molstar 2.3.3 → 2.3.8

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

@@ -1,20 +1,27 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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.StructureFromAssemblies = exports.StructureFromCellpack = exports.ParseCellPack = exports.CellPack = exports.DefaultCellPackBaseUrl = void 0;
+exports.CreateCompartmentSphere = exports.StructureFromAssemblies = exports.StructureFromCellpack = exports.ParseCellPack = exports.CellPack = exports.DefaultCellPackBaseUrl = void 0;
 var tslib_1 = require("tslib");
 var objects_1 = require("../../mol-plugin-state/objects");
 var param_definition_1 = require("../../mol-util/param-definition");
 var mol_task_1 = require("../../mol-task");
 var model_1 = require("./model");
+var assets_1 = require("../../mol-util/assets");
 var property_1 = require("./property");
 var structure_1 = require("../../mol-model/structure");
 var symmetry_1 = require("../../mol-model-formats/structure/property/symmetry");
-exports.DefaultCellPackBaseUrl = 'https://mesoscope.scripps.edu/data/cellPACK_data/cellPACK_database_1.1.0/';
+var linear_algebra_1 = require("../../mol-math/linear-algebra");
+var mol_state_1 = require("../../mol-state");
+var representation_1 = require("./representation");
+var binary_1 = require("../../mol-io/common/binary");
+var util_1 = require("./util");
+exports.DefaultCellPackBaseUrl = 'https://raw.githubusercontent.com/mesoscope/cellPACK_data/master/cellPACK_database_1.1.0';
 var CellPack = /** @class */ (function (_super) {
     (0, tslib_1.__extends)(CellPack, _super);
     function CellPack() {
@@ -27,32 +34,196 @@ var ParseCellPack = objects_1.PluginStateTransform.BuiltIn({
     name: 'parse-cellpack',
     display: { name: 'Parse CellPack', description: 'Parse CellPack from JSON data' },
     from: objects_1.PluginStateObject.Format.Json,
-    to: CellPack
+    to: CellPack,
+    params: function (a) {
+        return {
+            resultsFile: param_definition_1.ParamDefinition.File({ accept: '.bin' }),
+            baseUrl: param_definition_1.ParamDefinition.Text(exports.DefaultCellPackBaseUrl)
+        };
+    }
 })({
-    apply: function (_a) {
+    apply: function (_a, plugin) {
         var _this = this;
-        var a = _a.a;
+        var a = _a.a, params = _a.params, cache = _a.cache;
         return mol_task_1.Task.create('Parse CellPack', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            var cell, packings, compartments, cytoplasme, name_1, _a, surface, interior;
+            var cell, counter_id, fiber_counter_id, comp_counter, packings, compartments, cytoplasme, iName, name_1, _a, surface, interior, filename, compartment, iName, iName, options, resultsAsset, url, results, buffer, numbers, ninst, npoints, ncurve, offset, pos, quat, i, x, y, z, ingr_id, pid, ctr_pos, ctr_info, curve_ids, counter, ctr_points, prev_ctype, prev_cid, i, x, y, z, cid, ctype, pid_1, cname_1, pid_2, cname_2, pid, cname;
             return (0, tslib_1.__generator)(this, function (_b) {
-                cell = a.data;
-                packings = [];
-                compartments = cell.compartments, cytoplasme = cell.cytoplasme;
-                if (compartments) {
-                    for (name_1 in compartments) {
-                        _a = compartments[name_1], surface = _a.surface, interior = _a.interior;
-                        if (surface)
-                            packings.push({ name: name_1, location: 'surface', ingredients: surface.ingredients });
-                        if (interior)
-                            packings.push({ name: name_1, location: 'interior', ingredients: interior.ingredients });
-                    }
+                switch (_b.label) {
+                    case 0:
+                        cell = a.data;
+                        counter_id = 0;
+                        fiber_counter_id = 0;
+                        comp_counter = 0;
+                        packings = [];
+                        compartments = cell.compartments, cytoplasme = cell.cytoplasme;
+                        if (!cell.mapping_ids)
+                            cell.mapping_ids = {};
+                        if (cytoplasme) {
+                            packings.push({ name: 'Cytoplasme', location: 'cytoplasme', ingredients: cytoplasme.ingredients });
+                            for (iName in cytoplasme.ingredients) {
+                                if (cytoplasme.ingredients[iName].ingtype === 'fiber') {
+                                    cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
+                                    if (!cytoplasme.ingredients[iName].nbCurve)
+                                        cytoplasme.ingredients[iName].nbCurve = 0;
+                                    fiber_counter_id++;
+                                }
+                                else {
+                                    cell.mapping_ids[counter_id] = [comp_counter, iName];
+                                    if (!cytoplasme.ingredients[iName].results) {
+                                        cytoplasme.ingredients[iName].results = [];
+                                    }
+                                    counter_id++;
+                                }
+                            }
+                            comp_counter++;
+                        }
+                        if (compartments) {
+                            for (name_1 in compartments) {
+                                _a = compartments[name_1], surface = _a.surface, interior = _a.interior;
+                                filename = '';
+                                if (compartments[name_1].geom_type === 'file') {
+                                    filename = (compartments[name_1].geom) ? compartments[name_1].geom : '';
+                                }
+                                compartment = { filename: filename, geom_type: compartments[name_1].geom_type, compartment_primitives: compartments[name_1].mb };
+                                if (surface) {
+                                    packings.push({ name: name_1, location: 'surface', ingredients: surface.ingredients, compartment: compartment });
+                                    for (iName in surface.ingredients) {
+                                        if (surface.ingredients[iName].ingtype === 'fiber') {
+                                            cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
+                                            if (!surface.ingredients[iName].nbCurve)
+                                                surface.ingredients[iName].nbCurve = 0;
+                                            fiber_counter_id++;
+                                        }
+                                        else {
+                                            cell.mapping_ids[counter_id] = [comp_counter, iName];
+                                            if (!surface.ingredients[iName].results) {
+                                                surface.ingredients[iName].results = [];
+                                            }
+                                            counter_id++;
+                                        }
+                                    }
+                                    comp_counter++;
+                                }
+                                if (interior) {
+                                    if (!surface)
+                                        packings.push({ name: name_1, location: 'interior', ingredients: interior.ingredients, compartment: compartment });
+                                    else
+                                        packings.push({ name: name_1, location: 'interior', ingredients: interior.ingredients });
+                                    for (iName in interior.ingredients) {
+                                        if (interior.ingredients[iName].ingtype === 'fiber') {
+                                            cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
+                                            if (!interior.ingredients[iName].nbCurve)
+                                                interior.ingredients[iName].nbCurve = 0;
+                                            fiber_counter_id++;
+                                        }
+                                        else {
+                                            cell.mapping_ids[counter_id] = [comp_counter, iName];
+                                            if (!interior.ingredients[iName].results) {
+                                                interior.ingredients[iName].results = [];
+                                            }
+                                            counter_id++;
+                                        }
+                                    }
+                                    comp_counter++;
+                                }
+                            }
+                        }
+                        options = cell.options;
+                        if (!params.resultsFile) return [3 /*break*/, 2];
+                        return [4 /*yield*/, plugin.runTask(plugin.managers.asset.resolve(params.resultsFile, 'binary', true))];
+                    case 1:
+                        resultsAsset = _b.sent();
+                        return [3 /*break*/, 4];
+                    case 2:
+                        if (!(options === null || options === void 0 ? void 0 : options.resultfile)) return [3 /*break*/, 4];
+                        url = "".concat(params.baseUrl, "/results/").concat(options.resultfile);
+                        return [4 /*yield*/, plugin.runTask(plugin.managers.asset.resolve(assets_1.Asset.getUrlAsset(plugin.managers.asset, url), 'binary', true))];
+                    case 3:
+                        resultsAsset = _b.sent();
+                        _b.label = 4;
+                    case 4:
+                        if (resultsAsset) {
+                            cache.asset = resultsAsset;
+                            results = resultsAsset.data;
+                            buffer = binary_1.IsNativeEndianLittle ? results.buffer : (0, binary_1.flipByteOrder)(results, 4);
+                            numbers = new DataView(buffer);
+                            ninst = (0, util_1.getFloatValue)(numbers, 0);
+                            npoints = (0, util_1.getFloatValue)(numbers, 4);
+                            ncurve = (0, util_1.getFloatValue)(numbers, 8);
+                            offset = 12;
+                            if (ninst !== 0) {
+                                pos = new Float32Array(buffer, offset, ninst * 4);
+                                offset += ninst * 4 * 4;
+                                quat = new Float32Array(buffer, offset, ninst * 4);
+                                offset += ninst * 4 * 4;
+                                for (i = 0; i < ninst; i++) {
+                                    x = pos[i * 4 + 0];
+                                    y = pos[i * 4 + 1];
+                                    z = pos[i * 4 + 2];
+                                    ingr_id = pos[i * 4 + 3];
+                                    pid = cell.mapping_ids[ingr_id];
+                                    if (!packings[pid[0]].ingredients[pid[1]].results) {
+                                        packings[pid[0]].ingredients[pid[1]].results = [];
+                                    }
+                                    packings[pid[0]].ingredients[pid[1]].results.push([linear_algebra_1.Vec3.create(x, y, z),
+                                        linear_algebra_1.Quat.create(quat[i * 4 + 0], quat[i * 4 + 1], quat[i * 4 + 2], quat[i * 4 + 3])]);
+                                }
+                            }
+                            if (npoints !== 0) {
+                                ctr_pos = new Float32Array(buffer, offset, npoints * 4);
+                                offset += npoints * 4 * 4;
+                                offset += npoints * 4 * 4;
+                                ctr_info = new Float32Array(buffer, offset, npoints * 4);
+                                offset += npoints * 4 * 4;
+                                curve_ids = new Float32Array(buffer, offset, ncurve * 4);
+                                offset += ncurve * 4 * 4;
+                                counter = 0;
+                                ctr_points = [];
+                                prev_ctype = 0;
+                                prev_cid = 0;
+                                for (i = 0; i < npoints; i++) {
+                                    x = -ctr_pos[i * 4 + 0];
+                                    y = ctr_pos[i * 4 + 1];
+                                    z = ctr_pos[i * 4 + 2];
+                                    cid = ctr_info[i * 4 + 0];
+                                    ctype = curve_ids[cid * 4 + 0];
+                                    // cid  148 165 -1 0
+                                    // console.log("cid ",cid,ctype,prev_cid,prev_ctype);//165,148
+                                    if (prev_ctype !== ctype) {
+                                        pid_1 = cell.mapping_ids[-prev_ctype - 1];
+                                        cname_1 = "curve".concat(counter);
+                                        packings[pid_1[0]].ingredients[pid_1[1]].nbCurve = counter + 1;
+                                        packings[pid_1[0]].ingredients[pid_1[1]][cname_1] = ctr_points;
+                                        ctr_points = [];
+                                        counter = 0;
+                                    }
+                                    else if (prev_cid !== cid) {
+                                        ctr_points = [];
+                                        pid_2 = cell.mapping_ids[-prev_ctype - 1];
+                                        cname_2 = "curve".concat(counter);
+                                        packings[pid_2[0]].ingredients[pid_2[1]][cname_2] = ctr_points;
+                                        counter += 1;
+                                    }
+                                    ctr_points.push(linear_algebra_1.Vec3.create(x, y, z));
+                                    prev_ctype = ctype;
+                                    prev_cid = cid;
+                                }
+                                pid = cell.mapping_ids[-prev_ctype - 1];
+                                cname = "curve".concat(counter);
+                                packings[pid[0]].ingredients[pid[1]].nbCurve = counter + 1;
+                                packings[pid[0]].ingredients[pid[1]][cname] = ctr_points;
+                            }
+                        }
+                        return [2 /*return*/, new CellPack({ cell: cell, packings: packings })];
                 }
-                if (cytoplasme)
-                    packings.push({ name: 'Cytoplasme', location: 'cytoplasme', ingredients: cytoplasme.ingredients });
-                return [2 /*return*/, new CellPack({ cell: cell, packings: packings })];
             });
         }); });
-    }
+    },
+    dispose: function (_a) {
+        var _b, _c;
+        var cache = _a.cache;
+        (_c = (_b = cache) === null || _b === void 0 ? void 0 : _b.asset) === null || _c === void 0 ? void 0 : _c.dispose();
+    },
 });
 exports.ParseCellPack = ParseCellPack;
 var StructureFromCellpack = objects_1.PluginStateTransform.BuiltIn({
@@ -94,7 +265,7 @@ var StructureFromCellpack = objects_1.PluginStateTransform.BuiltIn({
                     case 2:
                         _c.sent();
                         cache.assets = assets;
-                        return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Structure(structure, { label: packing.name })];
+                        return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Structure(structure, { label: packing.name + '.' + packing.location })];
                 }
             });
         }); });
@@ -103,8 +274,8 @@ var StructureFromCellpack = objects_1.PluginStateTransform.BuiltIn({
         var b = _a.b, cache = _a.cache;
         var assets = cache.assets;
         if (assets) {
-            for (var _i = 0, assets_1 = assets; _i < assets_1.length; _i++) {
-                var a = assets_1[_i];
+            for (var _i = 0, assets_2 = assets; _i < assets_2.length; _i++) {
+                var a = assets_2[_i];
                 a.dispose();
             }
         }
@@ -157,7 +328,7 @@ var StructureFromAssemblies = objects_1.PluginStateTransform.BuiltIn({
                         _i++;
                         return [3 /*break*/, 1];
                     case 4:
-                        builder = structure_1.Structure.Builder();
+                        builder = structure_1.Structure.Builder({ label: 'Membrane' });
                         offsetInvariantId = 0;
                         for (_b = 0, structures_1 = structures; _b < structures_1.length; _b++) {
                             s = structures_1[_b];
@@ -176,7 +347,7 @@ var StructureFromAssemblies = objects_1.PluginStateTransform.BuiltIn({
                             structure_1.Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
                         }
                         _e.label = 5;
-                    case 5: return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Structure(structure, { label: a.label, description: "" + a.description })];
+                    case 5: return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Structure(structure, { label: a.label, description: "".concat(a.description) })];
                 }
             });
         }); });
@@ -187,4 +358,40 @@ var StructureFromAssemblies = objects_1.PluginStateTransform.BuiltIn({
     }
 });
 exports.StructureFromAssemblies = StructureFromAssemblies;
+var CreateTransformer = mol_state_1.StateTransformer.builderFactory('cellPACK');
+exports.CreateCompartmentSphere = CreateTransformer({
+    name: 'create-compartment-sphere',
+    display: 'CompartmentSphere',
+    from: objects_1.PluginStateObject.Root,
+    to: objects_1.PluginStateObject.Shape.Representation3D,
+    params: {
+        center: param_definition_1.ParamDefinition.Vec3((0, linear_algebra_1.Vec3)()),
+        radius: param_definition_1.ParamDefinition.Numeric(1),
+        label: param_definition_1.ParamDefinition.Text("Compartment Sphere")
+    }
+})({
+    canAutoUpdate: function (_a) {
+        var oldParams = _a.oldParams, newParams = _a.newParams;
+        return true;
+    },
+    apply: function (_a, plugin) {
+        var _this = this;
+        var a = _a.a, params = _a.params;
+        return mol_task_1.Task.create('Compartment Sphere', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            var data, repr;
+            var _a;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        data = params;
+                        repr = (0, representation_1.MBRepresentation)((0, tslib_1.__assign)({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl }, plugin.representation.structure.themes), function () { return (representation_1.MBParams); });
+                        return [4 /*yield*/, repr.createOrUpdate((0, tslib_1.__assign)((0, tslib_1.__assign)({}, params), { quality: 'custom', xrayShaded: true, doubleSided: true }), data).runInContext(ctx)];
+                    case 1:
+                        _b.sent();
+                        return [2 /*return*/, new objects_1.PluginStateObject.Shape.Representation3D({ repr: repr, sourceData: a }, { label: data.label })];
+                }
+            });
+        }); });
+    }
+});
 //# sourceMappingURL=state.js.map

package/lib/commonjs/extensions/cellpack/state.js.map

@@ -1 +1 @@
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package/lib/commonjs/extensions/cellpack/util.d.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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>
  */
 import { AssetManager, Asset } from '../../mol-util/assets';
 import { Structure } from '../../mol-model/structure';
@@ -28,3 +29,4 @@ export declare type IngredientFiles = {
     [name: string]: Asset.File;
 };
 export declare function getStructureMean(structure: Structure): Vec3;
+export declare function getFloatValue(value: DataView, offset: number): number;

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

@@ -1,11 +1,12 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * 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.getStructureMean = exports.getFromCellPackDB = exports.getFromOPM = exports.getFromPdb = exports.parsePDBfile = exports.parseCif = void 0;
+exports.getFloatValue = exports.getStructureMean = exports.getFromCellPackDB = exports.getFromOPM = exports.getFromPdb = exports.parsePDBfile = exports.parseCif = void 0;
 var tslib_1 = require("tslib");
 var cif_1 = require("../../mol-io/reader/cif");
 var parser_1 = require("../../mol-io/reader/pdb/parser");
@@ -86,7 +87,7 @@ function getFromPdb(plugin, pdbId, assetManager) {
         var _a, cif, asset;
         return (0, tslib_1.__generator)(this, function (_b) {
             switch (_b.label) {
-                case 0: return [4 /*yield*/, downloadCif(plugin, "https://models.rcsb.org/" + pdbId.toUpperCase() + ".bcif", true, assetManager)];
+                case 0: return [4 /*yield*/, downloadCif(plugin, "https://models.rcsb.org/".concat(pdbId, ".bcif"), true, assetManager)];
                 case 1:
                     _a = _b.sent(), cif = _a.cif, asset = _a.asset;
                     return [2 /*return*/, { mmcif: cif.blocks[0], asset: asset }];
@@ -101,7 +102,7 @@ function getFromOPM(plugin, pdbId, assetManager) {
         var _a;
         return (0, tslib_1.__generator)(this, function (_b) {
             switch (_b.label) {
-                case 0: return [4 /*yield*/, plugin.runTask(assetManager.resolve(assets_1.Asset.getUrlAsset(assetManager, "https://opm-assets.storage.googleapis.com/pdb/" + pdbId.toLowerCase() + ".pdb"), 'string'))];
+                case 0: return [4 /*yield*/, plugin.runTask(assetManager.resolve(assets_1.Asset.getUrlAsset(assetManager, "https://opm-assets.storage.googleapis.com/pdb/".concat(pdbId.toLowerCase(), ".pdb")), 'string'))];
                 case 1:
                     asset = _b.sent();
                     _a = {};
@@ -120,13 +121,13 @@ function getFromCellPackDB(plugin, id, baseUrl, assetManager) {
                 case 0:
                     if (!(id.toLowerCase().endsWith('.cif') || id.toLowerCase().endsWith('.bcif'))) return [3 /*break*/, 2];
                     isBinary = id.toLowerCase().endsWith('.bcif');
-                    return [4 /*yield*/, downloadCif(plugin, baseUrl + "/other/" + id, isBinary, assetManager)];
+                    return [4 /*yield*/, downloadCif(plugin, "".concat(baseUrl, "/other/").concat(id), isBinary, assetManager)];
                 case 1:
                     _a = _b.sent(), cif = _a.cif, asset = _a.asset;
                     return [2 /*return*/, { mmcif: cif.blocks[0], asset: asset }];
                 case 2:
                     name_1 = id.endsWith('.pdb') ? id.substring(0, id.length - 4) : id;
-                    return [4 /*yield*/, downloadPDB(plugin, baseUrl + "/other/" + name_1 + ".pdb", name_1, assetManager)];
+                    return [4 /*yield*/, downloadPDB(plugin, "".concat(baseUrl, "/other/").concat(name_1, ".pdb"), name_1, assetManager)];
                 case 3: return [2 /*return*/, _b.sent()];
             }
         });
@@ -150,4 +151,31 @@ function getStructureMean(structure) {
     return linear_algebra_1.Vec3.create(xSum / elementCount, ySum / elementCount, zSum / elementCount);
 }
 exports.getStructureMean = getStructureMean;
+function getFloatValue(value, offset) {
+    // if the last byte is a negative value (MSB is 1), the final
+    // float should be too
+    var negative = value.getInt8(offset + 2) >>> 31;
+    // this is how the bytes are arranged in the byte array/DataView
+    // buffer
+    var _a = [
+        // get first three bytes as unsigned since we only care
+        // about the last 8 bits of 32-bit js number returned by
+        // getUint8().
+        // Should be the same as: getInt8(offset) & -1 >>> 24
+        value.getUint8(offset),
+        value.getUint8(offset + 1),
+        value.getUint8(offset + 2),
+        // get the last byte, which is the exponent, as a signed int
+        // since it's already correct
+        value.getInt8(offset + 3)
+    ], b0 = _a[0], b1 = _a[1], b2 = _a[2], exponent = _a[3];
+    var mantissa = b0 | (b1 << 8) | (b2 << 16);
+    if (negative) {
+        // need to set the most significant 8 bits to 1's since a js
+        // number is 32 bits but our mantissa is only 24.
+        mantissa |= 255 << 24;
+    }
+    return mantissa * Math.pow(10, exponent);
+}
+exports.getFloatValue = getFloatValue;
 //# sourceMappingURL=util.js.map

package/lib/commonjs/extensions/cellpack/util.js.map

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package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts

@@ -9,7 +9,7 @@ import { StructureRepresentationPresetProvider } from '../../../mol-plugin-state
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 export declare const DnatcoConfalPyramidsPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;

package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts

@@ -10,7 +10,7 @@ import { StructureRepresentation, StructureRepresentationProvider } from '../../
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { ThemeRegistryContext } from '../../../mol-theme/theme';
 export declare const ConfalPyramidsParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -18,11 +18,11 @@ export declare const ConfalPyramidsParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type ConfalPyramidsParams = typeof ConfalPyramidsParams;
 export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, structure: Structure): {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -30,12 +30,12 @@ export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, struc
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type ConfalPyramidsRepresentation = StructureRepresentation<ConfalPyramidsParams>;
 export declare function ConfalPyramidsRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ConfalPyramidsParams>): ConfalPyramidsRepresentation;
 export declare const ConfalPyramidsRepresentationProvider: StructureRepresentationProvider<{
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -43,5 +43,5 @@ export declare const ConfalPyramidsRepresentationProvider: StructureRepresentati
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 }, "confal-pyramids">;

package/lib/commonjs/extensions/dnatco/confal-pyramids/util.js

@@ -68,12 +68,12 @@ var ConfalPyramidsUtil;
         Utility.prototype.stepToName = function (entry_id, modelNum, locFirst, locSecond, fakeAltId_1, fakeAltId_2) {
             var first = residueInfoFromLocation(locFirst);
             var second = residueInfoFromLocation(locSecond);
-            var model_id = this.hasMultipleModels ? "-m" + modelNum : '';
-            var alt_id_1 = fakeAltId_1 !== '' ? "." + fakeAltId_1 : (first.alt_id.length ? "." + first.alt_id : '');
-            var alt_id_2 = fakeAltId_2 !== '' ? "." + fakeAltId_2 : (second.alt_id.length ? "." + second.alt_id : '');
-            var ins_code_1 = first.ins_code.length ? "." + first.ins_code : '';
-            var ins_code_2 = second.ins_code.length ? "." + second.ins_code : '';
-            return "" + entry_id + model_id + "_" + first.auth_asym_id + "_" + first.comp_id + alt_id_1 + "_" + first.auth_seq_id + ins_code_1 + "_" + second.comp_id + alt_id_2 + "_" + second.auth_seq_id + ins_code_2;
+            var model_id = this.hasMultipleModels ? "-m".concat(modelNum) : '';
+            var alt_id_1 = fakeAltId_1 !== '' ? ".".concat(fakeAltId_1) : (first.alt_id.length ? ".".concat(first.alt_id) : '');
+            var alt_id_2 = fakeAltId_2 !== '' ? ".".concat(fakeAltId_2) : (second.alt_id.length ? ".".concat(second.alt_id) : '');
+            var ins_code_1 = first.ins_code.length ? ".".concat(first.ins_code) : '';
+            var ins_code_2 = second.ins_code.length ? ".".concat(second.ins_code) : '';
+            return "".concat(entry_id).concat(model_id, "_").concat(first.auth_asym_id, "_").concat(first.comp_id).concat(alt_id_1, "_").concat(first.auth_seq_id).concat(ins_code_1, "_").concat(second.comp_id).concat(alt_id_2, "_").concat(second.auth_seq_id).concat(ins_code_2);
         };
         return Utility;
     }());
@@ -100,7 +100,7 @@ var ConfalPyramidsUtil;
                     indices.push(eI);
             }
             if (indices.length === 0)
-                throw new Error("Element " + name + " not found on residue " + residue.index);
+                throw new Error("Element ".concat(name, " not found on residue ").concat(residue.index));
             return indices;
         };
         UnitWalker.prototype.getAtomPositions = function (indices) {