp('auth_asym_id')])
                             })
                         ]);
@@ -186,6 +191,8 @@ function getStructure(plugin, model, source, props) {
                     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];
             }
         });
@@ -200,9 +207,9 @@ function getTransformLegacy(trans, rot) {
     return m;
 }
 function getTransform(trans, rot) {
-    var q = linear_algebra_1.Quat.create(rot[0], rot[1], rot[2], rot[3]);
+    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]);
+    var p = linear_algebra_1.Vec3.create(-trans[0], trans[1], trans[2]);
     linear_algebra_1.Mat4.setTranslation(m, p);
     return m;
 }
@@ -226,9 +233,9 @@ function getCurveTransforms(ingredient) {
     }
     var resampling = false;
     for (var i = 0; i < n; ++i) {
-        var cname = "curve" + i;
+        var cname = "curve".concat(i);
         if (!(cname in ingredient)) {
-            // console.warn(`Expected '${cname}' in ingredient`)
+            console.warn("Expected '".concat(cname, "' in ingredient"));
             continue;
         }
         var _points = ingredient[cname];
@@ -239,7 +246,7 @@ function getCurveTransforms(ingredient) {
         // test for resampling
         var distance = linear_algebra_1.Vec3.distance(_points[0], _points[1]);
         if (distance >= segmentLength + 2.0) {
-            console.info(distance);
+            // console.info(distance);
             resampling = true;
         }
         var points = new Float32Array(_points.length * 3);
@@ -250,11 +257,11 @@ function getCurveTransforms(ingredient) {
     }
     return instances;
 }
-function getAssembly(transforms, structure) {
-    var builder = structure_1.Structure.Builder();
+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 = "" + (i + 1);
+        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];
@@ -369,14 +376,15 @@ function getCurve(plugin, name, ingredient, transforms, model) {
                     return [4 /*yield*/, plugin.runTask(curveModelTask)];
                 case 1:
                     curveModel = _a.sent();
-                    return [2 /*return*/, getStructure(plugin, curveModel, ingredient.source)];
+                    // ingredient.source.selection = undefined;
+                    return [2 /*return*/, getStructure(plugin, curveModel, ingredient)];
             }
         });
     });
 }
-function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, trajCache) {
+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, structureMean, m1, m, q, m;
+        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:
@@ -397,7 +405,7 @@ function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, tr
                         if (name === 'lypoglycane')
                             return [2 /*return*/];
                     }
-                    return [4 /*yield*/, getModel(plugin, source.pdb || name, ingredient, baseUrl, trajCache, file)];
+                    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)
@@ -408,6 +416,8 @@ function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, tr
                     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') {
@@ -417,11 +427,12 @@ function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, tr
                             bu = bu.slice(2);
                         }
                     }
-                    return [4 /*yield*/, getStructure(plugin, model, source, { assembly: bu })];
+                    return [4 /*yield*/, getStructure(plugin, model, ingredient, { assembly: bu })];
                 case 4:
                     structure = _b.sent();
                     legacy = true;
-                    if (ingredient.offset || ingredient.principalAxis) {
+                    pcp = ingredient.principalVector ? ingredient.principalVector : ingredient.principalAxis;
+                    if (pcp) {
                         legacy = false;
                         structureMean = (0, util_1.getStructureMean)(structure);
                         linear_algebra_1.Vec3.negate(structureMean, structureMean);
@@ -429,22 +440,27 @@ function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, tr
                         linear_algebra_1.Mat4.setTranslation(m1, structureMean);
                         structure = structure_1.Structure.transform(structure, m1);
                         if (ingredient.offset) {
-                            if (!linear_algebra_1.Vec3.exactEquals(ingredient.offset, linear_algebra_1.Vec3.zero())) {
+                            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, ingredient.offset);
+                                linear_algebra_1.Mat4.setTranslation(m, o);
                                 structure = structure_1.Structure.transform(structure, m);
                             }
                         }
-                        if (ingredient.principalAxis) {
-                            if (!linear_algebra_1.Vec3.exactEquals(ingredient.principalAxis, linear_algebra_1.Vec3.unitZ)) {
+                        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, ingredient.principalAxis, linear_algebra_1.Vec3.unitZ);
+                                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(getResultTransforms(results, legacy), structure);
+                    structure = getAssembly(name, getResultTransforms(results, legacy), structure);
                     _b.label = 5;
                 case 5: return [2 /*return*/, { structure: structure, assets: assets }];
             }
@@ -454,16 +470,15 @@ function getIngredientStructure(plugin, ingredient, baseUrl, ingredientFiles, tr
 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, name, assets, trajCache, structures, colors, skipColors, _a, _b, _i, iName, ingredientStructure, c, units, offsetInvariantId, offsetChainGroupId, _c, structures_1, s, maxInvariantId, maxChainGroupId, _d, _e, u, invariantId, chainGroupId, structure, i, il;
+        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, name = packing.name;
+                    ingredients = packing.ingredients, location = packing.location, name = packing.name;
                     assets = [];
                     trajCache = new TrajectoryCache();
                     structures = [];
                     colors = [];
-                    skipColors = false;
                     _a = [];
                     for (_b in ingredients)
                         _a.push(_b);
@@ -477,7 +492,7 @@ function createStructureFromCellPack(plugin, packing, baseUrl, ingredientFiles)
                 case 2:
                     _f.sent();
                     _f.label = 3;
-                case 3: return [4 /*yield*/, getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache)];
+                case 3: return [4 /*yield*/, getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache, location)];
                 case 4:
                     ingredientStructure = _f.sent();
                     if (ingredientStructure) {
@@ -488,7 +503,7 @@ function createStructureFromCellPack(plugin, packing, baseUrl, ingredientFiles)
                             colors.push(color_1.Color.fromNormalizedRgb(c[0], c[1], c[2]));
                         }
                         else {
-                            skipColors = true;
+                            colors.push(color_1.Color.fromNormalizedRgb(1, 0, 0));
                         }
                     }
                     _f.label = 5;
@@ -497,7 +512,7 @@ function createStructureFromCellPack(plugin, packing, baseUrl, ingredientFiles)
                     return [3 /*break*/, 1];
                 case 6:
                     if (!ctx.shouldUpdate) return [3 /*break*/, 8];
-                    return [4 /*yield*/, ctx.update(name + " - units")];
+                    return [4 /*yield*/, ctx.update("".concat(name, " - units"))];
                 case 7:
                     _f.sent();
                     _f.label = 8;
@@ -511,7 +526,7 @@ function createStructureFromCellPack(plugin, packing, baseUrl, ingredientFiles)
                     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("" + s.label)];
+                    return [4 /*yield*/, ctx.update("".concat(s.label))];
                 case 10:
                     _f.sent();
                     _f.label = 11;
@@ -534,16 +549,16 @@ function createStructureFromCellPack(plugin, packing, baseUrl, ingredientFiles)
                     return [3 /*break*/, 9];
                 case 13:
                     if (!ctx.shouldUpdate) return [3 /*break*/, 15];
-                    return [4 /*yield*/, ctx.update(name + " - structure")];
+                    return [4 /*yield*/, ctx.update("".concat(name, " - structure"))];
                 case 14:
                     _f.sent();
                     _f.label = 15;
                 case 15:
-                    structure = structure_1.Structure.create(units);
+                    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: skipColors ? undefined : colors }];
+                    return [2 /*return*/, { structure: structure, assets: assets, colors: colors }];
             }
         });
     }); });
@@ -559,8 +574,8 @@ function handleHivRna(plugin, packings, baseUrl) {
                     _a.label = 1;
                 case 1:
                     if (!(i < il)) return [3 /*break*/, 4];
-                    if (!(packings[i].name === 'HIV1_capsid_3j3q_PackInner_0_1_0')) return [3 /*break*/, 3];
-                    url = assets_1.Asset.getUrlAsset(plugin.managers.asset, baseUrl + "/extras/rna_allpoints.json");
+                    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();
@@ -587,13 +602,13 @@ function handleHivRna(plugin, packings, baseUrl) {
 }
 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, b, url, membrane, membraneParams;
+        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 = name + ".bcif";
+                        fileName = "".concat(name, ".bcif");
                         for (_i = 0, _a = params.ingredients; _i < _a.length; _i++) {
                             f = _a[_i];
                             if (fileName === f.name) {
@@ -602,7 +617,7 @@ function loadMembrane(plugin, name, state, params) {
                             }
                         }
                         if (!file) {
-                            cifileName = name + ".cif";
+                            cifileName = "".concat(name, ".cif");
                             for (_b = 0, _c = params.ingredients; _b < _c.length; _b++) {
                                 f = _c[_b];
                                 if (cifileName === f.name) {
@@ -612,6 +627,8 @@ function loadMembrane(plugin, name, state, params) {
                             }
                         }
                     }
+                    legacy_membrane = false;
+                    geometry_membrane = false;
                     b = state.build().toRoot();
                     if (file) {
                         if (file.name.endsWith('.cif')) {
@@ -622,9 +639,32 @@ function loadMembrane(plugin, name, state, params) {
                         }
                     }
                     else {
-                        url = assets_1.Asset.getUrlAsset(plugin.managers.asset, params.baseUrl + "/membranes/" + name + ".bcif");
-                        b = b.apply(transforms_1.StateTransforms.Data.Download, { url: url, isBinary: true, label: name }, { state: { isGhost: true } });
+                        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 } })
@@ -638,18 +678,73 @@ function loadMembrane(plugin, name, state, params) {
                     return [4 /*yield*/, preset_1.CellpackMembranePreset.apply(membrane, membraneParams, plugin)];
                 case 2:
                     _d.sent();
-                    return [2 /*return*/];
+                    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, url, file, jsonFile, data, cellPackBuilder, cellPackObject, packings, i, il, p, packing, packingParams;
+        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()
@@ -661,29 +756,39 @@ function loadPackings(plugin, runtime, state, params) {
                         plugin.log.error('No file selected');
                         return [2 /*return*/];
                     }
-                    jsonFile = void 0;
+                    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();
-                    jsonFile = assets_1.Asset.File(new File([data['model.json']], 'model.json'));
+                    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:
-                    jsonFile = file;
+                    modelFile = file;
                     _a.label = 4;
                 case 4:
                     cellPackJson = state.build().toRoot()
-                        .apply(transforms_1.StateTransforms.Data.ReadFile, { file: jsonFile, isBinary: false, label: jsonFile.name }, { state: { isGhost: true } });
+                        .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);
+                        .apply(state_1.ParseCellPack, { resultsFile: resultsFile, baseUrl: params.baseUrl });
                     return [4 /*yield*/, state.updateTree(cellPackBuilder).runInContext(runtime)];
                 case 6:
                     cellPackObject = _a.sent();
@@ -694,7 +799,7 @@ function loadPackings(plugin, runtime, state, params) {
                     i = 0, il = packings.length;
                     _a.label = 8;
                 case 8:
-                    if (!(i < il)) return [3 /*break*/, 13];
+                    if (!(i < il)) return [3 /*break*/, 23];
                     p = { packing: i, baseUrl: params.baseUrl, ingredientFiles: ingredientFiles };
                     return [4 /*yield*/, state.build()
                             .to(cellPackBuilder.ref)
@@ -709,15 +814,48 @@ function loadPackings(plugin, runtime, state, params) {
                     return [4 /*yield*/, preset_1.CellpackPackingPreset.apply(packing, packingParams, plugin)];
                 case 10:
                     _a.sent();
-                    if (!(packings[i].location === 'surface' && params.membrane)) return [3 /*break*/, 12];
-                    return [4 /*yield*/, loadMembrane(plugin, packings[i].name, state, params)];
+                    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();
-                    _a.label = 12;
+                    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 13: return [2 /*return*/];
+                case 23: return [2 /*return*/];
             }
         });
     });
@@ -727,19 +865,19 @@ var LoadCellPackModelParams = {
         'id': param_definition_1.ParamDefinition.Select('InfluenzaModel2.json', [
             ['blood_hiv_immature_inside.json', 'Blood HIV immature'],
             ['HIV_immature_model.json', 'HIV immature'],
-            ['BloodHIV1.0_mixed_fixed_nc1.cpr', 'Blood HIV'],
-            ['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV'],
+            ['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'],
+            ['InfluenzaModel2.json', 'Influenza complete'],
             ['ExosomeModel.json', 'Exosome Model'],
-            ['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma simple'],
-            ['MycoplasmaModel.json', 'Mycoplasma WholeCell 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.' }),
+        '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),
-    membrane: param_definition_1.ParamDefinition.Boolean(true),
-    ingredients: param_definition_1.ParamDefinition.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredients' }),
+    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']))