@datagrok/bio 2.13.2 → 2.13.5

package/dist/282.js

@@ -1,2 +0,0 @@
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indexes, num, index) {\n    if (num > distancesAr[distancesAr.length - 1])\n        return;\n    const newPosition = distancesAr.findIndex((v) => num < v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function insertLarger(distancesAr, indexes, num, index) {\n    if (num < distancesAr[distancesAr.length - 1])\n        return;\n    const newPosition = distancesAr.findIndex((v) => num > v);\n    distancesAr.pop();\n    distancesAr.splice(newPosition, 0, num);\n    indexes.pop();\n    indexes.splice(newPosition, 0, index);\n}\nexport function getAggregationFunction(aggregationMethod, weights) {\n    switch (aggregationMethod) {\n        case DistanceAggregationMethods.MANHATTAN:\n            return (vs) => vs.reduce((acc, val, idx) => acc + val * weights[idx], 0);\n        default:\n            return (vs) => {\n                // euclidean\n                const sum = vs.reduce((acc, val, idx) => acc + (val * weights[idx]) ** 2, 0);\n                return Math.sqrt(sum);\n            };\n    }\n}\n//# 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{ getAggregationFunction, insertSmaller, isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n    const { values, startIdx, endIdx, fnNames, opts, nNeighbours, weights, aggregationMethod } = event.data;\n    try {\n        const knnIndexes = new Array(values[0].length).fill(null).map(() => new Array(nNeighbours).fill(-1));\n        const knnDistances = new Array(values[0].length).fill(null).map(() => new Array(nNeighbours).fill(999999));\n        const aggregate = getAggregationFunction(aggregationMethod, weights);\n        const chunkSize = endIdx - startIdx;\n        values.forEach((v, colIdx) => {\n            if (isBitArrayMetric(fnNames[colIdx])) {\n                for (let i = 0; i < v.length; ++i) {\n                    if (isNil(v[i]))\n                        continue;\n                    values[colIdx][i] = new BitArray(values[colIdx][i]._data, values[colIdx][i]._length);\n                }\n            }\n        });\n        let cnt = 0;\n        const distanceFns = new Array(fnNames.length).fill(null).map((_, i) => new Measure(fnNames[i]).getMeasure(opts[i]));\n        const startRow = values[0].length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values[0].length * (values[0].length - 1) - 7) / 2 - 0.5);\n        const startCol = startIdx - values[0].length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);\n        let mi = startRow;\n        let mj = startCol;\n        while (cnt < chunkSize) {\n            //const value = seq1List[mi] && seq1List[mj] ? hamming(seq1List[mi], seq1List[mj]) : 0;\n            const distanceValues = distanceFns.map((fn, idx) => !isNil(values[idx][mi]) && !isNil(values[idx][mj]) ?\n                fn(values[idx][mi], values[idx][mj]) : 1);\n            // const value = !isNil(values[mi]) && !isNil(values[mj]) ?\n            //   distanceFn(values[mi], values[mj]) : 1;\n            const value = distanceValues.length === 1 ? distanceValues[0] : aggregate(distanceValues);\n            insertSmaller(knnDistances[mi], knnIndexes[mi], value, mj);\n            insertSmaller(knnDistances[mj], knnIndexes[mj], value, mi);\n            cnt++;\n            mj++;\n            if (mj === values[0].length) {\n                mi++;\n                mj = mi + 1;\n            }\n        }\n        postMessage({ knnDistances, knnIndexes });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# 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const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000,\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: 'd',\n    RIBOSE: 'r',\n    PHOSPHATE: 'p',\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null,\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\n/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n})(TAGS || (TAGS = {}));\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\n                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n            ]),\n            dna: new Set(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\n    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n//# sourceMappingURL=consts.js.map","import { monomerWorksConsts as C } from './consts';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET } from '../utils/macromolecule/consts';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                alphabet === ALPHABET.DNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE ||\n                alphabet === ALPHABET.RNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(it[\"symbol\" /* HELM_FIELDS.SYMBOL */], monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {string[]} monomerSeq - Sequence of monomer symbols\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @return {string} - Molfile V3000*/\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return '';\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock; // todo: types?\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    }\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === ALPHABET.DNA) ? monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);\n        phosphate = monomersDict.get(C.PHOSPHATE);\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        seqLength: monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const steabsCollection = [];\n    let nAtoms = 0;\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const monomer = monomersDict.get(monomerSeq[v.i]);\n        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n        //adding stereo atoms to array for further STEABS block generation\n        monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n        nAtoms += monomer.atoms.x.length;\n    }\n    capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (steabsCollection.length > 0)\n        result += getCollectionBlock(steabsCollection);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return result;\n}\nfunction getCollectionBlock(collection) {\n    //one row in STEABS block can be no longer than 80 symbols\n    //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n    const maxSymbols = 76;\n    const rowsArray = [];\n    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n    for (let i = 0; i < collection.length; i++) {\n        const updatedRow = `${newCollectionRow} ${collection[i]}`;\n        if (updatedRow.length > maxSymbols) {\n            rowsArray.push(`${newCollectionRow} -\\n`);\n            newCollectionRow = `M  V30 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        C.OXYGEN + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0) {\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    }\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift[0]; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * monomer.meta.backboneShift[1];\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n    * type of polymer (peptide/nucleotide)\n    * @param {string[]}monomerSeq - the sequence of monomers\n    * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers\n    * @param {ALPHABET}alphabet - the alphabet of the monomers\n    * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer\n    * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {\n    let atomCount = 0;\n    let bondCount = 0;\n    // sum up all the atoms/nodes provided by the sequence\n    for (const monomerSymbol of monomerSeq) {\n        if (monomerSymbol === '')\n            continue; // Skip for gap/empty monomer in MSA\n        const monomer = monomersDict.get(monomerSymbol);\n        atomCount += monomer.atoms.x.length;\n        bondCount += monomer.bonds.bondTypes.length;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerSeq.length;\n    }\n    else { // nucleotides\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);\n        const phosphate = monomersDict.get(C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount };\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n*/\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { monomerSequencesArray, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const molfileList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const monomerSeq = monomerSequencesArray[rowI];\n            molfileList[rowI - start] = monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? err.message : err.toString();\n            const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;\n            molfileWarningList.push(msg);\n        }\n    }\n    postMessage({ molfileList, molfileWarningList });\n};\n//# 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package/dist/356.js

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resolve;\n      readyPromiseReject = reject;\n    });\n    var moduleOverrides = Object.assign({}, Module);\n    var arguments_ = [];\n    var thisProgram = \"./this.program\";\n    var quit_ = (status, toThrow) => {\n      throw toThrow;\n    };\n    var ENVIRONMENT_IS_WEB = typeof window == \"object\";\n    var ENVIRONMENT_IS_WORKER = typeof importScripts == \"function\";\n    var ENVIRONMENT_IS_NODE =\n      typeof process == \"object\" &&\n      typeof process.versions == \"object\" &&\n      typeof process.versions.node == \"string\";\n    var scriptDirectory = \"\";\n    function locateFile(path) {\n      if (Module[\"locateFile\"]) {\n        return Module[\"locateFile\"](path, scriptDirectory);\n      }\n      return scriptDirectory + path;\n    }\n    var read_, readAsync, readBinary, setWindowTitle;\n    if (ENVIRONMENT_IS_WEB || ENVIRONMENT_IS_WORKER) {\n      if (ENVIRONMENT_IS_WORKER) {\n        scriptDirectory = self.location.href;\n      } else if (typeof document != \"undefined\" && document.currentScript) {\n        scriptDirectory = document.currentScript.src;\n      }\n      if (_scriptDir) {\n        scriptDirectory = _scriptDir;\n      }\n      if (scriptDirectory.indexOf(\"blob:\") !== 0) {\n        scriptDirectory = scriptDirectory.substr(\n          0,\n          scriptDirectory.replace(/[?#].*/, \"\").lastIndexOf(\"/\") + 1\n        );\n      } else {\n        scriptDirectory = \"\";\n      }\n      {\n        read_ = (url) => {\n          var xhr = new XMLHttpRequest();\n          xhr.open(\"GET\", url, false);\n          xhr.send(null);\n          return xhr.responseText;\n        };\n        if (ENVIRONMENT_IS_WORKER) {\n          readBinary = (url) => {\n            var xhr = new XMLHttpRequest();\n            xhr.open(\"GET\", url, false);\n            xhr.responseType = \"arraybuffer\";\n            xhr.send(null);\n            return new Uint8Array(xhr.response);\n          };\n        }\n        readAsync = (url, onload, onerror) 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Module[\"wasmBinary\"];\n    var noExitRuntime = Module[\"noExitRuntime\"] || true;\n    if (typeof WebAssembly != \"object\") {\n      abort(\"no native wasm support detected\");\n    }\n    var wasmMemory;\n    var ABORT = false;\n    var EXITSTATUS;\n    var HEAP8, HEAPU8, HEAP16, HEAPU16, HEAP32, HEAPU32, HEAPF32, HEAPF64;\n    function updateMemoryViews() {\n      var b = wasmMemory.buffer;\n      Module[\"HEAP8\"] = HEAP8 = new Int8Array(b);\n      Module[\"HEAP16\"] = HEAP16 = new Int16Array(b);\n      Module[\"HEAP32\"] = HEAP32 = new Int32Array(b);\n      Module[\"HEAPU8\"] = HEAPU8 = new Uint8Array(b);\n      Module[\"HEAPU16\"] = HEAPU16 = new Uint16Array(b);\n      Module[\"HEAPU32\"] = HEAPU32 = new Uint32Array(b);\n      Module[\"HEAPF32\"] = HEAPF32 = new Float32Array(b);\n      Module[\"HEAPF64\"] = HEAPF64 = new Float64Array(b);\n    }\n    var wasmTable;\n    var __ATPRERUN__ = [];\n    var __ATINIT__ = [];\n    var __ATPOSTRUN__ = [];\n    var runtimeInitialized = false;\n    function preRun() {\n      if (Module[\"preRun\"]) {\n        if (typeof Module[\"preRun\"] == \"function\")\n          Module[\"preRun\"] = [Module[\"preRun\"]];\n        while (Module[\"preRun\"].length) {\n          addOnPreRun(Module[\"preRun\"].shift());\n        }\n      }\n      callRuntimeCallbacks(__ATPRERUN__);\n    }\n    function initRuntime() {\n      runtimeInitialized = true;\n      callRuntimeCallbacks(__ATINIT__);\n    }\n    function postRun() {\n      if (Module[\"postRun\"]) {\n        if (typeof Module[\"postRun\"] == \"function\")\n          Module[\"postRun\"] = [Module[\"postRun\"]];\n        while (Module[\"postRun\"].length) {\n          addOnPostRun(Module[\"postRun\"].shift());\n        }\n      }\n      callRuntimeCallbacks(__ATPOSTRUN__);\n    }\n    function addOnPreRun(cb) {\n      __ATPRERUN__.unshift(cb);\n    }\n    function addOnInit(cb) {\n      __ATINIT__.unshift(cb);\n    }\n    function addOnPostRun(cb) {\n      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UTF8ArrayToString(HEAPU8, ptr, maxBytesToRead) : \"\";\n    }\n    function ccall(ident, returnType, argTypes, args, opts) {\n      var toC = {\n        string: (str) => {\n          var ret = 0;\n          if (str !== null && str !== undefined && str !== 0) {\n            ret = stringToUTF8OnStack(str);\n          }\n          return ret;\n        },\n        array: (arr) => {\n          var ret = stackAlloc(arr.length);\n          writeArrayToMemory(arr, ret);\n          return ret;\n        },\n      };\n      function convertReturnValue(ret) {\n        if (returnType === \"string\") {\n          return UTF8ToString(ret);\n        }\n        if (returnType === \"boolean\") return Boolean(ret);\n        return ret;\n      }\n      var func = getCFunc(ident);\n      var cArgs = [];\n      var stack = 0;\n      if (args) {\n        for (var i = 0; i < args.length; i++) {\n          var converter = toC[argTypes[i]];\n          if (converter) {\n            if (stack === 0) stack = stackSave();\n            cArgs[i] = converter(args[i]);\n          } else {\n            cArgs[i] = args[i];\n          }\n        }\n      }\n      var ret = func.apply(null, cArgs);\n      function onDone(ret) {\n        if (stack !== 0) stackRestore(stack);\n        return convertReturnValue(ret);\n      }\n      ret = onDone(ret);\n      return ret;\n    }\n    function cwrap(ident, returnType, argTypes, opts) {\n      var numericArgs =\n        !argTypes ||\n        argTypes.every((type) => type === \"number\" || type === \"boolean\");\n      var numericRet = returnType !== \"string\";\n      if (numericRet && numericArgs && !opts) {\n        return getCFunc(ident);\n      }\n      return function () {\n        return ccall(ident, returnType, argTypes, arguments, opts);\n      };\n    }\n    var wasmImports = {\n      d: ___cxa_throw,\n      a: _abort,\n      c: _emscripten_memcpy_big,\n      b: _emscripten_resize_heap,\n    };\n    var asm = createWasm();\n    var ___wasm_call_ctors = function () {\n      return (___wasm_call_ctors = Module[\"asm\"][\"f\"]).apply(null, arguments);\n    };\n    var _getDendrogram = (Module[\"_getDendrogram\"] = function () {\n      return (_getDendrogram = Module[\"_getDendrogram\"] =\n        Module[\"asm\"][\"g\"]).apply(null, arguments);\n    });\n    var _free = (Module[\"_free\"] = function () {\n      return (_free = Module[\"_free\"] = Module[\"asm\"][\"h\"]).apply(\n        null,\n        arguments\n      );\n    });\n    var ___errno_location = function () {\n      return (___errno_location = Module[\"asm\"][\"__errno_location\"]).apply(\n        null,\n        arguments\n      );\n    };\n    var _malloc = (Module[\"_malloc\"] = function () {\n      return (_malloc = Module[\"_malloc\"] = Module[\"asm\"][\"j\"]).apply(\n        null,\n        arguments\n      );\n    });\n    var stackSave = function () {\n      return (stackSave = Module[\"asm\"][\"k\"]).apply(null, arguments);\n    };\n    var stackRestore = function () {\n      return (stackRestore = Module[\"asm\"][\"l\"]).apply(null, arguments);\n    };\n    var stackAlloc = function () {\n      return (stackAlloc = Module[\"asm\"][\"m\"]).apply(null, arguments);\n    };\n    var ___cxa_is_pointer_type = function () {\n      return (___cxa_is_pointer_type = Module[\"asm\"][\"n\"]).apply(\n        null,\n        arguments\n      );\n    };\n    Module[\"ccall\"] = ccall;\n    Module[\"cwrap\"] = cwrap;\n    var calledRun;\n    dependenciesFulfilled = function runCaller() {\n      if (!calledRun) run();\n      if (!calledRun) dependenciesFulfilled = runCaller;\n    };\n    function run() {\n      if (runDependencies > 0) {\n        return;\n      }\n      preRun();\n      if (runDependencies > 0) {\n        return;\n      }\n      function doRun() {\n        if (calledRun) return;\n        calledRun = true;\n        Module[\"calledRun\"] = true;\n        if (ABORT) return;\n        initRuntime();\n        readyPromiseResolve(Module);\n        if (Module[\"onRuntimeInitialized\"]) Module[\"onRuntimeInitialized\"]();\n        postRun();\n      }\n      if (Module[\"setStatus\"]) {\n        Module[\"setStatus\"](\"Running...\");\n        setTimeout(function () {\n          setTimeout(function () {\n            Module[\"setStatus\"](\"\");\n          }, 1);\n          doRun();\n        }, 1);\n      } else {\n        doRun();\n      }\n    }\n    if (Module[\"preInit\"]) {\n      if (typeof Module[\"preInit\"] == \"function\")\n        Module[\"preInit\"] = [Module[\"preInit\"]];\n      while (Module[\"preInit\"].length > 0) {\n        Module[\"preInit\"].pop()();\n      }\n    }\n    run();\n\n    return exportCppLib.ready;\n  };\n})();\nif (typeof exports === \"object\" && typeof module === \"object\")\n  module.exports = exportCppLib;\nelse if (typeof define === \"function\" && define[\"amd\"])\n  define([], function () {\n    return exportCppLib;\n  });\nelse if (typeof exports === \"object\") exports[\"exportCppLib\"] = exportCppLib;\n","// The module cache\nvar __webpack_module_cache__ = {};\n\n// The require function\nfunction __webpack_require__(moduleId) {\n\t// Check if module is in cache\n\tvar cachedModule = __webpack_module_cache__[moduleId];\n\tif (cachedModule !== undefined) {\n\t\treturn cachedModule.exports;\n\t}\n\t// Create a new module (and put it into the cache)\n\tvar module = __webpack_module_cache__[moduleId] = {\n\t\tid: moduleId,\n\t\tloaded: false,\n\t\texports: {}\n\t};\n\n\t// Execute the module function\n\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n\n\t// Flag the module as loaded\n\tmodule.loaded = true;\n\n\t// Return the exports of the module\n\treturn module.exports;\n}\n\n// expose the modules object (__webpack_modules__)\n__webpack_require__.m = __webpack_modules__;\n\n","__webpack_require__.amdO = {};","// define getter functions for harmony exports\n__webpack_require__.d = (exports, definition) => {\n\tfor(var key in definition) {\n\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n\t\t}\n\t}\n};","__webpack_require__.g = (function() {\n\tif (typeof globalThis === 'object') return globalThis;\n\ttry {\n\t\treturn this || new Function('return this')();\n\t} catch (e) {\n\t\tif (typeof window === 'object') return window;\n\t}\n})();","__webpack_require__.hmd = (module) => {\n\tmodule = Object.create(module);\n\tif (!module.children) module.children = [];\n\tObject.defineProperty(module, 'exports', {\n\t\tenumerable: true,\n\t\tset: () => {\n\t\t\tthrow new Error('ES Modules may not assign module.exports or exports.*, Use ESM export syntax, instead: ' + module.id);\n\t\t}\n\t});\n\treturn module;\n};","__webpack_require__.o = (obj, prop) => (Object.prototype.hasOwnProperty.call(obj, prop))","var scriptUrl;\nif (__webpack_require__.g.importScripts) scriptUrl = __webpack_require__.g.location + \"\";\nvar document = __webpack_require__.g.document;\nif (!scriptUrl && document) {\n\tif (document.currentScript)\n\t\tscriptUrl = document.currentScript.src;\n\tif (!scriptUrl) {\n\t\tvar scripts = document.getElementsByTagName(\"script\");\n\t\tif(scripts.length) {\n\t\t\tvar i = scripts.length - 1;\n\t\t\twhile (i > -1 && !scriptUrl) scriptUrl = scripts[i--].src;\n\t\t}\n\t}\n}\n// When supporting browsers where an automatic publicPath is not supported you must specify an output.publicPath manually via configuration\n// or pass an empty string (\"\") and set the __webpack_public_path__ variable from your code to use your own logic.\nif (!scriptUrl) throw new Error(\"Automatic publicPath is not supported in this browser\");\nscriptUrl = scriptUrl.replace(/#.*$/, \"\").replace(/\\?.*$/, \"\").replace(/\\/[^\\/]+$/, \"/\");\n__webpack_require__.p = scriptUrl;","__webpack_require__.b = self.location + \"\";\n\n// object to store loaded chunks\n// \"1\" means \"already loaded\"\nvar installedChunks = {\n\t356: 1\n};\n\n// no chunk install function needed\n// no chunk loading\n\n// no HMR\n\n// no HMR manifest","import { getClustersFromDistMatWasm } from './clusterizerWasm';\nonmessage = (event) => {\n    const { distMatArray, n, methodCode } = event.data;\n    const data = {};\n    try {\n        getClustersFromDistMatWasm(distMatArray, n, methodCode)\n            .then((clusterMatrix) => {\n            data.clusterMatrix = clusterMatrix;\n            postMessage(data);\n        });\n    }\n    catch (e) {\n        data.error = e;\n        postMessage(data);\n    }\n};\n//# sourceMappingURL=clustering-worker.js.map","import {exportCppLib} from './wasmCluster.js';\n\n/**\n calls wasm function to get clustering merges and heights from distance matrix\n distmat: distance matrix as an array of floats comprising the top right triangle of the matrix\n n: number of observables\n method: 0 = single linkage, 1 = complete linkage, 2 = average linkage, 3 = median linkage\n result: { mergeResult: Int32Array, heightsResult: Float32Array }\n mergeResult has length of (n-1)*2 and heightResult has length of n-1\n together they describe the clustering as a dendrogram as a matrix of (n-1) X 3\n each row in the given matrix comprises the merge event at step i and last column is the height from the leaves.\n*/\nexport async function getClustersFromDistMatWasm(distmat, n, method) {\n  const wasmUrl = new URL('./wasmCluster.wasm', import.meta.url).href;\n  const wasmPath = wasmUrl.substring(0, wasmUrl.lastIndexOf('/') + 1) + 'wasmCluster.wasm';\n  let wasmInstance;\n  try {\n      wasmInstance = await exportCppLib({locateFile: () => wasmPath, printErr: (_) => {}});\n  } catch (e) {\n      try {\n          wasmInstance = await exportCppLib({locateFile: () => wasmUrl, printErr: (_) => {}});\n      }\n      catch (e) {\n          console.error(e);\n          throw new Error('Unable to load wasm file for hierarchical 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