molstar 3.4.0 → 3.6.1

package/lib/cli/cifschema/util/cif-dic.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,15 +10,17 @@ export function getFieldType(type, description, values, container) {
     switch (type) {
         // mmCIF
         case 'code':
-        case 'ucode':
         case 'line':
-        case 'uline':
         case 'text':
         case 'char':
-        case 'uchar3':
-        case 'uchar1':
         case 'boolean':
             return values && values.length ? EnumCol(values, 'str', description) : StrCol(description);
+        case 'ucode':
+        case 'uline':
+        case 'uchar3':
+        case 'uchar1':
+            // only force lower-case for enums
+            return values && values.length ? EnumCol(values.map(function (x) { return x.toLowerCase(); }), 'lstr', description) : StrCol(description);
         case 'aliasname':
         case 'name':
         case 'idname':

package/lib/cli/cifschema/util/generate.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/cli/cifschema/util/generate.js

@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { indentString } from '../../../mol-util/string';
 import { FieldPath } from '../../../mol-io/reader/cif/schema';
 function header(name, info, moldataImportPath) {
-    return "/**\n * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated '".concat(name, "' schema file. ").concat(info, "\n *\n * @author molstar/ciftools package\n */\n\nimport { Database, Column } from '").concat(moldataImportPath, "/db';\n\nimport Schema = Column.Schema;");
+    return "/**\n * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated '".concat(name, "' schema file. ").concat(info, "\n *\n * @author molstar/ciftools package\n */\n\nimport { Database, Column } from '").concat(moldataImportPath, "/db';\n\nimport Schema = Column.Schema;");
 }
 function footer(name) {
     return "\nexport type ".concat(name, "_Schema = typeof ").concat(name, "_Schema;\nexport interface ").concat(name, "_Database extends Database<").concat(name, "_Schema> {};");
@@ -20,7 +20,10 @@ function getTypeShorthands(schema, fields) {
         Object.keys(columns).forEach(function (columnName) {
             if (fields && !fields[table][columnName])
                 return;
-            types.add(schema.tables[table].columns[columnName].type);
+            var col = schema.tables[table].columns[columnName];
+            if (col.type === 'enum')
+                types.add(col.subType);
+            types.add(col.type);
         });
     });
     var shorthands = [];
@@ -29,6 +32,12 @@ function getTypeShorthands(schema, fields) {
             case 'str':
                 shorthands.push('const str = Schema.str;');
                 break;
+            case 'ustr':
+                shorthands.push('const ustr = Schema.ustr;');
+                break;
+            case 'lstr':
+                shorthands.push('const lstr = Schema.lstr;');
+                break;
             case 'int':
                 shorthands.push('const int = Schema.int;');
                 break;

package/lib/cli/cifschema/util/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -40,10 +40,10 @@ export declare type CoordCol = {
 export declare function CoordCol(description: string): CoordCol;
 export declare type EnumCol = {
     type: 'enum';
-    subType: 'int' | 'str';
+    subType: 'int' | 'str' | 'ustr' | 'lstr';
     values: string[];
 } & BaseCol;
-export declare function EnumCol(values: string[], subType: 'int' | 'str', description: string): EnumCol;
+export declare function EnumCol(values: string[], subType: 'int' | 'str' | 'ustr' | 'lstr', description: string): EnumCol;
 export declare type VectorCol = {
     type: 'vector';
     length: number;

package/lib/cli/cifschema/util/schema.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/apps/docking-viewer/index.js

@@ -10,7 +10,7 @@ exports.DockingViewer = exports.setProductionMode = exports.setDebugMode = expor
 var tslib_1 = require("tslib");
 var structure_1 = require("../../mol-model/structure");
 var objects_1 = require("../../mol-plugin-state/objects");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var behavior_1 = require("../../mol-plugin/behavior");
 var commands_1 = require("../../mol-plugin/commands");
@@ -118,7 +118,7 @@ var Viewer = /** @class */ (function () {
                             : elementOrId;
                         if (!element)
                             throw new Error("Could not get element with id '".concat(elementOrId, "'"));
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(element, spec)];
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(element, spec)];
                     case 1:
                         plugin = _b.sent();
                         plugin.customState = {

package/lib/commonjs/apps/viewer/app.js

@@ -28,7 +28,7 @@ var representation_preset_1 = require("../../mol-plugin-state/builder/structure/
 var volume_representation_params_1 = require("../../mol-plugin-state/helpers/volume-representation-params");
 var transforms_1 = require("../../mol-plugin-state/transforms");
 var model_1 = require("../../mol-plugin-state/transforms/model");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var config_1 = require("../../mol-plugin/config");
@@ -156,7 +156,7 @@ var Viewer = /** @class */ (function () {
                             : elementOrId;
                         if (!element)
                             throw new Error("Could not get element with id '".concat(elementOrId, "'"));
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(element, spec, {
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(element, spec, {
                                 onBeforeUIRender: function (plugin) {
                                     // the preset needs to be added before the UI renders otherwise
                                     // "Download Structure" wont be able to pick it up

package/lib/commonjs/cli/chem-comp-dict/util.d.ts

@@ -16,7 +16,7 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -26,12 +26,12 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         pdbx_model_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_model_coordinates_db_code: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ideal_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         pdbx_initial_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_modified_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_release_status: import("../../mol-data/db/column").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "EBI" | "PDBE" | "PDBJ" | "PDBC">;
+        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
     };
     chem_comp_atom: {
         alt_atom_id: import("../../mol-data/db/column").Column.Schema.Str;
@@ -47,9 +47,9 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         pdbx_model_Cartn_x_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_y_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_z_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     chem_comp_bond: {
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
@@ -57,13 +57,13 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "E" | "Z">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"z" | "n" | "e">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     pdbx_chem_comp_descriptor: {
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         descriptor: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"SMILES_CANNONICAL" | "SMILES_CANONICAL" | "SMILES" | "InChI" | "InChI_MAIN" | "InChI_MAIN_FORMULA" | "InChI_MAIN_CONNECT" | "InChI_MAIN_HATOM" | "InChI_CHARGE" | "InChI_STEREO" | "InChI_ISOTOPE" | "InChI_FIXEDH" | "InChI_RECONNECT" | "InChIKey">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
         program: import("../../mol-data/db/column").Column.Schema.Str;
         program_version: import("../../mol-data/db/column").Column.Schema.Str;
     };
@@ -84,7 +84,7 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -94,12 +94,12 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         pdbx_model_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_model_coordinates_db_code: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ideal_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         pdbx_initial_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_modified_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_release_status: import("../../mol-data/db/column").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "EBI" | "PDBE" | "PDBJ" | "PDBC">;
+        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
     };
     chem_comp_atom: {
         alt_atom_id: import("../../mol-data/db/column").Column.Schema.Str;
@@ -115,9 +115,9 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         pdbx_model_Cartn_x_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_y_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_z_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     chem_comp_bond: {
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
@@ -125,13 +125,13 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "E" | "Z">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"z" | "n" | "e">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     pdbx_chem_comp_descriptor: {
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         descriptor: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"SMILES_CANNONICAL" | "SMILES_CANONICAL" | "SMILES" | "InChI" | "InChI_MAIN" | "InChI_MAIN_FORMULA" | "InChI_MAIN_CONNECT" | "InChI_MAIN_HATOM" | "InChI_CHARGE" | "InChI_STEREO" | "InChI_ISOTOPE" | "InChI_FIXEDH" | "InChI_RECONNECT" | "InChIKey">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
         program: import("../../mol-data/db/column").Column.Schema.Str;
         program_version: import("../../mol-data/db/column").Column.Schema.Str;
     };

package/lib/commonjs/cli/cif2bcif/converter.js

@@ -99,7 +99,7 @@ function classify(name, field) {
 function convert(path, asText, hints, filter) {
     var _this = this;
     if (asText === void 0) { asText = false; }
-    return mol_task_1.Task.create('BinaryCIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Convert CIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var encodingProvider, cif, encoder, maxProgress, _i, _a, b, _b, _c, c, current, _d, _e, b, _f, _g, c, cat, fields, _h, _j, f, ret;
         return tslib_1.__generator(this, function (_k) {
             switch (_k.label) {

package/lib/commonjs/cli/cif2bcif/index.js

@@ -22,7 +22,7 @@ function process(srcPath, outPath, configPath, filterPath) {
                 case 0:
                     config = configPath ? JSON.parse(fs.readFileSync(configPath, 'utf8')) : void 0;
                     filter = filterPath ? fs.readFileSync(filterPath, 'utf8') : void 0;
-                    return [4 /*yield*/, (0, converter_1.convert)(srcPath, false, config, filter)];
+                    return [4 /*yield*/, (0, converter_1.convert)(srcPath, srcPath.toLowerCase().indexOf('.bcif') > 0, config, filter)];
                 case 1:
                     res = _a.sent();
                     return [4 /*yield*/, write(outPath, res)];
@@ -58,13 +58,13 @@ function run(args) {
 }
 var parser = new argparse.ArgumentParser({
     add_help: true,
-    description: 'Convert any CIF file to a BCIF file'
+    description: 'Convert any BCIF file to a CIF file or vice versa'
 });
 parser.add_argument('src', {
-    help: 'Source CIF path'
+    help: 'Source file path'
 });
 parser.add_argument('out', {
-    help: 'Output BCIF path'
+    help: 'Output file path'
 });
 parser.add_argument('-c', '--config', {
     help: 'Optional encoding strategy/precision config path',

package/lib/commonjs/cli/cifschema/util/cif-dic.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/cli/cifschema/util/cif-dic.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -13,15 +13,17 @@ function getFieldType(type, description, values, container) {
     switch (type) {
         // mmCIF
         case 'code':
-        case 'ucode':
         case 'line':
-        case 'uline':
         case 'text':
         case 'char':
-        case 'uchar3':
-        case 'uchar1':
         case 'boolean':
             return values && values.length ? (0, schema_1.EnumCol)(values, 'str', description) : (0, schema_1.StrCol)(description);
+        case 'ucode':
+        case 'uline':
+        case 'uchar3':
+        case 'uchar1':
+            // only force lower-case for enums
+            return values && values.length ? (0, schema_1.EnumCol)(values.map(function (x) { return x.toLowerCase(); }), 'lstr', description) : (0, schema_1.StrCol)(description);
         case 'aliasname':
         case 'name':
         case 'idname':

package/lib/commonjs/cli/cifschema/util/generate.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/cli/cifschema/util/generate.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,7 +9,7 @@ exports.generate = void 0;
 var string_1 = require("../../../mol-util/string");
 var schema_1 = require("../../../mol-io/reader/cif/schema");
 function header(name, info, moldataImportPath) {
-    return "/**\n * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated '".concat(name, "' schema file. ").concat(info, "\n *\n * @author molstar/ciftools package\n */\n\nimport { Database, Column } from '").concat(moldataImportPath, "/db';\n\nimport Schema = Column.Schema;");
+    return "/**\n * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated '".concat(name, "' schema file. ").concat(info, "\n *\n * @author molstar/ciftools package\n */\n\nimport { Database, Column } from '").concat(moldataImportPath, "/db';\n\nimport Schema = Column.Schema;");
 }
 function footer(name) {
     return "\nexport type ".concat(name, "_Schema = typeof ").concat(name, "_Schema;\nexport interface ").concat(name, "_Database extends Database<").concat(name, "_Schema> {};");
@@ -23,7 +23,10 @@ function getTypeShorthands(schema, fields) {
         Object.keys(columns).forEach(function (columnName) {
             if (fields && !fields[table][columnName])
                 return;
-            types.add(schema.tables[table].columns[columnName].type);
+            var col = schema.tables[table].columns[columnName];
+            if (col.type === 'enum')
+                types.add(col.subType);
+            types.add(col.type);
         });
     });
     var shorthands = [];
@@ -32,6 +35,12 @@ function getTypeShorthands(schema, fields) {
             case 'str':
                 shorthands.push('const str = Schema.str;');
                 break;
+            case 'ustr':
+                shorthands.push('const ustr = Schema.ustr;');
+                break;
+            case 'lstr':
+                shorthands.push('const lstr = Schema.lstr;');
+                break;
             case 'int':
                 shorthands.push('const int = Schema.int;');
                 break;

package/lib/commonjs/cli/cifschema/util/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -40,10 +40,10 @@ export declare type CoordCol = {
 export declare function CoordCol(description: string): CoordCol;
 export declare type EnumCol = {
     type: 'enum';
-    subType: 'int' | 'str';
+    subType: 'int' | 'str' | 'ustr' | 'lstr';
     values: string[];
 } & BaseCol;
-export declare function EnumCol(values: string[], subType: 'int' | 'str', description: string): EnumCol;
+export declare function EnumCol(values: string[], subType: 'int' | 'str' | 'ustr' | 'lstr', description: string): EnumCol;
 export declare type VectorCol = {
     type: 'vector';
     length: number;

package/lib/commonjs/cli/cifschema/util/schema.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/examples/alpha-orbitals/index.js

@@ -11,7 +11,7 @@ var rxjs_1 = require("rxjs");
 var operators_1 = require("rxjs/operators");
 var transforms_1 = require("../../extensions/alpha-orbitals/transforms");
 var grid3d_1 = require("../../mol-gl/compute/grid3d");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var config_1 = require("../../mol-plugin/config");
@@ -38,7 +38,7 @@ var AlphaOrbitalsExample = /** @class */ (function () {
                     case 0:
                         defaultSpec = (0, spec_1.DefaultPluginUISpec)();
                         _b = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, defaultSpec), { layout: {
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, defaultSpec), { layout: {
                                     initial: {
                                         isExpanded: false,
                                         showControls: false

package/lib/commonjs/examples/basic-wrapper/index.js

@@ -10,7 +10,7 @@ var pdbe_1 = require("../../extensions/pdbe");
 var loci_1 = require("../../mol-model/loci");
 var structure_1 = require("../../mol-model/structure");
 var model_index_1 = require("../../mol-plugin-state/animation/built-in/model-index");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var script_1 = require("../../mol-script/script");
@@ -186,7 +186,7 @@ var BasicWrapper = /** @class */ (function () {
                 switch (_b.label) {
                     case 0:
                         _a = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
                                     initial: {
                                         isExpanded: false,
                                         showControls: false

package/lib/commonjs/examples/lighting/index.js

@@ -6,7 +6,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var assets_1 = require("../../mol-util/assets");
@@ -66,7 +66,7 @@ var LightingDemo = /** @class */ (function () {
                 switch (_b.label) {
                     case 0:
                         _a = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
                                     initial: {
                                         isExpanded: false,
                                         showControls: false

package/lib/commonjs/examples/proteopedia-wrapper/index.js

@@ -11,7 +11,7 @@ var canvas3d_1 = require("../../mol-canvas3d/canvas3d");
 var model_index_1 = require("../../mol-plugin-state/animation/built-in/model-index");
 var structure_representation_params_1 = require("../../mol-plugin-state/helpers/structure-representation-params");
 var transforms_1 = require("../../mol-plugin-state/transforms");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var transformers_1 = require("../../mol-plugin/behavior/dynamic/volume-streaming/transformers");
 var commands_1 = require("../../mol-plugin/commands");
@@ -241,7 +241,7 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
                 switch (_b.label) {
                     case 0:
                         _a = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { animations: [
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, (0, spec_1.DefaultPluginUISpec)()), { animations: [
                                     model_index_1.AnimateModelIndex
                                 ], layout: {
                                     initial: {

package/lib/commonjs/extensions/anvil/behavior.d.ts

@@ -42,6 +42,7 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    allowTransparentBackfaces: boolean;
     bumpFrequency: number;
     bumpAmplitude: number;
 }>>;

package/lib/commonjs/extensions/anvil/representation.d.ts

@@ -18,6 +18,7 @@ declare const BilayerPlanesParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -98,6 +99,7 @@ export declare const MembraneOrientationParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 };
@@ -134,6 +136,7 @@ export declare function getMembraneOrientationParams(ctx: ThemeRegistryContext,
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 };
@@ -170,6 +173,7 @@ export declare const MembraneOrientationRepresentationProvider: StructureReprese
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
 }, "membrane-orientation">;

package/lib/commonjs/extensions/cellpack/representation.d.ts

@@ -44,6 +44,7 @@ export declare const MBParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;