@datagrok-libraries/bio 5.32.3 → 5.32.5

package/src/monomer-works/to-atomic-level-utils.js

@@ -0,0 +1,284 @@
+import { monomerWorksConsts as C } from './consts';
+import { HELM_CORE_FIELDS, } from '../utils/const';
+/** 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*/
+export 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 === "DNA" /* ALPHABET.DNA */ && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE ||
+                alphabet === "RNA" /* ALPHABET.RNA */ && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE ||
+                it["symbol" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE) ||
+            polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */ &&
+                it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== "Branch" /* HELM_MONOMER_TYPE.BRANCH */) {
+            const monomerObject = {};
+            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
+ * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects
+ * @param {ALPHABET} alphabet - Alphabet of the column
+ * @param {HELM_POLYMER_TYPE} polymerType - Polymer type
+ * @return {string} - Molfile V3000*/
+export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {
+    if (monomerSeq.length === 0) {
+        // throw new Error('monomerSeq is empty');
+        return '';
+    }
+    // define atom and bond counts, taking into account the bond type
+    const getAtomAndBondCounts = getResultingAtomBondCounts;
+    const { atomCount, bondCount } = 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; // todo: types?
+    let sugar = null;
+    let phosphate = null;
+    if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
+        addMonomerToMolblock = addAminoAcidToMolblock;
+    }
+    else { // nucleotides
+        addMonomerToMolblock = addNucleotideToMolblock;
+        sugar = (alphabet === "DNA" /* ALPHABET.DNA */) ? monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);
+        phosphate = monomersDict.get(C.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,
+    };
+    for (v.i = 0; v.i < LC.seqLength; ++v.i) {
+        const monomer = monomersDict.get(monomerSeq[v.i]);
+        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);
+    }
+    capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC);
+    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.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 += C.V3K_HEADER_FIRST_LINE;
+    result += C.V3K_HEADER_SECOND_LINE;
+    result += C.V3K_BEGIN_CTAB_BLOCK;
+    result += molfileCountsLine;
+    result += C.V3K_BEGIN_ATOM_BLOCK;
+    result += molfileAtomBlock.join('');
+    result += C.V3K_END_ATOM_BLOCK;
+    result += C.V3K_BEGIN_BOND_BLOCK;
+    result += molfileBondBlock.join('');
+    result += C.V3K_END_BOND_BLOCK;
+    result += C.V3K_END_CTAB_BLOCK;
+    result += C.V3K_END;
+    // return molfileParts.join('');
+    return result;
+}
+/** 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) {
+    // add terminal oxygen
+    const atomIdx = v.nodeShift + 1;
+    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +
+        C.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] = C.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] = C.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]; // todo: non-null check
+    v.backbonePositionShift[1] += v.flipFactor * monomer.meta.backboneShift[1];
+}
+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] = C.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] = C.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] = C.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] = C.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] = C.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;
+    // sum up all the atoms/nodes provided by the sequence
+    for (const monomerSymbol of monomerSeq) {
+        if (monomerSymbol === '')
+            continue; // Skip for gap/empty monomer in MSA
+        const monomer = monomersDict.get(monomerSymbol);
+        atomCount += monomer.atoms.x.length;
+        bondCount += monomer.bonds.bondTypes.length;
+    }
+    // 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 += monomerSeq.length;
+    }
+    else { // nucleotides
+        const sugar = (alphabet === "DNA" /* ALPHABET.DNA */) ?
+            monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);
+        const phosphate = monomersDict.get(C.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 };
+}
+/** 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
+*/
+export function keepPrecision(x) {
+    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;
+}
+//# sourceMappingURL=to-atomic-level-utils.js.map

package/src/monomer-works/to-atomic-level-utils.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"to-atomic-level-utils.js","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,kBAAkB,IAAI,CAAC,EAAC,MAAM,UAAU,CAAC;AAGjD,OAAO,EACQ,gBAAgB,GAC9B,MAAM,gBAAgB,CAAC;AAKxB;;;;iHAIiH;AACjH,MAAM,UAAU,sBAAsB,CACpC,UAAuB,EAAE,WAA8B,EAAE,QAAkB;IAE3E,MAAM,GAAG,GAAG,IAAI,GAAG,EAAe,CAAC;IACnC,KAAK,MAAM,aAAa,IAAI,UAAU,CAAC,uBAAuB,CAAC,WAAW,CAAC,EAAE;QAC3E,MAAM,EAAE,GAAY,UAAU,CAAC,UAAU,CAAC,WAAW,EAAE,aAAa,CAAE,CAAC;QACvE,IACE,WAAW,sCAA0B;YACnC,CAAC,EAAE,8CAA0B,4CAA6B;gBACxD,QAAQ,6BAAiB,IAAI,EAAE,mCAAoB,KAAK,CAAC,CAAC,WAAW;gBACrE,QAAQ,6BAAiB,IAAI,EAAE,mCAAoB,KAAK,CAAC,CAAC,MAAM;gBAChE,EAAE,mCAAoB,KAAK,CAAC,CAAC,SAAS,CAAC;YACzC,WAAW,8CAA8B;gBACzC,EAAE,8CAA0B,4CAA6B,EAC3D;YACA,MAAM,aAAa,GAA2B,EAAE,CAAC;YACjD,gBAAgB,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,EAAE;gBACjC,YAAY;gBACZ,aAAa,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC;YACnC,CAAC,CAAC,CAAC;YACH,GAAG,CAAC,GAAG,CAAC,EAAE,mCAAoB,EAAE,aAAa,CAAC,CAAC;SAChD;KACF;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED;;;;;qCAKqC;AACrC,MAAM,UAAU,mBAAmB,CACjC,UAAoB,EAAE,YAAmC,EACzD,QAAkB,EAAE,WAA8B;IAElD,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE;QAC3B,0CAA0C;QAC1C,OAAO,EAAE,CAAC;KACX;IAED,iEAAiE;IACjE,MAAM,oBAAoB,GAAG,0BAA0B,CAAC;IACxD,MAAM,EAAC,SAAS,EAAE,SAAS,EAAC,GAAG,oBAAoB,CAAC,UAAU,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAC;IAErG,wDAAwD;IACxD,MAAM,gBAAgB,GAAG,IAAI,KAAK,CAAS,SAAS,CAAC,CAAC;IACtD,MAAM,gBAAgB,GAAG,IAAI,KAAK,CAAS,SAAS,CAAC,CAAC;IAEtD,IAAI,oBAAoB,CAAC,CAAC,eAAe;IAEzC,IAAI,KAAK,GAAG,IAAI,CAAC;IACjB,IAAI,SAAS,GAAG,IAAI,CAAC;IAErB,IAAI,WAAW,8CAA8B,EAAE;QAC7C,oBAAoB,GAAG,sBAAsB,CAAC;KAC/C;SAAM,EAAE,cAAc;QACrB,oBAAoB,GAAG,uBAAuB,CAAC;QAC/C,KAAK,GAAG,CAAC,QAAQ,6BAAiB,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;QACnG,SAAS,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;KAC3C;IACD,MAAM,CAAC,GAAkB;QACvB,CAAC,EAAE,CAAC;QACJ,SAAS,EAAE,CAAC;QACZ,SAAS,EAAE,CAAC;QACZ,qBAAqB,EAAE,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;QACnD,mBAAmB,EAAE,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;QACjD,kBAAkB,EAAE,CAAC;QACrB,gBAAgB,EAAE,CAAC;QACnB,UAAU,EAAE,CAAC;KACd,CAAC;IAEF,MAAM,EAAE,GAAkB;QACxB,KAAK,EAAE,KAAM;QACb,SAAS,EAAE,SAAU;QACrB,SAAS,EAAE,UAAU,CAAC,MAAM;QAC5B,SAAS,EAAE,SAAS;QACpB,SAAS,EAAE,SAAS;KACrB,CAAC;IAEF,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,SAAS,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE;QACvC,MAAM,OAAO,GAAG,YAAY,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC;QACnD,oBAAoB,CAAC,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;KAC1E;IAED,oBAAoB,CAAC,gBAAgB,EAAE,gBAAgB,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;IAEhE,MAAM,iBAAiB,GAAG,CAAC,CAAC,qBAAqB,GAAG,SAAS,GAAG,GAAG,GAAG,SAAS,GAAG,CAAC,CAAC,sBAAsB,CAAC;IAE3G,6EAA6E;IAC7E,4EAA4E;IAC5E,gCAAgC;IAEhC,IAAI,MAAM,GAAG,EAAE,CAAC;IAChB,MAAM,IAAI,CAAC,CAAC,qBAAqB,CAAC;IAClC,MAAM,IAAI,CAAC,CAAC,sBAAsB,CAAC;IACnC,MAAM,IAAI,CAAC,CAAC,oBAAoB,CAAC;IACjC,MAAM,IAAI,iBAAiB,CAAC;IAC5B,MAAM,IAAI,CAAC,CAAC,oBAAoB,CAAC;IACjC,MAAM,IAAI,gBAAgB,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpC,MAAM,IAAI,CAAC,CAAC,kBAAkB,CAAC;IAC/B,MAAM,IAAI,CAAC,CAAC,oBAAoB,CAAC;IACjC,MAAM,IAAI,gBAAgB,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpC,MAAM,IAAI,CAAC,CAAC,kBAAkB,CAAC;IAC/B,MAAM,IAAI,CAAC,CAAC,kBAAkB,CAAC;IAC/B,MAAM,IAAI,CAAC,CAAC,OAAO,CAAC;IAEpB,gCAAgC;IAChC,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;+CAI+C;AAC/C,SAAS,oBAAoB,CAC3B,gBAA0B,EAAE,gBAA0B,EACtD,CAAgB,EAAE,EAAiB;IAEnC,sBAAsB;IACtB,MAAM,OAAO,GAAG,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC;IAChC,gBAAgB,CAAC,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,mBAAmB,GAAG,OAAO,GAAG,GAAG;QACpE,CAAC,CAAC,MAAM,GAAG,GAAG,GAAG,aAAa,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG;QAChE,CAAC,CAAC,UAAU,GAAG,aAAa,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,YAAY,GAAG,IAAI,CAAC;IAEvF,oBAAoB;IACpB,MAAM,SAAS,GAAG,CAAC,CAAC,kBAAkB,CAAC;IACvC,MAAM,UAAU,GAAG,OAAO,CAAC;IAC3B,gBAAgB,CAAC,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,mBAAmB,GAAG,CAAC,CAAC,SAAS,GAAG,GAAG;QACxE,CAAC,GAAG,GAAG,GAAG,SAAS,GAAG,GAAG,GAAG,UAAU,GAAG,IAAI,CAAC;AAClD,CAAC;AAED,SAAS,sBAAsB,CAAC,OAAiB,EAAE,gBAA0B,EAC3E,gBAA0B,EAAE,CAAgB;IAE5C,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,qCAAqC;IACvE,4BAA4B,CAAC,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;AAC/E,CAAC;AAED,SAAS,4BAA4B,CACnC,OAAiB,EAAE,gBAA0B,EAAE,gBAA0B,EAAE,CAAgB;IAE3F,uEAAuE;IACvE,iDAAiD;IACjD,aAAa,CAAC,OAAO,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;IAE5C,gDAAgD;IAChD,aAAa,CAAC,OAAO,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;IAE5C,eAAe;IACf,sBAAsB,CAAC,OAAO,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;IAErD,uCAAuC;IACvC,IAAI,OAAO,CAAC,IAAI,CAAC,WAAW,KAAK,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,MAAM,GAAG,CAAC;QAC5E,qBAAqB,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC;IAEpC,wBAAwB;IACxB,6BAA6B,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC;AAC5C,CAAC;AAED,SAAS,uBAAuB,CAC9B,UAAoB,EAAE,gBAA0B,EAAE,gBAA0B,EAAE,CAAgB,EAAE,EAAiB;IAEjH,4EAA4E;IAC5E,YAAY;IACZ,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;QACb,4BAA4B,CAAC,EAAE,CAAC,KAAM,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;KAChF;SAAM;QACL,KAAK,MAAM,OAAO,IAAI,CAAC,EAAE,CAAC,SAAS,EAAE,EAAE,CAAC,KAAK,CAAC;YAC5C,4BAA4B,CAAC,OAAQ,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;KACjF;IAED,0BAA0B,CAAC,UAAU,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;AAChF,CAAC;AAED,SAAS,0BAA0B,CACjC,OAAiB,EAAE,gBAA0B,EAAE,gBAA0B,EAAE,CAAgB;IAE3F,mBAAmB,CAAC,OAAO,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;IAClD,aAAa,CAAC,OAAO,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;IAC5C,wBAAwB,CAAC,OAAO,EAAE,gBAAgB,EAAE,CAAC,CAAC,CAAC;IAEvD,WAAW;IACX,MAAM,OAAO,GAAG,CAAC,CAAC,SAAS,CAAC;IAC5B,MAAM,SAAS,GAAG,CAAC,CAAC,gBAAgB,CAAC;IACrC,MAAM,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC;IAC/D,gBAAgB,CAAC,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,mBAAmB,GAAG,OAAO,GAAG,GAAG;QACjE,CAAC,GAAG,GAAG,GAAG,SAAS,GAAG,GAAG,GAAG,UAAU,GAAG,IAAI,CAAC;IAElD,wBAAwB;IACxB,CAAC,CAAC,SAAS,IAAI,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC;IAClD,CAAC,CAAC,SAAS,IAAI,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC;AAChD,CAAC;AAED,SAAS,6BAA6B,CAAC,OAAiB,EAAE,CAAgB;IACxE,CAAC,CAAC,kBAAkB,GAAG,CAAC,CAAC,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC;IACnE,CAAC,CAAC,SAAS,IAAI,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC;IAElD,CAAC,CAAC,SAAS,IAAI,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC;IAC9C,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,aAAc,CAAC,CAAC,CAAC,CAAC,CAAC,uBAAuB;IACrF,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,aAAc,CAAC,CAAC,CAAC,CAAC;AAC9E,CAAC;AAED,SAAS,qBAAqB,CAAC,OAAiB,EAAE,CAAgB;IAChE,CAAC,CAAC,gBAAgB,GAAG,CAAC,CAAC,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC;IACjE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACxB,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC,WAAY,CAAC,CAAC,CAAC,CAAC;AACzF,CAAC;AAED,SAAS,aAAa,CAAC,OAAiB,EAAE,gBAA0B,EAAE,CAAgB;IACpF,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACvD,MAAM,OAAO,GAAG,CAAC,CAAC,SAAS,GAAG,CAAC,GAAG,CAAC,CAAC;QACpC,gBAAgB,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,mBAAmB,GAAG,OAAO,GAAG,GAAG;YACrE,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,GAAG;YAChC,aAAa,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG;YACpE,aAAa,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,UAAU,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC7E,GAAG,GAAG,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;KACnC;AACH,CAAC;AAED,2BAA2B;AAC3B,SAAS,mBAAmB,CAAC,OAAiB,EAAE,gBAA0B,EAAE,CAAgB;IAC1F,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACvD,MAAM,OAAO,GAAG,CAAC,CAAC,SAAS,GAAG,CAAC,GAAG,CAAC,CAAC;QACpC,gBAAgB,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,mBAAmB,GAAG,OAAO,GAAG,GAAG;YACrE,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,GAAG;YAChC,aAAa,CAAC,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG;YAClE,aAAa,CAAC,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,UAAU,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC3E,GAAG,GAAG,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;KACnC;AACH,CAAC;AAED,SAAS,aAAa,CAAC,OAAiB,EAAE,gBAA0B,EAAE,CAAgB;IACpF,gDAAgD;IAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;QACvD,MAAM,OAAO,GAAG,CAAC,CAAC,SAAS,GAAG,CAAC,GAAG,CAAC,CAAC;QACpC,MAAM,SAAS,GAAG,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC;QAC9D,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC;QAC/D,IAAI,OAAO,GAAG,EAAE,CAAC;QACjB,IAAI,OAAO,CAAC,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAC1C,kCAAkC;YAClC,IAAI,WAAW,GAAG,OAAO,CAAC,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;YACzD,IAAI,CAAC,CAAC,UAAU,GAAG,CAAC;gBAClB,WAAW,GAAG,CAAC,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC5C,OAAO,GAAG,OAAO,GAAG,WAAW,CAAC;SACjC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;YAC1C,GAAG,GAAG,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QACzC,gBAAgB,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,mBAAmB,GAAG,OAAO,GAAG,GAAG;YACrE,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,GAAG;YAChC,SAAS,GAAG,GAAG,GAAG,UAAU,GAAG,OAAO,GAAG,MAAM,GAAG,IAAI,CAAC;KAC5D;AACH,CAAC;AAED,SAAS,sBAAsB,CAAC,OAAiB,EAAE,gBAA0B,EAAE,CAAgB;IAC7F,IAAI,CAAC,CAAC,kBAAkB,KAAK,CAAC,EAAE;QAC9B,MAAM,OAAO,GAAG,CAAC,CAAC,SAAS,CAAC;QAC5B,MAAM,SAAS,GAAG,CAAC,CAAC,kBAAkB,CAAC;QACvC,MAAM,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC;QAC/D,gBAAgB,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,mBAAmB,GAAG,OAAO,GAAG,GAAG;YACrE,CAAC,GAAG,GAAG,GAAG,SAAS,GAAG,GAAG,GAAG,UAAU,GAAG,IAAI,CAAC;KACnD;AACH,CAAC;AAED,eAAe;AACf,SAAS,wBAAwB,CAAC,aAAuB,EAAE,gBAA0B,EAAE,CAAgB;IACrG,MAAM,OAAO,GAAG,CAAC,CAAC,SAAS,CAAC;IAC5B,MAAM,SAAS,GAAG,CAAC,CAAC,gBAAgB,CAAC;IACrC,MAAM,UAAU,GAAG,aAAa,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,SAAS,CAAC;IACrE,gBAAgB,CAAC,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,mBAAmB,GAAG,OAAO,GAAG,GAAG;QACjE,CAAC,GAAG,GAAG,GAAG,SAAS,GAAG,GAAG,GAAG,UAAU,GAAG,IAAI,CAAC;AACpD,CAAC;AAED;;;;;;+EAM+E;AAC/E,SAAS,0BAA0B,CACjC,UAAoB,EAAE,YAAmC,EACzD,QAAkB,EAAE,WAA8B;IAElD,IAAI,SAAS,GAAG,CAAC,CAAC;IAClB,IAAI,SAAS,GAAG,CAAC,CAAC;IAElB,sDAAsD;IACtD,KAAK,MAAM,aAAa,IAAI,UAAU,EAAE;QACtC,IAAI,aAAa,KAAK,EAAE;YAAE,SAAS,CAAC,oCAAoC;QACxE,MAAM,OAAO,GAAG,YAAY,CAAC,GAAG,CAAC,aAAa,CAAE,CAAC;QACjD,SAAS,IAAI,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC;QACpC,SAAS,IAAI,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC;KAC7C;IAED,iDAAiD;IACjD,IAAI,WAAW,8CAA8B,EAAE;QAC7C,0DAA0D;QAC1D,SAAS,IAAI,CAAC,CAAC;QACf,2EAA2E;QAC3E,SAAS,IAAI,UAAU,CAAC,MAAM,CAAC;KAChC;SAAM,EAAE,cAAc;QACrB,MAAM,KAAK,GAAG,CAAC,QAAQ,6BAAiB,CAAC,CAAC,CAAC;YACvC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,CAAE,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAE,CAAC;QACnE,MAAM,SAAS,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAE,CAAC;QAEjD,oDAAoD;QACpD,SAAS,IAAI,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC;QAEhE,uCAAuC;QACvC,SAAS,IAAI,UAAU,CAAC,MAAM,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC;QAEtD,6CAA6C;QAC7C,SAAS,IAAI,CAAC,CAAC;QAEf,oCAAoC;QACpC,SAAS,IAAI,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC;QAExE,gCAAgC;QAChC,SAAS,IAAI,UAAU,CAAC,MAAM,GAAG,KAAK,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC;QAE9D,+EAA+E;QAC/E,SAAS,IAAI,CAAC,CAAC;QAEf,8EAA8E;QAC9E,SAAS,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;KACpC;IAED,OAAO,EAAC,SAAS,EAAE,SAAS,EAAC,CAAC;AAChC,CAAC;AAED;;;EAGE;AACF,MAAM,UAAU,aAAa,CAAC,CAAS;IACrC,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,gBAAgB,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,gBAAgB,CAAC;AACjE,CAAC"}

package/src/monomer-works/to-atomic-level.d.ts

@@ -1,14 +1,58 @@
 import * as DG from 'datagrok-api/dg';
+import { HELM_POLYMER_TYPE } from '../utils/const';
+import { ALPHABET } from '../utils/macromolecule/consts';
 import { IMonomerLib, Monomer } from '../types';
-/** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library  */
+import { Bonds, MolGraph } from './types';
+/** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
+ * @param {DG.DataFrame} df - DataFrame containing the column to be converted
+ * @param {DG.Column} seqCol - Column containing the macromolecule sequence
+ * @param {IMonomerLib} monomerLib - Monomer library
+*/
 export declare function _toAtomicLevel(df: DG.DataFrame, seqCol: DG.Column<string>, monomerLib: IMonomerLib): Promise<{
     col: DG.Column | null;
     warnings: string[];
 }>;
-/** Parse element symbols for R-groups from the HELM monomer library R-groups
- * field  */
+/** Get jagged array of monomer symbols for the dataframe
+ * @param {DG.Column} macroMolCol - Column with macro-molecules
+ * @return {string[]} - Jagged array of monomer symbols for the dataframe */
+export declare function getMonomerSequencesArray(macroMolCol: DG.Column<string>): string[][];
+/** Get a mapping of monomer symbols to MolGraph objects. Notice, the
+ * transformation from molfile V2000 to V3000 takes place,
+ * with the help of async function call from Chem (RdKit module)
+ * @param {string[]} monomerSequencesArray - Jagged array of monomer symbols for the dataframe
+ * @param {IMonomerLib} monomerLib - Monomer library
+ * @param {HELM_POLYMER_TYPE} polymerType - Polymer type
+ * @param {ALPHABET} alphabet - Alphabet
+ * @return {Map<string, MolGraph>} - Mapping of monomer symbols to MolGraph objects*/
+export declare function getMonomersDictFromLib(monomerSequencesArray: string[][], monomerLib: IMonomerLib, polymerType: HELM_POLYMER_TYPE, alphabet: ALPHABET): Promise<Map<string, MolGraph>>;
+/** Parse element symbols for R-groups from the HELM monomer library R-group field
+ * @param {any[]} rGroupObjList - R-group object list
+ * @return {Map<number, number>} - Cap group index map*/
 export declare function parseCapGroups(rGroupObjList: any[]): string[];
+/** V2000 to V3000 converter
+ * @param {string} molfileV2K - V2000 molfile
+ * @param {any} moduleRdkit - RDKit module
+ * @return {string} - V3000 molfile*/
+export declare function convertMolfileToV3K(molfileV2K: string, moduleRdkit: any): string;
+/** Parse V3000 bond block and construct the Bonds object
+ * @param {string} molfileV3K - V3000 molfile
+ * @param {number} bondCount - Number of bonds
+ * @return {Bonds} - Bonds object*/
+export declare function parseBondBlock(molfileV3K: string, bondCount: number): Bonds;
+/** Constructs mapping of r-group nodes to default capGroups, all numeration starting from 1.
+  * According to https://pubs.acs.org/doi/10.1021/ci3001925, R1 and R2 are the chain extending attachment points,
+  * while R3 is the branching attachment point.
+  * @param {string} molfileV2K - V2000 molfile
+  * @return {Map<number, number>} - Map of r-group nodes to default capGroups*/
+export declare function parseCapGroupIdxMap(molfileV2K: string): Map<number, number>;
+export declare function parseAtomAndBondCounts(molfileV3K: string): {
+    atomCount: number;
+    bondCount: number;
+};
+export declare function convertMolGraphToMolfileV3K(molGraph: MolGraph): string;
 export declare function getSymbolToCappedMolfileMap(monomersLibList: any[]): Promise<Map<string, string> | undefined>;
-/** Get the V3K molfile corresponding to the capped Monomer (default cap groups)  */
+/** Get the V3K molfile corresponding to the capped Monomer (default cap groups)
+ * @param {Monomer} monomer
+ * @return {string} V3K molfile*/
 export declare function capPeptideMonomer(monomer: Monomer): string;
 //# sourceMappingURL=to-atomic-level.d.ts.map

package/src/monomer-works/to-atomic-level.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"to-atomic-level.d.ts","sourceRoot":"","sources":["to-atomic-level.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAStC,OAAO,EAAC,WAAW,EAAE,OAAO,EAAC,MAAM,UAAU,CAAC;AAuH9C,kHAAkH;AAClH,wBAAsB,cAAc,CAClC,EAAE,EAAE,EAAE,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,WAAW,GACnE,OAAO,CAAC;IAAE,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC;IAAC,QAAQ,EAAE,MAAM,EAAG,CAAA;CAAE,CAAC,CAkEzD;AAwND;YACY;AACZ,wBAAgB,cAAc,CAAC,aAAa,EAAE,GAAG,EAAE,GAAG,MAAM,EAAE,CAe7D;AA09BD,wBAAsB,2BAA2B,CAAC,eAAe,EAAE,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,CAAC,CA6BlH;AAED,oFAAoF;AACpF,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,OAAO,GAAG,MAAM,CAmB1D"}
+{"version":3,"file":"to-atomic-level.d.ts","sourceRoot":"","sources":["to-atomic-level.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAc,iBAAiB,EAAqB,MAAM,gBAAgB,CAAC;AAClF,OAAO,EAAC,QAAQ,EAAiB,MAAM,+BAA+B,CAAC;AAEvE,OAAO,EAAC,WAAW,EAAE,OAAO,EAAC,MAAM,UAAU,CAAC;AAK9C,OAAO,EAAQ,KAAK,EAAe,QAAQ,EAAwC,MAAM,SAAS,CAAC;AAOnG;;;;EAIE;AACF,wBAAsB,cAAc,CAClC,EAAE,EAAE,EAAE,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,WAAW,GACnE,OAAO,CAAC;IAAE,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC;IAAC,QAAQ,EAAE,MAAM,EAAG,CAAA;CAAE,CAAC,CAuDzD;AAED;;4EAE4E;AAC5E,wBAAgB,wBAAwB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,MAAM,EAAE,EAAE,CAenF;AAGD;;;;;;;qFAOqF;AACrF,wBAAsB,sBAAsB,CAC1C,qBAAqB,EAAE,MAAM,EAAE,EAAE,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,QAAQ,EAAE,QAAQ,GAC7G,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAqChC;AAoID;;wDAEwD;AACxD,wBAAgB,cAAc,CAAC,aAAa,EAAE,GAAG,EAAE,GAAG,MAAM,EAAE,CAe7D;AAyGD;;;qCAGqC;AACrC,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,GAAG,MAAM,CAMhF;AAED;;;mCAGmC;AACnC,wBAAgB,cAAc,CAAC,UAAU,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,GAAG,KAAK,CA8C3E;AAED;;;;+EAI+E;AAC/E,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAyC3E;AAED,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,MAAM,GAAG;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAA;CAAE,CAcnG;AA2cD,wBAAgB,2BAA2B,CAAC,QAAQ,EAAE,QAAQ,GAAG,MAAM,CAmEtE;AAED,wBAAsB,2BAA2B,CAAC,eAAe,EAAE,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,CAAC,CA6BlH;AAED;;iCAEiC;AACjC,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,OAAO,GAAG,MAAM,CAmB1D"}