molstar 3.3.1 → 3.6.0

package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js

@@ -1,8 +1,8 @@
 "use strict";
 /**
- * Copyright (c) 2017-2020 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.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
  *
  * @author molstar/ciftools package
  */
@@ -17,6 +17,7 @@ var coord = Schema.coord;
 var Aliased = Schema.Aliased;
 var Matrix = Schema.Matrix;
 var Vector = Schema.Vector;
+var lstr = Schema.lstr;
 var List = Schema.List;
 exports.mmCIF_Schema = {
     /**
@@ -511,7 +512,7 @@ exports.mmCIF_Schema = {
          * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
          * _chem_comp.mon_nstd_details data items.
          */
-        mon_nstd_flag: Aliased(str),
+        mon_nstd_flag: Aliased(lstr),
         /**
          * The full name of the component.
          */
@@ -522,7 +523,7 @@ exports.mmCIF_Schema = {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Synonym list for the component.
          */
@@ -559,7 +560,7 @@ exports.mmCIF_Schema = {
          * bond associated with the specified atoms, expressed as a bond
          * order.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * Ordinal index for the component bond list.
          */
@@ -567,11 +568,11 @@ exports.mmCIF_Schema = {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Aliased(str),
+        pdbx_stereo_config: Aliased(lstr),
         /**
          * A flag indicating an aromatic bond.
          */
-        pdbx_aromatic_flag: Aliased(str),
+        pdbx_aromatic_flag: Aliased(lstr),
     },
     /**
      * Data items in the CITATION category record details about the
@@ -703,7 +704,7 @@ exports.mmCIF_Schema = {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Aliased(str),
+        database_id: Aliased(lstr),
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.
@@ -766,7 +767,7 @@ exports.mmCIF_Schema = {
          * manipulated sources are expected to have further information in
          * the ENTITY_SRC_GEN category.
          */
-        src_method: Aliased(str),
+        src_method: Aliased(lstr),
         /**
          * Defines the type of the entity.
          *
@@ -779,7 +780,7 @@ exports.mmCIF_Schema = {
          * Water entities are not expected to have corresponding
          * entries in the ENTITY category.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * A description of the entity.
          *
@@ -819,12 +820,12 @@ exports.mmCIF_Schema = {
          * one monomer-to-monomer link different from that implied by
          * _entity_poly.type.
          */
-        nstd_linkage: Aliased(str),
+        nstd_linkage: Aliased(lstr),
         /**
          * A flag to indicate whether the polymer contains at least
          * one monomer that is not considered standard.
          */
-        nstd_monomer: Aliased(str),
+        nstd_monomer: Aliased(lstr),
         /**
          * The type of the polymer.
          */
@@ -893,6 +894,10 @@ exports.mmCIF_Schema = {
          * parent is not specified. Deoxynucleotides are
          * represented by their canonical one-letter codes of A,
          * C, G, or T.
+         *
+         * For modifications with several parent amino acids,
+         * all corresponding parent amino acid codes will be listed
+         * (ex. chromophores).
          */
         pdbx_seq_one_letter_code_can: str,
         /**
@@ -918,7 +923,7 @@ exports.mmCIF_Schema = {
          * A flag to indicate whether this monomer in the polymer is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -995,7 +1000,7 @@ exports.mmCIF_Schema = {
          * The classification of the software according to the most
          * common types.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * The version of the software.
          */
@@ -1118,7 +1123,7 @@ exports.mmCIF_Schema = {
          * This data item is a pointer to _struct_conf_type.id in the
          * STRUCT_CONF_TYPE category.
          */
-        conf_type_id: Aliased(str),
+        conf_type_id: Aliased(lstr),
         /**
          * A description of special aspects of the conformation assignment.
          */
@@ -1218,7 +1223,7 @@ exports.mmCIF_Schema = {
          * This data item is a pointer to _struct_conn_type.id in the
          * STRUCT_CONN_TYPE category.
          */
-        conn_type_id: Aliased(str),
+        conn_type_id: Aliased(lstr),
         /**
          * A description of special aspects of the connection.
          */
@@ -1438,7 +1443,7 @@ exports.mmCIF_Schema = {
          * The chemical bond order associated with the specified atoms in
          * this contact.
          */
-        pdbx_value_order: Aliased(str),
+        pdbx_value_order: Aliased(lstr),
     },
     /**
      * Data items in the STRUCT_CONN_TYPE category record details
@@ -1453,7 +1458,7 @@ exports.mmCIF_Schema = {
         /**
          * The chemical or structural type of the interaction.
          */
-        id: Aliased(str),
+        id: Aliased(lstr),
         /**
          * A reference that specifies the criteria used to define the
          * interaction.
@@ -1807,7 +1812,7 @@ exports.mmCIF_Schema = {
         /**
          * The cell settings for this space-group symmetry.
          */
-        cell_setting: Aliased(str),
+        cell_setting: Aliased(lstr),
         /**
          * Space-group number from International Tables for Crystallography
          * Vol. A (2002).
@@ -1867,7 +1872,7 @@ exports.mmCIF_Schema = {
          * This code indicates whether the entry belongs to
          * Structural Genomics Project.
          */
-        SG_entry: Aliased(str),
+        SG_entry: Aliased(lstr),
         /**
          * The site where the file was deposited.
          */
@@ -1891,7 +1896,7 @@ exports.mmCIF_Schema = {
          * A value of 'N' indicates that the no PDB format data file is
          * corresponding to this entry is available in the PDB archive.
          */
-        pdb_format_compatible: Aliased(str),
+        pdb_format_compatible: Aliased(lstr),
     },
     /**
      * The PDBX_NONPOLY_SCHEME category provides residue level nomenclature
@@ -2044,7 +2049,7 @@ exports.mmCIF_Schema = {
          * The value of polymer flag indicates whether the unobserved or
          * zero occupancy residue is part of a polymer chain or not
          */
-        polymer_flag: Aliased(str),
+        polymer_flag: Aliased(lstr),
         /**
          * The value of occupancy flag indicates whether the residue
          * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
@@ -2297,7 +2302,7 @@ exports.mmCIF_Schema = {
         /**
          * Defines the polymer characteristic of the entity.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Additional details about this entity.
          */
@@ -2392,7 +2397,7 @@ exports.mmCIF_Schema = {
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * The entity component identifier for the first of two entities containing the linkage.
          */
@@ -2478,7 +2483,7 @@ exports.mmCIF_Schema = {
         /**
          * The bond order target for the non-standard linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_MOLECULE category identify reference molecules
@@ -2513,11 +2518,11 @@ exports.mmCIF_Schema = {
         /**
          * Broadly defines the function of the molecule.
          */
-        class: Aliased(str),
+        class: Aliased(lstr),
         /**
          * Defines the structural classification of the molecule.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * A name of the molecule.
          */
@@ -2664,7 +2669,7 @@ exports.mmCIF_Schema = {
         /**
          * This data item contains the descriptor type.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * This data item contains the name of the program
          * or library used to compute the descriptor.
@@ -2739,7 +2744,7 @@ exports.mmCIF_Schema = {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -2811,7 +2816,7 @@ exports.mmCIF_Schema = {
         /**
          * The chiral configuration of the first atom making the linkage.
          */
-        atom_stereo_config_1: Aliased(str),
+        atom_stereo_config_1: Aliased(lstr),
         /**
          * The atom identifier/name for the second atom making the linkage.
          */
@@ -2823,11 +2828,11 @@ exports.mmCIF_Schema = {
         /**
          * The chiral configuration of the second atom making the linkage.
          */
-        atom_stereo_config_2: Aliased(str),
+        atom_stereo_config_2: Aliased(lstr),
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_ENTITY_BRANCH category specify the list
@@ -2858,7 +2863,7 @@ exports.mmCIF_Schema = {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * Pointer to _atom_site.label_asym_id.
          */
@@ -3331,15 +3336,15 @@ exports.mmCIF_Schema = {
         /**
          * A flag to indicate if the modeling is multi scale.
          */
-        multi_scale_flag: Aliased(str),
+        multi_scale_flag: Aliased(lstr),
         /**
          * A flag to indicate if the modeling is multi state.
          */
-        multi_state_flag: Aliased(str),
+        multi_state_flag: Aliased(lstr),
         /**
          * A flag to indicate if the modeling involves an ensemble ordered by time or other order.
          */
-        ordered_flag: Aliased(str),
+        ordered_flag: Aliased(lstr),
         /**
          * The file id corresponding to the script used in the modeling protocol step.
          * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category.
@@ -3628,7 +3633,7 @@ exports.mmCIF_Schema = {
          * A flag that indicates whether the dataset is archived in
          * an IHM related database or elsewhere.
          */
-        database_hosted: Aliased(str),
+        database_hosted: Aliased(lstr),
     },
     /**
      * Category to define groups or collections of input datasets.
@@ -4235,7 +4240,7 @@ exports.mmCIF_Schema = {
          * whether the whole image is used or only a portion of it is used (by masking
          * or by other means) as restraint in the modeling.
          */
-        image_segment_flag: Aliased(str),
+        image_segment_flag: Aliased(lstr),
         /**
          * Number of 2D projections of the model used in the fitting.
          */
@@ -4388,7 +4393,7 @@ exports.mmCIF_Schema = {
          * whether the whole SAS profile is used or only a portion of it is used
          * (by masking or by other means) as restraint in the modeling.
          */
-        profile_segment_flag: Aliased(str),
+        profile_segment_flag: Aliased(lstr),
         /**
          * The type of atoms in the model fit to the SAS data.
          */

package/lib/commonjs/mol-io/reader/cif/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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/commonjs/mol-io/reader/cif/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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,7 +11,7 @@ var tslib_1 = require("tslib");
 var db_1 = require("../../../mol-data/db");
 var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var mol_util_1 = require("../../../mol-util");
-var Data = (0, tslib_1.__importStar)(require("./data-model"));
+var Data = tslib_1.__importStar(require("./data-model"));
 var FieldPath;
 (function (FieldPath) {
     function canonical(path) {
@@ -48,13 +48,33 @@ function toTable(schema, category) {
 exports.toTable = toTable;
 function getColumnCtor(t) {
     switch (t.valueType) {
-        case 'str': return function (f, c, k) { return createColumn(t, f, f.str, f.toStringArray); };
+        case 'str': return function (f, c, k) { return createStringColumn(t, f, f.str, f.toStringArray); };
         case 'int': return function (f, c, k) { return createColumn(t, f, f.int, f.toIntArray); };
         case 'float': return function (f, c, k) { return createColumn(t, f, f.float, f.toFloatArray); };
         case 'list': throw new Error('Use createListColumn instead.');
         case 'tensor': throw new Error('Use createTensorColumn instead.');
     }
 }
+function createStringColumn(schema, field, value, toArray) {
+    return {
+        schema: schema,
+        __array: field.__array,
+        isDefined: field.isDefined,
+        rowCount: field.rowCount,
+        value: schema.transform === 'lowercase'
+            ? function (row) { return value(row).toLowerCase(); }
+            : schema.transform === 'uppercase'
+                ? function (row) { return value(row).toUpperCase(); }
+                : value,
+        valueKind: field.valueKind,
+        areValuesEqual: field.areValuesEqual,
+        toArray: schema.transform === 'lowercase'
+            ? function (p) { return Array.from(toArray(p)).map(function (x) { return x.toLowerCase(); }); }
+            : schema.transform === 'uppercase'
+                ? function (p) { return Array.from(toArray(p)).map(function (x) { return x.toUpperCase(); }); }
+                : toArray,
+    };
+}
 function createColumn(schema, field, value, toArray) {
     return {
         schema: schema,
@@ -200,7 +220,7 @@ function createTable(key, schema, frame, aliases) {
         cat = {
             rowCount: rowCount,
             name: key,
-            fieldNames: (0, tslib_1.__spreadArray)([], fieldNames, true),
+            fieldNames: tslib_1.__spreadArray([], fieldNames, true),
             getField: function (name) {
                 return fields_1[name];
             }

package/lib/commonjs/mol-io/reader/cif/text/parser.js

@@ -25,7 +25,7 @@ var tslib_1 = require("tslib");
  * - Similarly, things like punctuation (\', ..) are left to be processed by the user if needed.
  *
  */
-var Data = (0, tslib_1.__importStar)(require("../data-model"));
+var Data = tslib_1.__importStar(require("../data-model"));
 var tokenizer_1 = require("../../common/text/tokenizer");
 var result_1 = require("../../result");
 var mol_task_1 = require("../../../../mol-task");
@@ -553,9 +553,9 @@ function updateLoopChunk(ctx, state) {
  * Reads a loop.
  */
 function handleLoop(tokenizer, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var loopLine, name, isFlat, fieldNames, rowCountEstimate, tokens, fieldCount, i, state, rowCount, i, fields, fields, i;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     loopLine = tokenizer.lineNumber;
@@ -631,9 +631,9 @@ function result(data) {
  * @returns CifParserResult wrapper of the result.
  */
 function parseInternal(data, runtimeCtx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var dataBlocks, tokenizer, blockHeader, blockCtx, saveFrames, saveCtx, saveFrame, saveHeader, token, cat, cat;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     dataBlocks = [];
@@ -719,8 +719,8 @@ function parseInternal(data, runtimeCtx) {
 }
 function parseCifText(data) {
     var _this = this;
-    return mol_task_1.Task.create('Parse CIF', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Parse CIF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, parseInternal(data, ctx)];
                 case 1: return [2 /*return*/, _a.sent()];

package/lib/commonjs/mol-io/reader/cif.js

@@ -32,4 +32,4 @@ exports.CIF = {
         densityServer: function (frame) { return (0, schema_1.toDatabase)(density_server_1.DensityServer_Data_Schema, frame); },
     }
 };
-(0, tslib_1.__exportStar)(require("./cif/data-model"), exports);
+tslib_1.__exportStar(require("./cif/data-model"), exports);

package/lib/commonjs/mol-io/reader/common/text/tokenizer.js

@@ -118,9 +118,9 @@ exports.Tokenizer = Tokenizer;
     /** Advance the state by the given number of lines and return line starts/ends as tokens. */
     function readLinesAsync(state, count, ctx, initialLineCount) {
         if (initialLineCount === void 0) { initialLineCount = 100000; }
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var length, lineTokens, linesAlreadyRead;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         length = state.length;
@@ -161,9 +161,9 @@ exports.Tokenizer = Tokenizer;
     }
     function readAllLinesAsync(data, ctx, chunkSize) {
         if (chunkSize === void 0) { chunkSize = 100000; }
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var state, tokens;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         state = Tokenizer(data);

package/lib/commonjs/mol-io/reader/csv/data-model.js

@@ -14,6 +14,6 @@ function CsvFile(table) {
 }
 exports.CsvFile = CsvFile;
 function CsvTable(rowCount, columnNames, columns) {
-    return { rowCount: rowCount, columnNames: (0, tslib_1.__spreadArray)([], columnNames, true), getColumn: function (name) { return columns[name]; } };
+    return { rowCount: rowCount, columnNames: tslib_1.__spreadArray([], columnNames, true), getColumn: function (name) { return columns[name]; } };
 }
 exports.CsvTable = CsvTable;

package/lib/commonjs/mol-io/reader/csv/parser.js

@@ -9,7 +9,7 @@ exports.parseCsv = void 0;
 var tslib_1 = require("tslib");
 // import { Column } from 'mol-data/db'
 var tokenizer_1 = require("../common/text/tokenizer");
-var Data = (0, tslib_1.__importStar)(require("./data-model"));
+var Data = tslib_1.__importStar(require("./data-model"));
 var field_1 = require("./field");
 var result_1 = require("../result");
 var mol_task_1 = require("../../../mol-task");
@@ -208,9 +208,9 @@ function init(state) {
     }
 }
 function handleRecords(state) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var columns, i;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     init(state);
@@ -227,9 +227,9 @@ function handleRecords(state) {
     });
 }
 function parseInternal(data, ctx, opts) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var state, table, result;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     state = State(data, ctx, opts);
@@ -246,8 +246,8 @@ function parseInternal(data, ctx, opts) {
 function parseCsv(data, opts) {
     var _this = this;
     var completeOpts = Object.assign({}, { quote: '"', comment: '#', delimiter: ',', noColumnNames: false }, opts);
-    return mol_task_1.Task.create('Parse CSV', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Parse CSV', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, parseInternal(data, ctx, completeOpts)];
                 case 1: return [2 /*return*/, _a.sent()];

package/lib/commonjs/mol-io/reader/cube/parser.js

@@ -93,9 +93,9 @@ function readValues(ctx, tokenizer, header) {
 }
 function parseCube(data, name) {
     var _this = this;
-    return mol_task_1.Task.create('Parse Cube', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse Cube', function (taskCtx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var tokenizer, _a, header, atoms, values;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, taskCtx.update('Reading header...')];
                 case 1:

package/lib/commonjs/mol-io/reader/dcd/parser.js

@@ -152,9 +152,9 @@ function _parseDcd(data) {
 exports._parseDcd = _parseDcd;
 function parseDcd(data) {
     var _this = this;
-    return mol_task_1.Task.create('Parse DCD', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse DCD', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var dcdFile;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             try {
                 dcdFile = _parseDcd(data);
                 return [2 /*return*/, result_1.ReaderResult.success(dcdFile)];

package/lib/commonjs/mol-io/reader/dsn6/parser.js

@@ -66,9 +66,9 @@ function getBlocks(header) {
     return { xBlocks: xBlocks, yBlocks: yBlocks, zBlocks: zBlocks };
 }
 function readDsn6Header(file) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var buffer, brixStr, isBrix, littleEndian, header;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, file.readBuffer(0, exports.dsn6HeaderSize)];
                 case 1:
@@ -84,9 +84,9 @@ function readDsn6Header(file) {
 }
 exports.readDsn6Header = readDsn6Header;
 function parseDsn6Values(header, source, target, littleEndian) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var divisor, summand, xExtent, yExtent, zExtent, _a, xBlocks, yBlocks, zBlocks, offset, zz, yy, xx, k, z, j, y, i, x, idx;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             if (!littleEndian) {
                 // even though the values are one byte they need to be swapped like they are 2
                 simple_buffer_1.SimpleBuffer.flipByteOrderInPlace2(source.buffer);
@@ -137,9 +137,9 @@ function getDsn6Counts(header) {
 }
 exports.getDsn6Counts = getDsn6Counts;
 function parseInternal(file, size, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _a, header, littleEndian, buffer, valueCount, values, result;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, ctx.update({ message: 'Parsing DSN6/BRIX file...' })];
                 case 1:
@@ -163,9 +163,9 @@ function parseInternal(file, size, ctx) {
 }
 function parseFile(file, size) {
     var _this = this;
-    return mol_task_1.Task.create('Parse DSN6/BRIX', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse DSN6/BRIX', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var _a, _b, e_1;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     _c.trys.push([0, 2, , 3]);

package/lib/commonjs/mol-io/reader/dx/parser.js

@@ -71,9 +71,9 @@ function readValuesText(ctx, tokenizer, header) {
     }, function (ctx, _, i) { return ctx.update({ current: Math.min(i, N), max: N }); });
 }
 function parseText(taskCtx, data, name) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var tokenizer, header, values;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, taskCtx.update('Reading header...')];
                 case 1:
@@ -92,9 +92,9 @@ function parseText(taskCtx, data, name) {
     });
 }
 function parseBinary(taskCtx, data, name) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var headerString, tokenizer, _a, header, headerByteCount, size, dv, values, i;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, taskCtx.update('Reading header...')];
                 case 1:

package/lib/commonjs/mol-io/reader/gro/parser.js

@@ -78,9 +78,9 @@ function handleNumberOfAtoms(state) {
  *     velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4 decimal places)
  */
 function handleAtoms(state) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var tokenizer, numberOfAtoms, lines, positionSample, precisions, hasVelocities, pO, pW, vO, vW, col, undef, ret;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     tokenizer = state.tokenizer, numberOfAtoms = state.numberOfAtoms;
@@ -129,9 +129,9 @@ function handleBoxVectors(state) {
     state.header.box = [+values[0], +values[1], +values[2]];
 }
 function parseInternal(data, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var tokenizer, structures, state, atoms, result;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     tokenizer = (0, tokenizer_1.Tokenizer)(data);
@@ -160,8 +160,8 @@ function parseInternal(data, ctx) {
 }
 function parseGRO(data) {
     var _this = this;
-    return mol_task_1.Task.create('Parse GRO', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Parse GRO', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, parseInternal(data, ctx)];
                 case 1: return [2 /*return*/, _a.sent()];