@datagrok-libraries/bio 5.43.0 → 5.44.0

package/src/monomer-works/seq-to-molfile.js

@@ -1,31 +1,75 @@
-export async function seqToMolFileWorker(monomerSequencesArray, monomersDict, alphabet, polymerType, srcColLength) {
+import * as DG from 'datagrok-api/dg';
+import wu from 'wu';
+import { getMolColName, hexToPercentRgb } from './utils';
+import { SeqHandler } from '../utils/seq-handler';
+import { HelmTypes } from '../helm/consts';
+export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, rdKitModule) {
+    const srcColLength = seqCol.length;
+    const df = seqCol.dataFrame;
     const threadCount = Math.max(navigator.hardwareConcurrency - 2, 1);
     const workers = new Array(threadCount).fill(null)
         .map(() => new Worker(new URL('./seq-to-molfile-worker', import.meta.url)));
     const chunkSize = srcColLength / threadCount;
-    let res = [];
-    let warnings = [];
     const promises = new Array(threadCount);
+    const seqSH = SeqHandler.forColumn(seqCol);
+    const biotype = polymerType == "RNA" /* PolymerTypes.RNA */ ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
+    const seqList = wu.count(0).take(seqCol.length).map((rowIdx) => {
+        const seqSS = seqSH.getSplitted(rowIdx);
+        return wu.count(0).take(seqSS.length)
+            .map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
+            .toArray();
+    }).toArray();
     for (let i = 0; i < threadCount; i++) {
+        const worker = workers[i];
         const start = Math.floor(i * chunkSize);
         const end = (i === threadCount - 1) ? srcColLength : Math.floor((i + 1) * chunkSize);
-        workers[i].postMessage({ monomerSequencesArray, monomersDict, alphabet, polymerType, start, end });
-        promises[i] = new Promise((resolveWorker) => {
-            workers[i].onmessage = ({ data: { molfileList, molfileWarningList } }) => {
-                resolveWorker({ molfileList, molfileWarningList });
+        promises[i] = new Promise((resolve) => {
+            worker.onmessage = (res) => {
+                resolve(res.data);
             };
         });
+        worker.postMessage({ seqList, monomersDict, alphabet, polymerType, start, end });
     }
-    const resArray = await Promise.all(promises);
-    resArray.forEach((resItem) => {
-        res = res.concat(...resItem.molfileList);
-        warnings = warnings.concat(...resItem.molfileWarningList);
+    let molList = [];
+    let warnings = [];
+    await Promise.all(promises).then((resArray) => {
+        for (const resItem of resArray) {
+            molList.push(...resItem.molfiles);
+            warnings.push(...resItem.warnings);
+        }
     });
+    const molHlList = molList.map((item) => getMolHighlight(item.monomers.values(), monomerLib));
     setTimeout(() => {
         workers.forEach((worker) => {
             worker.terminate();
         });
     }, 0);
-    return { molfileList: res, molfileWarningList: warnings };
+    const molColName = getMolColName(df, seqCol.name);
+    const molCol = DG.Column.fromType(DG.COLUMN_TYPE.STRING, molColName, seqCol.length)
+        .init((rowIdx) => molList[rowIdx].molfile);
+    molCol.semType = DG.SEMTYPE.MOLECULE;
+    molCol.meta.units = DG.UNITS.Molecule.MOLBLOCK;
+    molCol.setTag(".sequence-src-col" /* ChemTags.SEQUENCE_SRC_COL */, seqCol.name);
+    return { molCol: molCol, warnings: warnings };
+}
+export function getMolHighlight(monomerMaps, monomerLib) {
+    const hlAtoms = {};
+    const hlBonds = {};
+    for (const monomerMapValue of monomerMaps) {
+        const wem = monomerLib.getWebEditorMonomer(monomerMapValue.biotype, monomerMapValue.symbol);
+        const mColorStr = wem.backgroundcolor;
+        const mColorA = hexToPercentRgb(mColorStr ?? DG.Color.toRgb(DG.Color.mouseOverRows)) ?? [1.0, 0.0, 0.0, 0.7];
+        for (const mAtom of monomerMapValue.atoms)
+            hlAtoms[mAtom] = mColorA;
+        for (const mBond of monomerMapValue.bonds)
+            hlBonds[mBond] = mColorA;
+    }
+    let resSubstruct = {
+        atoms: Object.keys(hlAtoms).map((k) => parseInt(k)),
+        bonds: Object.keys(hlBonds).map((k) => parseInt(k)),
+        highlightAtomColors: hlAtoms,
+        highlightBondColors: hlBonds,
+    };
+    return resSubstruct;
 }
 //# sourceMappingURL=seq-to-molfile.js.map

package/src/monomer-works/seq-to-molfile.js.map

@@ -1 +1 @@
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package/src/monomer-works/to-atomic-level-utils.d.ts

@@ -1,23 +1,23 @@
-import { MolGraph } from './types';
-import { HELM_POLYMER_TYPE } from '../utils/const';
+import { MolfileWithMap, MonomerMolGraphMap } from './types';
 import { ALPHABET } from '../utils/macromolecule/consts';
 import { IMonomerLib } from '../types';
+import { ISeqMonomer, PolymerType } from '../helm/types';
 /** 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 declare function getFormattedMonomerLib(monomerLib: IMonomerLib, polymerType: HELM_POLYMER_TYPE, alphabet: ALPHABET): Map<string, any>;
+export declare function getFormattedMonomerLib(monomerLib: IMonomerLib, polymerType: PolymerType, alphabet: ALPHABET): Map<string, any>;
 /** Translate a sequence of monomer symbols into Molfile V3000
- * @param {string[]} monomerSeq - Sequence of monomer symbols
+ * @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 {HELM_POLYMER_TYPE} polymerType - Polymer type
+ * @param {PolymerType} polymerType - Polymer type
  * @return {string} - Molfile V3000*/
-export declare function monomerSeqToMolfile(monomerSeq: string[], monomersDict: Map<string, MolGraph>, alphabet: ALPHABET, polymerType: HELM_POLYMER_TYPE): string;
+export declare function monomerSeqToMolfile(monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType): MolfileWithMap;
 /** 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 declare function keepPrecision(x: number): number;
 //# sourceMappingURL=to-atomic-level-utils.d.ts.map

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

@@ -1 +1 @@
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package/src/monomer-works/to-atomic-level-utils.js

@@ -1,6 +1,8 @@
 import { monomerWorksConsts as C } from './consts';
+import { getMolGraph, MolfileWithMap, MonomerMap } from './types';
 import { HELM_CORE_FIELDS, } from '../utils/const';
-import { ALPHABET } from '../utils/macromolecule/consts';
+import { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';
+import { helmTypeToPolymerType } from './monomer-works';
 /** 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
@@ -12,9 +14,9 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
         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 === ALPHABET.DNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE ||
-                alphabet === ALPHABET.RNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE ||
-                it["symbol" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE) ||
+                alphabet === ALPHABET.DNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE.symbol ||
+                alphabet === ALPHABET.RNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE.symbol ||
+                it["symbol" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE.symbol) ||
             polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */ &&
                 it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== "Branch" /* HELM_MONOMER_TYPE.BRANCH */) {
             const monomerObject = {};
@@ -28,15 +30,15 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
     return map;
 }
 /** Translate a sequence of monomer symbols into Molfile V3000
- * @param {string[]} monomerSeq - Sequence of monomer symbols
+ * @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 {HELM_POLYMER_TYPE} polymerType - Polymer type
+ * @param {PolymerType} 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 '';
+        return MolfileWithMap.createEmpty();
     }
     // define atom and bond counts, taking into account the bond type
     const getAtomAndBondCounts = getResultingAtomBondCounts;
@@ -44,7 +46,7 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     // create arrays to store lines of the resulting molfile
     const molfileAtomBlock = new Array(atomCount);
     const molfileBondBlock = new Array(bondCount);
-    let addMonomerToMolblock; // todo: types?
+    let addMonomerToMolblock;
     let sugar = null;
     let phosphate = null;
     if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
@@ -52,8 +54,8 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     }
     else { // nucleotides
         addMonomerToMolblock = addNucleotideToMolblock;
-        sugar = (alphabet === ALPHABET.DNA) ? monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);
-        phosphate = monomersDict.get(C.PHOSPHATE);
+        sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);
+        phosphate = getMolGraph(monomersDict, C.PHOSPHATE);
     }
     const v = {
         i: 0,
@@ -72,14 +74,33 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
         atomCount: atomCount,
         bondCount: bondCount,
     };
+    const monomers = new MonomerMap();
     const steabsCollection = [];
     let nAtoms = 0;
     for (v.i = 0; v.i < LC.seqLength; ++v.i) {
-        const monomer = monomersDict.get(monomerSeq[v.i]);
+        const seqMonomer = monomerSeq[v.i];
+        if (seqMonomer.symbol === GAP_SYMBOL)
+            continue;
+        const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });
+        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
+        });
     }
     capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC);
     const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;
@@ -102,7 +123,7 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     result += C.V3K_END_CTAB_BLOCK;
     result += C.V3K_END;
     // return molfileParts.join('');
-    return result;
+    return { molfile: result, monomers: monomers };
 }
 function getCollectionBlock(collection) {
     //one row in STEABS block can be no longer than 80 symbols
@@ -257,34 +278,38 @@ function fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {
         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*/
+ * 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;
     // sum up all the atoms/nodes provided by the sequence
-    for (const monomerSymbol of monomerSeq) {
-        if (monomerSymbol === '')
+    for (const seqMonomer of monomerSeq) {
+        if (seqMonomer.symbol === GAP_SYMBOL)
             continue; // Skip for gap/empty monomer in MSA
-        const monomer = monomersDict.get(monomerSymbol);
+        if (seqMonomer.symbol == '*')
+            throw new Error(`Gap canonical symbol is '', not '*`);
+        const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });
         atomCount += monomer.atoms.x.length;
         bondCount += monomer.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 += monomerSeq.length;
+        bondCount += monomerCount;
     }
     else { // nucleotides
         const sugar = (alphabet === ALPHABET.DNA) ?
-            monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);
-        const phosphate = monomersDict.get(C.PHOSPHATE);
+            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);
+        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);
         // add phosphate per each pair of nucleobase symbols
         atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;
         // add sugar per each nucleobase symbol
@@ -305,7 +330,7 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
 /** 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;
 }

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

@@ -1,30 +1,29 @@
 import * as DG from 'datagrok-api/dg';
-import { HELM_POLYMER_TYPE } from '../utils/const';
+import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import { ALPHABET } from '../utils/macromolecule/consts';
 import { IMonomerLib, Monomer } from '../types';
-import { Bonds, MolGraph } from './types';
+import { Bonds, MolGraph, MonomerMolGraphMap } from './types';
+import { ToAtomicLevelRes } from '../utils/seq-helper';
+import { ISeqMonomer, PolymerType } from '../helm/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[];
-}>;
+export declare function _toAtomicLevel(df: DG.DataFrame, seqCol: DG.Column<string>, monomerLib: IMonomerLib, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
 /** 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[][];
+export declare function getMonomerSequencesArray(macroMolCol: DG.Column<string>): ISeqMonomer[][];
 /** 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 {PolymerType} 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>>;
+export declare function getMonomersDictFromLib(monomerSequencesArray: ISeqMonomer[][], polymerType: PolymerType, alphabet: ALPHABET, monomerLib: IMonomerLib, rdKitModule: RDModule): MonomerMolGraphMap;
 /** 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*/

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

@@ -1 +1 @@
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