@datagrok/sequence-translator 1.9.7 → 1.9.9

package/dist/vendors-node_modules_datagrok-libraries_bio_src_monomer-works_seq-to-molfile-worker_js.js

@@ -1,833 +0,0 @@
-var sequencetranslator;
-/******/ (() => { // webpackBootstrap
-/******/ 	"use strict";
-/******/ 	var __webpack_modules__ = ({
-
-/***/ "./node_modules/@datagrok-libraries/bio/src/helm/consts.js":
-/*!*****************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/helm/consts.js ***!
-  \*****************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   HelmTypes: () => (/* reexport safe */ _datagrok_libraries_js_draw_lite_src_types_org__WEBPACK_IMPORTED_MODULE_0__.HelmTypes)
-/* harmony export */ });
-/* harmony import */ var _datagrok_libraries_js_draw_lite_src_types_org__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! @datagrok-libraries/js-draw-lite/src/types/org */ "./node_modules/@datagrok-libraries/js-draw-lite/src/types/org.js");
-
-
-//# sourceMappingURL=consts.js.map
-
-/***/ }),
-
-/***/ "./node_modules/@datagrok-libraries/bio/src/monomer-works/consts.js":
-/*!**************************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/monomer-works/consts.js ***!
-  \**************************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   monomerWorksConsts: () => (/* binding */ monomerWorksConsts)
-/* harmony export */ });
-const monomerWorksConsts = {
-    // constants for parsing molfile V2000
-    V2K_RGP_SHIFT: 8,
-    V2K_RGP_LINE: 'M  RGP',
-    V2K_A_LINE: 'A  ',
-    // constants for parsing/reconstruction of molfile V3000
-    V3K_COUNTS_SHIFT: 14,
-    V3K_IDX_SHIFT: 7,
-    V3K_HEADER_FIRST_LINE: '\nDatagrok macromolecule handler\n\n',
-    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\n',
-    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\n',
-    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\n',
-    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',
-    V3K_COUNTS_LINE_ENDING: ' 0 0 0\n',
-    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\n',
-    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\n',
-    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\n',
-    V3K_END_BOND_BLOCK: 'M  V30 END BOND\n',
-    V3K_BOND_CONFIG: ' CFG=',
-    V3K_BEGIN_DATA_LINE: 'M  V30 ',
-    V3K_END: 'M  END',
-    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates
-    // symbols for the corresponding monomers in HELM library
-    DEOXYRIBOSE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'd' },
-    RIBOSE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'r' },
-    PHOSPHATE: { polymerType: "RNA" /* PolymerTypes.RNA */, symbol: 'p' },
-    OXYGEN: 'O',
-    HYDROGEN: 'H',
-};
-//# sourceMappingURL=consts.js.map
-
-/***/ }),
-
-/***/ "./node_modules/@datagrok-libraries/bio/src/monomer-works/monomer-works.js":
-/*!*********************************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/monomer-works/monomer-works.js ***!
-  \*********************************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   MonomerWorks: () => (/* binding */ MonomerWorks),
-/* harmony export */   helmTypeToPolymerType: () => (/* binding */ helmTypeToPolymerType)
-/* harmony export */ });
-/* harmony import */ var _helm_consts__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! ../helm/consts */ "./node_modules/@datagrok-libraries/bio/src/helm/consts.js");
-
-class MonomerWorks {
-    //private molfileConverter: IMolfileConverter;
-    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {
-        this.monomerLib = monomerLib;
-        //this.molfileConverter = molfileConverter;
-    }
-    //types according to Monomer possible
-    getCappedRotatedMonomer(monomerType, monomerName) {
-        // TODO: Check type of monomerType arg
-        const monomer = this.monomerLib.getMonomer(monomerType, monomerName);
-        if (monomer)
-            return monomer.molfile; //TODO cap
-        return null;
-    }
-}
-function helmTypeToPolymerType(helmType) {
-    let polymerType = undefined;
-    switch (helmType) {
-        case _helm_consts__WEBPACK_IMPORTED_MODULE_0__.HelmTypes.BASE:
-        case _helm_consts__WEBPACK_IMPORTED_MODULE_0__.HelmTypes.SUGAR: // r - ribose, d - deoxyribose
-        case _helm_consts__WEBPACK_IMPORTED_MODULE_0__.HelmTypes.LINKER: // p - phosphate
-        case _helm_consts__WEBPACK_IMPORTED_MODULE_0__.HelmTypes.NUCLEOTIDE:
-        // @ts-ignore
-        case 'nucleotide':
-            polymerType = "RNA" /* PolymerTypes.RNA */;
-            break;
-        case _helm_consts__WEBPACK_IMPORTED_MODULE_0__.HelmTypes.AA:
-            polymerType = "PEPTIDE" /* PolymerTypes.PEPTIDE */;
-            break;
-        case _helm_consts__WEBPACK_IMPORTED_MODULE_0__.HelmTypes.CHEM:
-            polymerType = "CHEM" /* PolymerTypes.CHEM */;
-            break;
-        case _helm_consts__WEBPACK_IMPORTED_MODULE_0__.HelmTypes.BLOB:
-            polymerType = "BLOB" /* PolymerTypes.BLOB */;
-            break;
-        default:
-            polymerType = "PEPTIDE" /* PolymerTypes.PEPTIDE */;
-            console.warn(`Unexpected HelmType '${helmType}'`);
-    }
-    return polymerType;
-}
-//# sourceMappingURL=monomer-works.js.map
-
-/***/ }),
-
-/***/ "./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js":
-/*!*****************************************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js ***!
-  \*****************************************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   getFormattedMonomerLib: () => (/* binding */ getFormattedMonomerLib),
-/* harmony export */   keepPrecision: () => (/* binding */ keepPrecision),
-/* harmony export */   monomerSeqToMolfile: () => (/* binding */ monomerSeqToMolfile)
-/* harmony export */ });
-/* harmony import */ var _consts__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! ./consts */ "./node_modules/@datagrok-libraries/bio/src/monomer-works/consts.js");
-/* harmony import */ var _types__WEBPACK_IMPORTED_MODULE_1__ = __webpack_require__(/*! ./types */ "./node_modules/@datagrok-libraries/bio/src/monomer-works/types.js");
-/* harmony import */ var _utils_const__WEBPACK_IMPORTED_MODULE_2__ = __webpack_require__(/*! ../utils/const */ "./node_modules/@datagrok-libraries/bio/src/utils/const.js");
-/* harmony import */ var _utils_macromolecule_consts__WEBPACK_IMPORTED_MODULE_3__ = __webpack_require__(/*! ../utils/macromolecule/consts */ "./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/consts.js");
-/* harmony import */ var _monomer_works__WEBPACK_IMPORTED_MODULE_4__ = __webpack_require__(/*! ./monomer-works */ "./node_modules/@datagrok-libraries/bio/src/monomer-works/monomer-works.js");
-/* eslint-disable max-len */
-
-
-
-
-
-/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.
- * @param {IMonomerLib} monomerLib - Monomer library
- * @param {HELM_POLYMER_TYPE} polymerType - Polymer type
- * @param {ALPHABET} alphabet - Alphabet of the column
- * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/
-function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
-    const map = new Map();
-    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {
-        const it = monomerLib.getMonomer(polymerType, monomerSymbol);
-        if (polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ &&
-            (it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] === "Branch" /* HELM_MONOMER_TYPE.BRANCH */ ||
-                alphabet === _utils_macromolecule_consts__WEBPACK_IMPORTED_MODULE_3__.ALPHABET.DNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.DEOXYRIBOSE.symbol ||
-                alphabet === _utils_macromolecule_consts__WEBPACK_IMPORTED_MODULE_3__.ALPHABET.RNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.RIBOSE.symbol ||
-                it["symbol" /* HELM_FIELDS.SYMBOL */] === _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.PHOSPHATE.symbol) ||
-            polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */ &&
-                it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== "Branch" /* HELM_MONOMER_TYPE.BRANCH */) {
-            const monomerObject = {};
-            _utils_const__WEBPACK_IMPORTED_MODULE_2__.HELM_CORE_FIELDS.forEach((field) => {
-                //@ts-ignore
-                monomerObject[field] = it[field];
-            });
-            map.set(it["symbol" /* HELM_FIELDS.SYMBOL */], monomerObject);
-        }
-    }
-    return map;
-}
-/** Translate a sequence of monomer symbols into Molfile V3000
- * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)
- * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects
- * @param {ALPHABET} alphabet - Alphabet of the column
- * @param {PolymerType} polymerType - Polymer type
- * @return {string} - Molfile V3000*/
-function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {
-    if (monomerSeq.length === 0) {
-        // throw new Error('monomerSeq is empty');
-        return _types__WEBPACK_IMPORTED_MODULE_1__.MolfileWithMap.createEmpty();
-    }
-    // define atom and bond counts, taking into account the bond type
-    const getAtomAndBondCounts = getResultingAtomBondCounts;
-    const { atomCount, bondCount, needsCapping } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);
-    // create arrays to store lines of the resulting molfile
-    const molfileAtomBlock = new Array(atomCount);
-    const molfileBondBlock = new Array(bondCount);
-    let addMonomerToMolblock;
-    let sugar = null;
-    let phosphate = null;
-    if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */)
-        addMonomerToMolblock = addAminoAcidToMolblock;
-    else { // nucleotides
-        addMonomerToMolblock = addNucleotideToMolblock;
-        sugar = (alphabet === _utils_macromolecule_consts__WEBPACK_IMPORTED_MODULE_3__.ALPHABET.DNA) ? (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.DEOXYRIBOSE) : (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.RIBOSE);
-        phosphate = (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.PHOSPHATE);
-    }
-    const v = {
-        i: 0,
-        nodeShift: 0,
-        bondShift: 0,
-        backbonePositionShift: new Array(2).fill(0),
-        branchPositionShift: new Array(2).fill(0),
-        backboneAttachNode: 0,
-        branchAttachNode: 0,
-        flipFactor: 1,
-    };
-    const LC = {
-        sugar: sugar,
-        phosphate: phosphate,
-        seqLength: monomerSeq.length,
-        atomCount: atomCount,
-        bondCount: bondCount,
-    };
-    const monomers = new _types__WEBPACK_IMPORTED_MODULE_1__.MonomerMap();
-    const steabsCollection = [];
-    let nAtoms = 0;
-    let lastMonomerCappingAtom = undefined;
-    for (v.i = 0; v.i < LC.seqLength; ++v.i) {
-        const seqMonomer = monomerSeq[v.i];
-        if (seqMonomer.symbol === _utils_macromolecule_consts__WEBPACK_IMPORTED_MODULE_3__.GAP_SYMBOL)
-            continue;
-        const monomer = (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, { symbol: seqMonomer.symbol, polymerType: (0,_monomer_works__WEBPACK_IMPORTED_MODULE_4__.helmTypeToPolymerType)(seqMonomer.biotype) });
-        lastMonomerCappingAtom = monomer.terminalR2Atom;
-        const mAtomFirst = v.nodeShift;
-        const mBondFirst = v.bondShift;
-        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);
-        //adding stereo atoms to array for further STEABS block generation
-        monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));
-        nAtoms += monomer.atoms.x.length;
-        const mAtomCount = v.nodeShift - mAtomFirst;
-        const mAtomList = new Array(mAtomCount);
-        for (let maI = 0; maI < mAtomCount; ++maI)
-            mAtomList[maI] = mAtomFirst + maI;
-        const mBondCount = v.bondShift - mBondFirst;
-        const mBondList = new Array(mBondCount);
-        for (let mbI = 0; mbI < mBondCount; ++mbI)
-            mBondList[mbI] = mBondFirst + mbI;
-        monomers.set(v.i, {
-            biotype: seqMonomer.biotype,
-            symbol: seqMonomer.symbol,
-            atoms: mAtomList, bonds: mBondList
-        });
-    }
-    // if the last monomer needs to be capped, add the terminal OH to the resulting molfile
-    if (needsCapping)
-        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.OXYGEN);
-    const molfileCountsLine = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_COUNTS_LINE_ENDING;
-    // todo: possible optimization may be achieved by replacing .join('') with +=
-    // since counterintuitively joining an array into a new string is reportedly
-    // slower than using += as below
-    let result = '';
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_HEADER_FIRST_LINE;
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_HEADER_SECOND_LINE;
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_CTAB_BLOCK;
-    result += molfileCountsLine;
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_ATOM_BLOCK;
-    result += molfileAtomBlock.join('');
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_END_ATOM_BLOCK;
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_BOND_BLOCK;
-    result += molfileBondBlock.join('');
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_END_BOND_BLOCK;
-    if (steabsCollection.length > 0)
-        result += getCollectionBlock(steabsCollection);
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_END_CTAB_BLOCK;
-    result += _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_END;
-    // return molfileParts.join('');
-    return { molfile: result, monomers: monomers };
-}
-function getCollectionBlock(collection) {
-    //one row in STEABS block can be no longer than 80 symbols
-    //maxSymbols = 80 symbols minus ' -\n' (4 symbols)
-    const maxSymbols = 76;
-    const rowsArray = [];
-    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;
-    for (let i = 0; i < collection.length; i++) {
-        const updatedRow = `${newCollectionRow} ${collection[i]}`;
-        if (updatedRow.length > maxSymbols) {
-            rowsArray.push(`${newCollectionRow} -\n`);
-            newCollectionRow = `M  V30 ${collection[i]}`;
-        }
-        else
-            newCollectionRow = updatedRow;
-        //in case last atom was added - close the block
-        if (i === collection.length - 1)
-            rowsArray.push(`${newCollectionRow})\n`);
-    }
-    return `M  V30 BEGIN COLLECTION\n${rowsArray.join('')}M  V30 END COLLECTION\n`;
-}
-/** Cap the resulting (after sewing up all the monomers) molfile with 'O'
- * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block
- * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block
- * @param {LoopVariables} v - Loop variables
- * @param {LoopConstants} LC - Loop constants*/
-function capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.OXYGEN) {
-    // add terminal oxygen
-    const atomIdx = v.nodeShift + 1;
-    molfileAtomBlock[LC.atomCount] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +
-        (cappingAtomType ?? _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +
-        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\n';
-    // add terminal bond
-    const firstAtom = v.backboneAttachNode;
-    const secondAtom = atomIdx;
-    molfileBondBlock[LC.bondCount] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +
-        1 + ' ' + firstAtom + ' ' + secondAtom + '\n';
-}
-function addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {
-    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX
-    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);
-}
-function addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {
-    // todo: remove these comments to the docstrings of the corr. functions
-    // construnct the lines of V3K molfile atom block
-    fillAtomLines(monomer, molfileAtomBlock, v);
-    // construct the lines of V3K molfile bond block
-    fillBondLines(monomer, molfileBondBlock, v);
-    // peptide bond
-    fillChainExtendingBond(monomer, molfileBondBlock, v);
-    // update branch variables if necessary
-    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)
-        updateBranchVariables(monomer, v);
-    // update loop variables
-    updateChainExtendingVariables(monomer, v);
-}
-function addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {
-    // construnct the lines of V3K molfile atom block corresponding to phosphate
-    // and sugar
-    if (v.i === 0)
-        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);
-    else {
-        for (const monomer of [LC.phosphate, LC.sugar])
-            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);
-    }
-    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);
-}
-function addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {
-    fillBranchAtomLines(monomer, molfileAtomBlock, v);
-    fillBondLines(monomer, molfileBondBlock, v);
-    fillBackboneToBranchBond(monomer, molfileBondBlock, v);
-    // C-N bond
-    const bondIdx = v.bondShift;
-    const firstAtom = v.branchAttachNode;
-    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;
-    molfileBondBlock[bondIdx - 1] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +
-        1 + ' ' + firstAtom + ' ' + secondAtom + '\n';
-    // update loop variables
-    v.bondShift += monomer.bonds.atomPairs.length + 1;
-    v.nodeShift += monomer.atoms.atomTypes.length;
-}
-function updateChainExtendingVariables(monomer, v) {
-    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];
-    v.bondShift += monomer.bonds.atomPairs.length + 1;
-    v.nodeShift += monomer.atoms.atomTypes.length;
-    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check
-    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);
-}
-function updateBranchVariables(monomer, v) {
-    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];
-    for (let i = 0; i < 2; ++i)
-        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];
-}
-function fillAtomLines(monomer, molfileAtomBlock, v) {
-    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {
-        const atomIdx = v.nodeShift + j + 1;
-        molfileAtomBlock[v.nodeShift + j] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +
-            monomer.atoms.atomTypes[j] + ' ' +
-            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +
-            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +
-            ' ' + monomer.atoms.kwargs[j];
-    }
-}
-// todo: remove as quickfix
-function fillBranchAtomLines(monomer, molfileAtomBlock, v) {
-    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {
-        const atomIdx = v.nodeShift + j + 1;
-        molfileAtomBlock[v.nodeShift + j] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +
-            monomer.atoms.atomTypes[j] + ' ' +
-            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +
-            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +
-            ' ' + monomer.atoms.kwargs[j];
-    }
-}
-function fillBondLines(monomer, molfileBondBlock, v) {
-    // construct the lines of V3K molfile bond block
-    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {
-        const bondIdx = v.bondShift + j + 1;
-        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;
-        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;
-        let bondCfg = '';
-        if (monomer.bonds.bondConfiguration.has(j)) {
-            // flip orientation when necessary
-            let orientation = monomer.bonds.bondConfiguration.get(j);
-            if (v.flipFactor < 0)
-                orientation = (orientation === 1) ? 3 : 1;
-            bondCfg = ' CFG=' + orientation;
-        }
-        const kwargs = monomer.bonds.kwargs.has(j) ?
-            ' ' + monomer.bonds.kwargs.get(j) : '';
-        molfileBondBlock[v.bondShift + j] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +
-            monomer.bonds.bondTypes[j] + ' ' +
-            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\n';
-    }
-}
-function fillChainExtendingBond(monomer, molfileBondBlock, v) {
-    if (v.backboneAttachNode !== 0) {
-        const bondIdx = v.bondShift;
-        const firstAtom = v.backboneAttachNode;
-        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;
-        molfileBondBlock[v.bondShift - 1] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +
-            1 + ' ' + firstAtom + ' ' + secondAtom + '\n';
-    }
-}
-// todo: remove
-function fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {
-    const bondIdx = v.bondShift;
-    const firstAtom = v.branchAttachNode;
-    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;
-    molfileBondBlock[bondIdx - 1] = _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +
-        1 + ' ' + firstAtom + ' ' + secondAtom + '\n';
-}
-/** Compute the atom/bond counts for the resulting molfile, depending on the
- * type of polymer (peptide/nucleotide)
- * @param {string[]}monomerSeq - the sequence of monomers
- * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers
- * @param {ALPHABET}alphabet - the alphabet of the monomers
- * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer
- * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/
-function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {
-    let atomCount = 0;
-    let bondCount = 0;
-    let monomerCount = 0;
-    let needsCapping = true;
-    let lastMonomerGraph = null;
-    // sum up all the atoms/nodes provided by the sequence
-    for (const seqMonomer of monomerSeq) {
-        if (seqMonomer.symbol === _utils_macromolecule_consts__WEBPACK_IMPORTED_MODULE_3__.GAP_SYMBOL)
-            continue; // Skip for gap/empty monomer in MSA
-        if (seqMonomer.symbol == '*')
-            throw new Error(`Gap canonical symbol is '', not '*`);
-        lastMonomerGraph = (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, { symbol: seqMonomer.symbol, polymerType: (0,_monomer_works__WEBPACK_IMPORTED_MODULE_4__.helmTypeToPolymerType)(seqMonomer.biotype) });
-        atomCount += lastMonomerGraph.atoms.x.length;
-        bondCount += lastMonomerGraph.bonds.bondTypes.length;
-        monomerCount++;
-    }
-    // add extra values depending on the polymer type
-    if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
-        // add the rightmost/terminating cap group 'OH' (i.e. 'O')
-        atomCount += 1;
-        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)
-        bondCount += monomerCount;
-        // if the last monomer is something like NH2, which only has R1, there is no need to cap it
-        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen
-        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted
-        if (monomerCount > 0) {
-            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.HYDROGEN.toLowerCase()) {
-                needsCapping = false;
-                atomCount -= 1; // remove the last atom (the terminal 'O')
-                bondCount -= 1; // remove the last bond (the terminal C-OH)
-            }
-        }
-    }
-    else { // nucleotides
-        const sugar = (alphabet === _utils_macromolecule_consts__WEBPACK_IMPORTED_MODULE_3__.ALPHABET.DNA) ?
-            (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.DEOXYRIBOSE) : (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.RIBOSE);
-        const phosphate = (0,_types__WEBPACK_IMPORTED_MODULE_1__.getMolGraph)(monomersDict, _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.PHOSPHATE);
-        // add phosphate per each pair of nucleobase symbols
-        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;
-        // add sugar per each nucleobase symbol
-        atomCount += monomerSeq.length * sugar.atoms.x.length;
-        // add the leftmost cap group 'OH' (i.e. 'O')
-        atomCount += 1;
-        // add bonds from phosphate monomers
-        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;
-        // add bonds from sugar monomers
-        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;
-        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)
-        bondCount -= 1;
-        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)
-        bondCount += monomerSeq.length * 3;
-    }
-    return { atomCount, bondCount, needsCapping };
-}
-/** Keep precision upon floating point operations over atom coordinates
- * @param {number}x - the floating point number
- * @return {number} - the floating point number with the same precision
- */
-function keepPrecision(x) {
-    return Math.round(_consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.PRECISION_FACTOR * x) / _consts__WEBPACK_IMPORTED_MODULE_0__.monomerWorksConsts.PRECISION_FACTOR;
-}
-//# sourceMappingURL=to-atomic-level-utils.js.map
-
-/***/ }),
-
-/***/ "./node_modules/@datagrok-libraries/bio/src/monomer-works/types.js":
-/*!*************************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/monomer-works/types.js ***!
-  \*************************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   MolfileWithMap: () => (/* binding */ MolfileWithMap),
-/* harmony export */   MonomerMap: () => (/* binding */ MonomerMap),
-/* harmony export */   getMolGraph: () => (/* binding */ getMolGraph),
-/* harmony export */   hasMolGraph: () => (/* binding */ hasMolGraph),
-/* harmony export */   setMolGraph: () => (/* binding */ setMolGraph)
-/* harmony export */ });
-function getMolGraph(dict, libKey) {
-    return dict[libKey.polymerType]?.[libKey.symbol];
-}
-function hasMolGraph(dict, libKey) {
-    return !!dict[libKey.polymerType]?.[libKey.symbol];
-}
-function setMolGraph(dict, libKey, value) {
-    let pt = dict[libKey.polymerType];
-    if (!pt)
-        pt = dict[libKey.polymerType] = {};
-    pt[libKey.symbol] = value;
-}
-class MonomerMap extends Map {
-    constructor(entries) {
-        super(entries);
-    }
-}
-/** @property monomers key - helm seq position, */
-class MolfileWithMap {
-    constructor(molfile, monomers) {
-        this.molfile = molfile;
-        this.monomers = monomers;
-    }
-    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }
-}
-//# sourceMappingURL=types.js.map
-
-/***/ }),
-
-/***/ "./node_modules/@datagrok-libraries/bio/src/utils/const.js":
-/*!*****************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/utils/const.js ***!
-  \*****************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   DEOXYRIBOSE_SYMBOL: () => (/* binding */ DEOXYRIBOSE_SYMBOL),
-/* harmony export */   DUMMY_MONOMER: () => (/* binding */ DUMMY_MONOMER),
-/* harmony export */   HELM_CORE_FIELDS: () => (/* binding */ HELM_CORE_FIELDS),
-/* harmony export */   HELM_WRAPPERS_REGEXP: () => (/* binding */ HELM_WRAPPERS_REGEXP),
-/* harmony export */   MONOMER_ENCODE_MAX: () => (/* binding */ MONOMER_ENCODE_MAX),
-/* harmony export */   MONOMER_ENCODE_MIN: () => (/* binding */ MONOMER_ENCODE_MIN),
-/* harmony export */   PHOSPHATE_SYMBOL: () => (/* binding */ PHOSPHATE_SYMBOL),
-/* harmony export */   RIBOSE_SYMBOL: () => (/* binding */ RIBOSE_SYMBOL),
-/* harmony export */   SDF_MONOMER_NAME: () => (/* binding */ SDF_MONOMER_NAME),
-/* harmony export */   jsonSdfMonomerLibDict: () => (/* binding */ jsonSdfMonomerLibDict)
-/* harmony export */ });
-// core fields of HELM library object used in toAtomicLevel function
-const HELM_CORE_FIELDS = [
-    "symbol" /* HELM_FIELDS.SYMBOL */,
-    "molfile" /* HELM_FIELDS.MOLFILE */,
-    "rgroups" /* HELM_FIELDS.RGROUPS */,
-    "name" /* HELM_FIELDS.NAME */,
-    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be
-    // supported
-];
-const SDF_MONOMER_NAME = 'MonomerName';
-// todo: ideally, keys should be expressed via constants
-const jsonSdfMonomerLibDict = {
-    'monomerType': null, // -> Backbone
-    'smiles': null,
-    'name': 'Name',
-    'author': null,
-    'molfile': 'molecule',
-    'naturalAnalog': 'MonomerNaturalAnalogCode',
-    'rgroups': 'MonomerCaps',
-    'createDate': null,
-    'id': null,
-    'polymerType': 'MonomerType',
-    'symbol': 'MonomerName'
-};
-const DUMMY_MONOMER = {
-    'monomerType': 'Backbone',
-    'smiles': '',
-    'name': '',
-    'author': 'Datagrok',
-    'molfile': '',
-    'naturalAnalog': '',
-    'rgroups': [],
-    'createDate': null,
-    'id': 0,
-    'polymerType': 'PEPTIDE',
-    'symbol': ''
-};
-// range of hex nubers used in PepSea library to endode monomers
-const MONOMER_ENCODE_MIN = 0x100;
-const MONOMER_ENCODE_MAX = 0x40A;
-const RIBOSE_SYMBOL = 'r';
-const DEOXYRIBOSE_SYMBOL = 'd';
-const PHOSPHATE_SYMBOL = 'p';
-const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\((\\w)\\)${PHOSPHATE_SYMBOL}?`, 'g');
-//# sourceMappingURL=const.js.map
-
-/***/ }),
-
-/***/ "./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/consts.js":
-/*!********************************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/consts.js ***!
-  \********************************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   ALPHABET: () => (/* binding */ ALPHABET),
-/* harmony export */   Alphabets: () => (/* binding */ Alphabets),
-/* harmony export */   BioTags: () => (/* binding */ TAGS),
-/* harmony export */   GAP_SYMBOL: () => (/* binding */ GAP_SYMBOL),
-/* harmony export */   GapOriginals: () => (/* binding */ GapOriginals),
-/* harmony export */   MONOMER_MOTIF_SPLITTER: () => (/* binding */ MONOMER_MOTIF_SPLITTER),
-/* harmony export */   NOTATION: () => (/* binding */ NOTATION),
-/* harmony export */   TAGS: () => (/* binding */ TAGS),
-/* harmony export */   candidateAlphabets: () => (/* binding */ candidateAlphabets),
-/* harmony export */   helmPp1Re: () => (/* binding */ helmPp1Re),
-/* harmony export */   helmRe: () => (/* binding */ helmRe),
-/* harmony export */   monomerRe: () => (/* binding */ monomerRe),
-/* harmony export */   positionSeparator: () => (/* binding */ positionSeparator)
-/* harmony export */ });
-/* harmony import */ var _types__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! ./types */ "./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/types.js");
-
-/** enum type to simplify setting "user-friendly" notation if necessary */
-var NOTATION;
-(function (NOTATION) {
-    NOTATION["FASTA"] = "fasta";
-    NOTATION["SEPARATOR"] = "separator";
-    NOTATION["HELM"] = "helm";
-    /* Requires notation handler */ NOTATION["CUSTOM"] = "custom";
-})(NOTATION || (NOTATION = {}));
-var ALPHABET;
-(function (ALPHABET) {
-    ALPHABET["DNA"] = "DNA";
-    ALPHABET["RNA"] = "RNA";
-    ALPHABET["PT"] = "PT";
-    /** Unknown */
-    ALPHABET["UN"] = "UN";
-})(ALPHABET || (ALPHABET = {}));
-var TAGS;
-(function (TAGS) {
-    TAGS["aligned"] = "aligned";
-    TAGS["alphabet"] = "alphabet";
-    TAGS["alphabetSize"] = ".alphabetSize";
-    TAGS["alphabetIsMultichar"] = ".alphabetIsMultichar";
-    TAGS["separator"] = "separator";
-    TAGS["isHelmCompatible"] = ".isHelmCompatible";
-    TAGS["positionNames"] = ".positionNames";
-    TAGS["positionLabels"] = ".positionLabels";
-    TAGS["regions"] = ".regions";
-    TAGS["positionShift"] = ".positionShift";
-    TAGS["selectedPosition"] = ".selectedPosition";
-})(TAGS || (TAGS = {}));
-
-const positionSeparator = ', ';
-const monomerRe = /(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g;
-const helmRe = /(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g;
-const helmPp1Re = /\[([^\[\]]+)]/g;
-const Alphabets = new class {
-    constructor() {
-        this.fasta = {
-            peptide: new Set([
-                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',
-                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',
-            ]),
-            dna: new Set(['A', 'C', 'G', 'T']),
-            rna: new Set(['A', 'C', 'G', 'U']),
-        };
-    }
-}();
-const candidateAlphabets = [
-    new _types__WEBPACK_IMPORTED_MODULE_0__.CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),
-    new _types__WEBPACK_IMPORTED_MODULE_0__.CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),
-    new _types__WEBPACK_IMPORTED_MODULE_0__.CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),
-];
-/** Canonical gap symbol */
-const GAP_SYMBOL = '';
-const GapOriginals = {
-    [NOTATION.FASTA]: '-',
-    [NOTATION.SEPARATOR]: '',
-    [NOTATION.HELM]: '*',
-};
-const MONOMER_MOTIF_SPLITTER = ' , ';
-//# sourceMappingURL=consts.js.map
-
-/***/ }),
-
-/***/ "./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/types.js":
-/*!*******************************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/types.js ***!
-  \*******************************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   CandidateSimType: () => (/* binding */ CandidateSimType),
-/* harmony export */   CandidateType: () => (/* binding */ CandidateType)
-/* harmony export */ });
-/** Alphabet candidate type */
-class CandidateType {
-    constructor(name, alphabet, cutoff) {
-        this.name = name;
-        this.alphabet = alphabet;
-        this.cutoff = cutoff;
-    }
-}
-/** Alphabet candidate similarity type */
-class CandidateSimType extends CandidateType {
-    constructor(candidate, freq, similarity) {
-        super(candidate.name, candidate.alphabet, candidate.cutoff);
-        this.freq = freq;
-        this.similarity = similarity;
-    }
-}
-//# sourceMappingURL=types.js.map
-
-/***/ }),
-
-/***/ "./node_modules/@datagrok-libraries/js-draw-lite/src/types/org.js":
-/*!************************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/js-draw-lite/src/types/org.js ***!
-  \************************************************************************/
-/***/ ((__unused_webpack_module, __webpack_exports__, __webpack_require__) => {
-
-__webpack_require__.r(__webpack_exports__);
-/* harmony export */ __webpack_require__.d(__webpack_exports__, {
-/* harmony export */   HelmTypes: () => (/* binding */ HelmTypes)
-/* harmony export */ });
-var HelmTypes;
-(function (HelmTypes) {
-    HelmTypes["BASE"] = "HELM_BASE";
-    HelmTypes["SUGAR"] = "HELM_SUGAR";
-    HelmTypes["LINKER"] = "HELM_LINKER";
-    HelmTypes["AA"] = "HELM_AA";
-    HelmTypes["CHEM"] = "HELM_CHEM";
-    HelmTypes["BLOB"] = "HELM_BLOB";
-    HelmTypes["NUCLEOTIDE"] = "HELM_NUCLETIDE";
-})(HelmTypes || (HelmTypes = {}));
-//# sourceMappingURL=org.js.map
-
-/***/ })
-
-/******/ 	});
-/************************************************************************/
-/******/ 	// The module cache
-/******/ 	var __webpack_module_cache__ = {};
-/******/ 	
-/******/ 	// The require function
-/******/ 	function __webpack_require__(moduleId) {
-/******/ 		// Check if module is in cache
-/******/ 		var cachedModule = __webpack_module_cache__[moduleId];
-/******/ 		if (cachedModule !== undefined) {
-/******/ 			return cachedModule.exports;
-/******/ 		}
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-/******/ 		};
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-/******/ 		__webpack_modules__[moduleId](module, module.exports, __webpack_require__);
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-/******/ 	})();
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-/******/ 	(() => {
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-/******/ 				Object.defineProperty(exports, Symbol.toStringTag, { value: 'Module' });
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-/******/ 	})();
-/******/ 	
-/************************************************************************/
-var __webpack_exports__ = {};
-/*!*****************************************************************************************!*\
-  !*** ./node_modules/@datagrok-libraries/bio/src/monomer-works/seq-to-molfile-worker.js ***!
-  \*****************************************************************************************/
-__webpack_require__.r(__webpack_exports__);
-/* harmony import */ var _to_atomic_level_utils__WEBPACK_IMPORTED_MODULE_0__ = __webpack_require__(/*! ./to-atomic-level-utils */ "./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js");
-
-onmessage = (event) => {
-    const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;
-    const resMolList = new Array(end - start);
-    const molfileWarningList = new Array(0);
-    for (let rowI = start; rowI < end; ++rowI) {
-        try {
-            const seq = seqList[rowI];
-            resMolList[rowI - start] = (0,_to_atomic_level_utils__WEBPACK_IMPORTED_MODULE_0__.monomerSeqToMolfile)(seq, monomersDict, alphabet, polymerType);
-        }
-        catch (err) {
-            const errMsg = err instanceof Error ? err.message : err.toString();
-            const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;
-            molfileWarningList.push(msg);
-        }
-    }
-    postMessage({ molfiles: resMolList, warnings: molfileWarningList });
-};
-//# sourceMappingURL=seq-to-molfile-worker.js.map
-sequencetranslator = __webpack_exports__;
-/******/ })()
-;
-//# sourceMappingURL=vendors-node_modules_datagrok-libraries_bio_src_monomer-works_seq-to-molfile-worker_js.js.map