molstar 4.2.0 → 4.4.0

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

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseCifBinary = void 0;
+exports.parseCifBinary = parseCifBinary;
 const tslib_1 = require("tslib");
 const Data = tslib_1.__importStar(require("../data-model"));
 const field_1 = require("./field");
@@ -60,4 +60,3 @@ function parseCifBinary(data) {
         }
     });
 }
-exports.parseCifBinary = parseCifBinary;

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

@@ -6,14 +6,20 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getCifFieldType = exports.getTensor = exports.tensorFieldNameGetter = exports.CifField = exports.CifCategory = exports.CifSaveFrame = exports.CifBlock = exports.CifFile = void 0;
+exports.CifField = void 0;
+exports.CifFile = CifFile;
+exports.CifBlock = CifBlock;
+exports.CifSaveFrame = CifSaveFrame;
+exports.CifCategory = CifCategory;
+exports.tensorFieldNameGetter = tensorFieldNameGetter;
+exports.getTensor = getTensor;
+exports.getCifFieldType = getCifFieldType;
 const db_1 = require("../../../mol-data/db");
 const number_parser_1 = require("../common/text/number-parser");
 const token_1 = require("../common/text/column/token");
 function CifFile(blocks, name) {
     return { name, blocks: blocks };
 }
-exports.CifFile = CifFile;
 function CifBlock(categoryNames, categories, header, saveFrames = []) {
     return {
         categoryNames, header, categories, saveFrames,
@@ -23,15 +29,12 @@ function CifBlock(categoryNames, categories, header, saveFrames = []) {
         }
     };
 }
-exports.CifBlock = CifBlock;
 function CifSaveFrame(categoryNames, categories, header) {
     return { categoryNames, header, categories };
 }
-exports.CifSaveFrame = CifSaveFrame;
 function CifCategory(name, rowCount, fieldNames, fields) {
     return { rowCount, name, fieldNames: [...fieldNames], getField(name) { return fields[name]; } };
 }
-exports.CifCategory = CifCategory;
 (function (CifCategory) {
     function empty(name) {
         return { rowCount: 0, name, fieldNames: [], getField(name) { return void 0; } };
@@ -236,7 +239,6 @@ function tensorFieldNameGetter(field, rank, zeroIndexed, namingVariant) {
             throw new Error('Tensors with rank > 3 or rank 0 are currently not supported.');
     }
 }
-exports.tensorFieldNameGetter = tensorFieldNameGetter;
 function getTensor(category, space, row, getName) {
     const ret = space.create();
     if (space.rank === 1) {
@@ -271,7 +273,6 @@ function getTensor(category, space, row, getName) {
     }
     return ret;
 }
-exports.getTensor = getTensor;
 function getCifFieldType(field) {
     let floatCount = 0, hasStringOrScientific = false, undefinedCount = 0;
     for (let i = 0, _i = field.rowCount; i < _i; i++) {
@@ -297,4 +298,3 @@ function getCifFieldType(field) {
         return db_1.Column.Schema.float;
     return db_1.Column.Schema.int;
 }
-exports.getCifFieldType = getCifFieldType;

package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */
@@ -780,6 +780,14 @@ export declare const mmCIF_Schema: {
          * the entry.
          */
         pdbx_number_of_molecules: Schema.Int;
+        /**
+         * An identifier for the parent entity if this entity
+         * is part of a complex entity.  For instance a chimeric
+         * entity may be decomposed into several independent
+         * chemical entities where each component entity was
+         * obtained from a different source.
+         */
+        pdbx_parent_entity_id: Schema.Str;
         /**
          * Details about any entity mutation(s).
          */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */
@@ -792,6 +792,14 @@ exports.mmCIF_Schema = {
          * the entry.
          */
         pdbx_number_of_molecules: int,
+        /**
+         * An identifier for the parent entity if this entity
+         * is part of a complex entity.  For instance a chimeric
+         * entity may be decomposed into several independent
+         * chemical entities where each component entity was
+         * obtained from a different source.
+         */
+        pdbx_parent_entity_id: str,
         /**
          * Details about any entity mutation(s).
          */

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

@@ -6,7 +6,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.toTable = exports.toDatabase = exports.toDatabaseCollection = exports.FieldPath = void 0;
+exports.FieldPath = void 0;
+exports.toDatabaseCollection = toDatabaseCollection;
+exports.toDatabase = toDatabase;
+exports.toTable = toTable;
 const tslib_1 = require("tslib");
 const db_1 = require("../../../mol-data/db");
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
@@ -35,15 +38,12 @@ function toDatabaseCollection(schema, file, aliases) {
     }
     return dbc;
 }
-exports.toDatabaseCollection = toDatabaseCollection;
 function toDatabase(schema, frame, aliases) {
     return createDatabase(schema, frame, aliases);
 }
-exports.toDatabase = toDatabase;
 function toTable(schema, category) {
     return new CategoryTable(category, schema, true);
 }
-exports.toTable = toTable;
 function getColumnCtor(t) {
     switch (t.valueType) {
         case 'str': return (f, c, k) => createStringColumn(t, f, f.str, f.toStringArray);

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseCifText = void 0;
+exports.parseCifText = parseCifText;
 const tslib_1 = require("tslib");
 /**
  * mmCIF parser.
@@ -698,4 +698,3 @@ function parseCifText(data) {
         return await parseInternal(data, ctx);
     });
 }
-exports.parseCifText = parseCifText;

package/lib/commonjs/mol-io/reader/common/text/column/fixed.d.ts

@@ -5,5 +5,5 @@
  */
 import { Column } from '../../../../../mol-data/db';
 import { Tokens } from '../tokenizer';
-export declare function FixedColumnProvider(lines: Tokens): <T extends Column.Schema<any>>(offset: number, width: number, type: T) => Column<T["T"]>;
+export declare function FixedColumnProvider(lines: Tokens): <T extends Column.Schema>(offset: number, width: number, type: T) => Column<T["T"]>;
 export declare function FixedColumn<T extends Column.Schema>(lines: Tokens, offset: number, width: number, schema: T): Column<T['T']>;

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

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.FixedColumn = exports.FixedColumnProvider = void 0;
+exports.FixedColumnProvider = FixedColumnProvider;
+exports.FixedColumn = FixedColumn;
 const db_1 = require("../../../../../mol-data/db");
 const tokenizer_1 = require("../tokenizer");
 const number_parser_1 = require("../number-parser");
@@ -14,7 +15,6 @@ function FixedColumnProvider(lines) {
         return FixedColumn(lines, offset, width, type);
     };
 }
-exports.FixedColumnProvider = FixedColumnProvider;
 function FixedColumn(lines, offset, width, schema) {
     const { data, indices, count: rowCount } = lines;
     const { valueType: type } = schema;
@@ -48,4 +48,3 @@ function FixedColumn(lines, offset, width, schema) {
         areValuesEqual: (rowA, rowB) => value(rowA) === value(rowB)
     };
 }
-exports.FixedColumn = FixedColumn;

package/lib/commonjs/mol-io/reader/common/text/column/token.d.ts

@@ -6,7 +6,7 @@
  */
 import { Column } from '../../../../../mol-data/db';
 import { Tokens } from '../tokenizer';
-export declare function TokenColumnProvider(tokens: Tokens): <T extends Column.Schema<any>>(type: T) => Column<T["T"]>;
+export declare function TokenColumnProvider(tokens: Tokens): <T extends Column.Schema>(type: T) => Column<T["T"]>;
 export declare function TokenColumn<T extends Column.Schema>(tokens: Tokens, schema: T): Column<T['T']>;
 export declare function areValuesEqualProvider(tokens: Tokens): (rowA: number, rowB: number) => boolean;
 export declare function areTokensEmpty(tokens: Tokens): boolean;

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

@@ -6,7 +6,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.areTokensEmpty = exports.areValuesEqualProvider = exports.TokenColumn = exports.TokenColumnProvider = void 0;
+exports.TokenColumnProvider = TokenColumnProvider;
+exports.TokenColumn = TokenColumn;
+exports.areValuesEqualProvider = areValuesEqualProvider;
+exports.areTokensEmpty = areTokensEmpty;
 const db_1 = require("../../../../../mol-data/db");
 const number_parser_1 = require("../number-parser");
 function TokenColumnProvider(tokens) {
@@ -14,7 +17,6 @@ function TokenColumnProvider(tokens) {
         return TokenColumn(tokens, type);
     };
 }
-exports.TokenColumnProvider = TokenColumnProvider;
 function TokenColumn(tokens, schema) {
     const { data, indices, count: rowCount } = tokens;
     const { valueType: type } = schema;
@@ -34,7 +36,6 @@ function TokenColumn(tokens, schema) {
         areValuesEqual: areValuesEqualProvider(tokens)
     };
 }
-exports.TokenColumn = TokenColumn;
 function areValuesEqualProvider(tokens) {
     const { data, indices } = tokens;
     return function (rowA, rowB) {
@@ -50,7 +51,6 @@ function areValuesEqualProvider(tokens) {
         return true;
     };
 }
-exports.areValuesEqualProvider = areValuesEqualProvider;
 function areTokensEmpty(tokens) {
     const { count, indices } = tokens;
     for (let i = 0; i < count; ++i) {
@@ -59,4 +59,3 @@ function areTokensEmpty(tokens) {
     }
     return true;
 }
-exports.areTokensEmpty = areTokensEmpty;

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

@@ -8,7 +8,12 @@
  * based in part on https://github.com/dsehnal/CIFTools.js
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getNumberType = exports.NumberType = exports.parseFloat = exports.parseFloatSkipLeadingWhitespace = exports.parseInt = exports.parseIntSkipLeadingWhitespace = void 0;
+exports.NumberType = void 0;
+exports.parseIntSkipLeadingWhitespace = parseIntSkipLeadingWhitespace;
+exports.parseInt = parseInt;
+exports.parseFloatSkipLeadingWhitespace = parseFloatSkipLeadingWhitespace;
+exports.parseFloat = parseFloat;
+exports.getNumberType = getNumberType;
 /**
  * Efficient integer and float parsers.
  *
@@ -20,7 +25,6 @@ function parseIntSkipLeadingWhitespace(str, start, end) {
         start++;
     return parseInt(str, start, end);
 }
-exports.parseIntSkipLeadingWhitespace = parseIntSkipLeadingWhitespace;
 function parseInt(str, start, end) {
     let _start = start, ret = 0, neg = 1;
     if (str.charCodeAt(_start) === 45 /* - */) {
@@ -39,7 +43,6 @@ function parseInt(str, start, end) {
     }
     return neg * ret;
 }
-exports.parseInt = parseInt;
 function parseScientific(main, str, start, end) {
     // handle + in '1e+1' separately.
     if (str.charCodeAt(start) === 43 /* + */)
@@ -51,7 +54,6 @@ function parseFloatSkipLeadingWhitespace(str, start, end) {
         start++;
     return parseFloat(str, start, end);
 }
-exports.parseFloatSkipLeadingWhitespace = parseFloatSkipLeadingWhitespace;
 function parseFloat(str, start, end) {
     let _start = start, neg = 1.0, ret = 0.0, point = 0.0, div = 1.0;
     if (str.charCodeAt(_start) === 45 /* - */) {
@@ -94,7 +96,6 @@ function parseFloat(str, start, end) {
     }
     return neg * ret;
 }
-exports.parseFloat = parseFloat;
 exports.NumberType = {
     Int: 0 /* NumberTypes.Int */,
     Float: 1 /* NumberTypes.Float */,
@@ -165,4 +166,3 @@ function getNumberType(str) {
     }
     return start === end ? 0 /* NumberTypes.Int */ : 3 /* NumberTypes.NaN */;
 }
-exports.getNumberType = getNumberType;

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

@@ -7,7 +7,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.TokenBuilder = exports.trimStr = exports.Tokenizer = void 0;
+exports.TokenBuilder = void 0;
+exports.Tokenizer = Tokenizer;
+exports.trimStr = trimStr;
 const mol_task_1 = require("../../../../mol-task");
 function Tokenizer(data) {
     return {
@@ -19,7 +21,6 @@ function Tokenizer(data) {
         tokenEnd: 0
     };
 }
-exports.Tokenizer = Tokenizer;
 (function (Tokenizer) {
     function getTokenString(state) {
         return state.data.substring(state.tokenStart, state.tokenEnd);
@@ -237,7 +238,6 @@ function trimStr(data, start, end) {
         c = data.charCodeAt(--e);
     return data.substring(s, e + 1);
 }
-exports.trimStr = trimStr;
 var TokenBuilder;
 (function (TokenBuilder) {
     function resize(builder) {

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

@@ -5,14 +5,14 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CsvTable = exports.CsvFile = exports.CsvColumn = void 0;
+exports.CsvColumn = void 0;
+exports.CsvFile = CsvFile;
+exports.CsvTable = CsvTable;
 const data_model_1 = require("../cif/data-model");
 Object.defineProperty(exports, "CsvColumn", { enumerable: true, get: function () { return data_model_1.CifField; } });
 function CsvFile(table) {
     return { table };
 }
-exports.CsvFile = CsvFile;
 function CsvTable(rowCount, columnNames, columns) {
     return { rowCount, columnNames: [...columnNames], getColumn(name) { return columns[name]; } };
 }
-exports.CsvTable = CsvTable;

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseCsv = void 0;
+exports.parseCsv = parseCsv;
 const tslib_1 = require("tslib");
 // import { Column } from 'mol-data/db'
 const tokenizer_1 = require("../common/text/tokenizer");
@@ -229,4 +229,3 @@ function parseCsv(data, opts) {
         return await parseInternal(data, ctx, completeOpts);
     });
 }
-exports.parseCsv = parseCsv;

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

@@ -8,7 +8,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseCube = void 0;
+exports.parseCube = parseCube;
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
 const tokenizer_1 = require("../common/text/tokenizer");
 const db_1 = require("../../../mol-data/db");
@@ -99,4 +99,3 @@ function parseCube(data, name) {
         return result_1.ReaderResult.success({ header, atoms, values, name });
     });
 }
-exports.parseCube = parseCube;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseDcd = exports._parseDcd = void 0;
+exports._parseDcd = _parseDcd;
+exports.parseDcd = parseDcd;
 const result_1 = require("../result");
 const mol_task_1 = require("../../../mol-task");
 const binary_1 = require("../../common/binary");
@@ -148,7 +149,6 @@ function _parseDcd(data) {
     }
     return { header, frames };
 }
-exports._parseDcd = _parseDcd;
 function parseDcd(data) {
     return mol_task_1.Task.create('Parse DCD', async (ctx) => {
         try {
@@ -160,4 +160,3 @@ function parseDcd(data) {
         }
     });
 }
-exports.parseDcd = parseDcd;

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

@@ -5,7 +5,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parse = exports.parseFile = exports.getDsn6Counts = exports.parseDsn6Values = exports.readDsn6Header = exports.dsn6HeaderSize = void 0;
+exports.dsn6HeaderSize = void 0;
+exports.readDsn6Header = readDsn6Header;
+exports.parseDsn6Values = parseDsn6Values;
+exports.getDsn6Counts = getDsn6Counts;
+exports.parseFile = parseFile;
+exports.parse = parse;
 const mol_task_1 = require("../../../mol-task");
 const result_1 = require("../result");
 const file_handle_1 = require("../../common/file-handle");
@@ -72,7 +77,6 @@ async function readDsn6Header(file) {
     const header = isBrix ? parseBrixHeader(brixStr) : parseDsn6Header(buffer, littleEndian);
     return { header, littleEndian };
 }
-exports.readDsn6Header = readDsn6Header;
 async function parseDsn6Values(header, source, target, littleEndian) {
     if (!littleEndian) {
         // even though the values are one byte they need to be swapped like they are 2
@@ -109,7 +113,6 @@ async function parseDsn6Values(header, source, target, littleEndian) {
         }
     }
 }
-exports.parseDsn6Values = parseDsn6Values;
 function getDsn6Counts(header) {
     const { xExtent, yExtent, zExtent } = header;
     const { xBlocks, yBlocks, zBlocks } = getBlocks(header);
@@ -119,7 +122,6 @@ function getDsn6Counts(header) {
     const byteCount = count * elementByteSize;
     return { count, byteCount, valueCount };
 }
-exports.getDsn6Counts = getDsn6Counts;
 async function parseInternal(file, size, ctx) {
     await ctx.update({ message: 'Parsing DSN6/BRIX file...' });
     const { header, littleEndian } = await readDsn6Header(file);
@@ -140,8 +142,6 @@ function parseFile(file, size) {
         }
     });
 }
-exports.parseFile = parseFile;
 function parse(buffer, name) {
     return parseFile(file_handle_1.FileHandle.fromBuffer(simple_buffer_1.SimpleBuffer.fromUint8Array(buffer), name), buffer.length);
 }
-exports.parse = parse;

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

@@ -8,7 +8,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseDx = void 0;
+exports.parseDx = parseDx;
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
 const mol_task_1 = require("../../../mol-task");
 const number_parser_1 = require("../common/text/number-parser");
@@ -100,4 +100,3 @@ function parseDx(data, name) {
         return parseBinary(taskCtx, data, name);
     });
 }
-exports.parseDx = parseDx;

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

@@ -6,7 +6,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseGRO = void 0;
+exports.parseGRO = parseGRO;
 const db_1 = require("../../../mol-data/db");
 const tokenizer_1 = require("../common/text/tokenizer");
 const fixed_1 = require("../common/text/column/fixed");
@@ -137,4 +137,3 @@ function parseGRO(data) {
         return await parseInternal(data, ctx);
     });
 }
-exports.parseGRO = parseGRO;

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

@@ -6,7 +6,12 @@
  * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseMol = exports.handlePropertiesBlock = exports.handleFormalCharges = exports.handleBonds = exports.handleAtoms = exports.formalChargeMapper = void 0;
+exports.formalChargeMapper = formalChargeMapper;
+exports.handleAtoms = handleAtoms;
+exports.handleBonds = handleBonds;
+exports.handleFormalCharges = handleFormalCharges;
+exports.handlePropertiesBlock = handlePropertiesBlock;
+exports.parseMol = parseMol;
 const db_1 = require("../../../mol-data/db");
 const mol_task_1 = require("../../../mol-task");
 const token_1 = require("../common/text/column/token");
@@ -57,7 +62,6 @@ function formalChargeMapper(key) {
             return 0;
     }
 }
-exports.formalChargeMapper = formalChargeMapper;
 function handleAtoms(tokenizer, count) {
     const x = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     const y = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
@@ -88,7 +92,6 @@ function handleAtoms(tokenizer, count) {
         formal_charge: (0, token_1.TokenColumnProvider)(formal_charge)(db_1.Column.Schema.int)
     };
 }
-exports.handleAtoms = handleAtoms;
 function handleBonds(tokenizer, count) {
     const atomIdxA = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     const atomIdxB = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
@@ -111,7 +114,6 @@ function handleBonds(tokenizer, count) {
         order: (0, token_1.TokenColumnProvider)(order)(db_1.Column.Schema.int)
     };
 }
-exports.handleBonds = handleBonds;
 function handleFormalCharges(tokenizer, lineStart, formalCharges) {
     tokenizer_1.Tokenizer.trim(tokenizer, lineStart + 6, lineStart + 9);
     const numOfCharges = parseInt(tokenizer_1.Tokenizer.getTokenString(tokenizer));
@@ -140,7 +142,6 @@ function handleFormalCharges(tokenizer, lineStart, formalCharges) {
     /* Once the line is read, move to the next one. */
     tokenizer_1.Tokenizer.eatLine(tokenizer);
 }
-exports.handleFormalCharges = handleFormalCharges;
 /** Call an appropriate handler based on the property type.
  * (For now it only calls the formal charge handler, additional handlers can
  * be added for other properties.)
@@ -170,7 +171,6 @@ function handlePropertiesBlock(tokenizer) {
     };
     return formalCharges;
 }
-exports.handlePropertiesBlock = handlePropertiesBlock;
 function parseInternal(data) {
     const tokenizer = (0, tokenizer_1.Tokenizer)(data);
     const title = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
@@ -196,4 +196,3 @@ function parseMol(data) {
         return parseInternal(data);
     });
 }
-exports.parseMol = parseMol;

package/lib/commonjs/mol-io/reader/mol2/parser.js

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseMol2 = void 0;
+exports.parseMol2 = parseMol2;
 //               NOTES
 // When want to created undefined string column, must use
 // undefStr = UndefinedColumn(molecule.num_atoms, ColumnType.str)
@@ -278,4 +278,3 @@ function parseMol2(data, name) {
         return await parseInternal(ctx, data, name);
     });
 }
-exports.parseMol2 = parseMol2;

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseNctraj = void 0;
+exports.parseNctraj = parseNctraj;
 const mol_task_1 = require("../../../mol-task");
 const reader_1 = require("../../common/netcdf/reader");
 const result_1 = require("../result");
@@ -72,4 +72,3 @@ function parseNctraj(data) {
         }
     });
 }
-exports.parseNctraj = parseNctraj;

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parse = void 0;
+exports.parse = parse;
 const result_1 = require("../result");
 const mol_task_1 = require("../../../mol-task");
 const mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
@@ -20,4 +20,3 @@ function parse(data) {
         return await parseInternal(data, ctx);
     });
 }
-exports.parse = parse;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parsePDB = void 0;
+exports.parsePDB = parsePDB;
 const mol_task_1 = require("../../../mol-task");
 const result_1 = require("../result");
 const tokenizer_1 = require("../common/text/tokenizer");
@@ -17,4 +17,3 @@ function parsePDB(data, id, isPdbqt = false) {
         isPdbqt
     }));
 }
-exports.parsePDB = parsePDB;

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parsePly = void 0;
+exports.parsePly = parsePly;
 const result_1 = require("../result");
 const mol_task_1 = require("../../../mol-task");
 const schema_1 = require("./schema");
@@ -237,4 +237,3 @@ function parsePly(data) {
         return await parseInternal(data, ctx);
     });
 }
-exports.parsePly = parsePly;

package/lib/commonjs/mol-io/reader/ply/schema.d.ts

@@ -24,7 +24,7 @@ export declare const PlyTypeByteLength: {
 };
 export type PlyType = keyof typeof PlyTypeByteLength;
 export declare const PlyTypes: Set<string>;
-export declare function PlyType(str: string): "double" | "float" | "char" | "int" | "uint8" | "int8" | "uint16" | "int16" | "uint32" | "int32" | "float32" | "ushort" | "uchar" | "short" | "uint" | "float64";
+export declare function PlyType(str: string): PlyType;
 export interface PlyFile {
     readonly comments: ReadonlyArray<string>;
     readonly elementNames: ReadonlyArray<string>;