@datagrok/sequence-translator 1.0.13 → 1.0.15

package/src/main/main-view.ts

@@ -1,21 +1,30 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+
+import * as rxjs from 'rxjs';
 import {convertSequence, undefinedInputSequence, isValidSequence} from '../structures-works/sequence-codes-tools';
-import {map, MODIFICATIONS} from '../structures-works/map';
+import {map} from '../structures-works/map';
+import {MODIFICATIONS} from '../structures-works/const';
 import {sequenceToSmiles, sequenceToMolV3000} from '../structures-works/from-monomers';
 import $ from 'cash-dom';
 import {download} from '../helpers';
+import {extractAtomDataV3000} from '../structures-works/mol-transformations';
+import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 
-const defaultInput = 'fAmCmGmAmCpsmU';
-const sequenceWasCopied = 'Copied';
+const defaultInput = 'fAmCmGmAmCpsmU'; // todo: capitalize constants
+const sequenceWasCopied = 'Copied'; // todo: wrap hardcoded literals into constants
 const tooltipSequence = 'Copy sequence';
 
-export function mainView() {
-  function updateTableAndMolecule(sequence: string, inputFormat: string): void {
+export async function mainView(): Promise<HTMLDivElement> {
+  const onInput: rxjs.Subject<string> = new rxjs.Subject<string>();
+
+  async function updateTableAndMolecule(sequence: string, inputFormat: string): Promise<void> {
     moleculeSvgDiv.innerHTML = '';
     outputTableDiv.innerHTML = '';
     const pi = DG.TaskBarProgressIndicator.create('Rendering table and molecule...');
+    let errorsExist = false;
+
     try {
       sequence = sequence.replace(/\s/g, '');
       const output = isValidSequence(sequence, null);
@@ -52,24 +61,71 @@ export function mainView() {
       );
 
       if (outputSequenceObj.type != undefinedInputSequence && outputSequenceObj.Error != undefinedInputSequence) {
-        const canvas = ui.canvas(300, 170);
-        canvas.addEventListener('click', () => {
-          const canv = ui.canvas($(window).width(), $(window).height());
-          const mol = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, true,
-            output.synthesizer![0]);
-          // @ts-ignore
-          OCL.StructureView.drawMolecule(canv, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
-          ui.dialog('Molecule: ' + inputSequenceField.value)
-            .add(canv)
-            .showModal(true);
+        const formCanvasWidth = 500;
+        const formCanvasHeight = 170;
+        const formCanvas = ui.canvas(
+          formCanvasWidth * window.devicePixelRatio, formCanvasHeight * window.devicePixelRatio);
+        formCanvas.style.width = `${formCanvasWidth}px`;
+        formCanvas.style.height = `${formCanvasHeight}px`;
+
+        formCanvas.addEventListener('click', async () => {
+          try {
+            const mol = sequenceToMolV3000(
+              inputSequenceField.value.replace(/\s/g, ''), false, true,
+              output.synthesizer![0],
+            );
+            console.log(mol);
+
+            const addDiv = ui.div([], {style: {overflowX: 'scroll'}});
+
+            // addDiv size required, but now available before dialog show()
+            const coordinates = extractAtomDataV3000(mol);
+            const cw: number = $(window).width() * 0.80; // addDiv.clientWidth
+            const ch: number = $(window).height() * 0.70; // addDiv.clientHeight
+            const molWidth: number = Math.max(...coordinates.x) - Math.min(...coordinates.x);
+            const molHeight: number = Math.max(...coordinates.y) - Math.min(...coordinates.y);
+
+            const wR: number = cw / molWidth;
+            const hR: number = ch / molHeight;
+            const r: number = hR; // Math.max(wR, hR);
+            const dlgCanvasWidth = r * molWidth;
+            const dlgCanvasHeight = r * molHeight;
+
+            const dlgCanvas = ui.canvas(dlgCanvasWidth * window.devicePixelRatio, dlgCanvasHeight * window.devicePixelRatio);
+            dlgCanvas.style.width = `${dlgCanvasWidth}px`;
+            dlgCanvas.style.height = `${dlgCanvasHeight}px`;
+
+            // // @ts-ignore
+            // OCL.StructureView.drawMolecule(dlgCanvas, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
+            // await grok.chem.canvasMol(0, 0, dlgCanvas.width, dlgCanvas.height, dlgCanvas, mol, null,
+            //   {setNewCoords: false, normalizeDepiction: false, straightenDepiction: false});
+            await grok.functions.call('Chem:canvasMol', {
+              x: 0, y: 0, w: dlgCanvas.width, h: dlgCanvas.height, canvas: dlgCanvas,
+              molString: mol, scaffoldMolString: '',
+              options: {setNewCoords: false, normalizeDepiction: false, straightenDepiction: false}
+            });
+
+            addDiv.appendChild(dlgCanvas);
+            ui.dialog('Molecule: ' + inputSequenceField.value)
+              .add(addDiv)
+              .showModal(true);
+          } catch (err) {
+            const errStr = errorToConsole(err);
+            console.error(errStr);
+          }
         });
-        $(canvas).on('mouseover', () => $(canvas).css('cursor', 'zoom-in'));
-        $(canvas).on('mouseout', () => $(canvas).css('cursor', 'default'));
+        $(formCanvas).on('mouseover', () => $(formCanvas).css('cursor', 'zoom-in'));
+        $(formCanvas).on('mouseout', () => $(formCanvas).css('cursor', 'default'));
         const mol = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, true,
-        output.synthesizer![0]);
-        // @ts-ignore
-        OCL.StructureView.drawMolecule(canvas, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
-        moleculeSvgDiv.append(canvas);
+          output.synthesizer![0]);
+        // // @ts-ignore
+        // OCL.StructureView.drawMolecule(formCanvas, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
+        await grok.functions.call('Chem:canvasMol', {
+          x: 0, y: 0, w: formCanvas.width, h: formCanvas.height, canvas: formCanvas,
+          molString: mol, scaffoldMolString: '',
+          options: {setNewCoords: false, normalizeDepiction: false, straightenDepiction: false}
+        });
+        moleculeSvgDiv.append(formCanvas);
       } else
         moleculeSvgDiv.innerHTML = '';
     } finally {
@@ -84,6 +140,11 @@ export function mainView() {
   const moleculeSvgDiv = ui.block([]);
   const outputTableDiv = ui.div([]);
   const inputSequenceField = ui.textInput('', defaultInput, (sequence: string) => {
+    // Send event to DG.debounce()
+    onInput.next(sequence);
+  });
+
+  DG.debounce<string>(onInput, 300).subscribe((sequence) => {
     updateTableAndMolecule(sequence, inputFormatChoiceInput.value!);
   });
 
@@ -121,9 +182,9 @@ export function mainView() {
   );
 
   const overhangModificationsGrid = DG.Viewer.grid(
-      DG.DataFrame.fromColumns([
-        DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
-      ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
+    DG.DataFrame.fromColumns([
+      DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
+    ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
   );
   updateTableAndMolecule(defaultInput, inputFormatChoiceInput.value!);
 
@@ -151,9 +212,10 @@ export function mainView() {
     $(codesTablesDiv).hide(),
   );
 
-  const downloadMolFileIcon = ui.iconFA('download', () => {
+  const downloadMolFileIcon = ui.iconFA('download', async () => {
     const clearSequence = inputSequenceField.value.replace(/\s/g, '');
-    const result = sequenceToMolV3000(clearSequence, false, false, inputFormatChoiceInput.value!);
+    const result = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, false,
+      inputFormatChoiceInput.value!);
     download(clearSequence + '.mol', encodeURIComponent(result));
   }, 'Save .mol file');
 
@@ -183,9 +245,8 @@ export function mainView() {
           appMainDescription,
           ui.div([
             ui.h1('Input sequence'),
-            ui.div([
-              inputSequenceField.root,
-            ], 'input-base'),
+            ui.div([], 'input-base'),
+            inputSequenceField.root,
           ], 'inputSequence'),
           ui.div([inputFormatChoiceInput], {style: {padding: '5px 0'}}),
           ui.block([

package/src/package.ts

@@ -5,13 +5,31 @@ import {autostartOligoSdFileSubscription} from './autostart/registration';
 import {defineAxolabsPattern} from './axolabs/define-pattern';
 import {saveSenseAntiSense} from './structures-works/save-sense-antisense';
 import {mainView} from './main/main-view';
+import {IMonomerLib, MonomerWorks, readLibrary} from '@datagrok-libraries/bio';
 
 export const _package = new DG.Package();
 
+const LIB_PATH = 'System:AppData/SequenceTranslator';
+
+let monomerLib: IMonomerLib | null = null;
+export let monomerWorks: MonomerWorks | null = null;
+
+export function getMonomerWorks() {
+  return monomerWorks;
+}
+
+export function getMonomerLib() {
+  return monomerLib;
+}
 
 //name: Sequence Translator
 //tags: app
-export function sequenceTranslator(): void {
+export async function sequenceTranslator(): Promise<void> {
+  monomerLib = await readLibrary(LIB_PATH, 'helmLib.json');
+
+  if (monomerWorks == null)
+    monomerWorks = new MonomerWorks(monomerLib);
+
   const windows = grok.shell.windows;
   windows.showProperties = false;
   windows.showToolbox = false;
@@ -20,7 +38,7 @@ export function sequenceTranslator(): void {
   const v = grok.shell.newView('Sequence Translator', []);
   v.box = true;
   v.append(ui.tabControl({
-    'MAIN': mainView(),
+    'MAIN': await mainView(),
     'AXOLABS': defineAxolabsPattern(),
     'SDF': saveSenseAntiSense(),
   }));

package/src/structures-works/const.ts

@@ -0,0 +1,5 @@
+import * as map from './map';
+
+export const MODIFICATIONS = map.MODIFICATIONS;
+
+export const standardPhosphateLinkSmiles = 'OP(=O)(O)O';

package/src/structures-works/converters.ts

@@ -1,33 +1,35 @@
-import {lcmsToGcrs} from './map';
+import {lcmsToGcrs, MODIFICATIONS} from './map';
 import * as DG from 'datagrok-api/dg';
-import {delimiter} from './map';
+import {DELIMITER} from './map';
+import {sortByStringLengthInDescendingOrder} from '../helpers';
 //name: gcrsToLcms
 //input: string nucleotides {semType: GCRS}
 //output: string result {semType: LCMS}
 export function gcrsToLcms(sequence: string): string {
-  const df = DG.DataFrame.fromCsv(lcmsToGcrs);
-  const arr1 = df.getCol('GCRS').toList();
-  const arr2 = df.getCol('LCMS').toList();
-  const obj: {[i: string]: string} = {};
-  arr1.forEach((element, index) => obj[element] = arr2[index]);
-  obj[delimiter] = delimiter;
-  // for (let i = 0; i < arr1.length; i++) {
-  //   arr1[i] = arr1[i].replace('(', '\\(');
-  //   arr1[i] = arr1[i].replace(')', '\\)');
-  // }
-  // const regExp = new RegExp('(' + arr1.join('|') + ')', 'g');
-  // let r1 = sequence.replace(regExp, function(code) {return obj[code];});
-  const codes = arr1.concat(delimiter).sort(function(a, b) {return b.length - a.length;});
-  let i = 0;
-  let r1 = '';
-  while (i < sequence.length) {
-    const matchedCode = codes.find((c) => c == sequence.slice(i, i + c.length));
-    r1 += obj[sequence.slice(i, i + matchedCode.length)];
-    i += matchedCode.length;
+  try {
+    const df = DG.DataFrame.fromCsv(lcmsToGcrs);
+    const arr1: string[] = df.getCol('GCRS').toList();
+    const arr2: string[] = df.getCol('LCMS').toList();
+    const obj: { [i: string]: string } = {};
+    arr1.forEach((element, index) => obj[element] = arr2[index]);
+    obj[DELIMITER] = DELIMITER;
+    const codes = arr1
+      .concat(DELIMITER)
+      .concat(Object.keys(MODIFICATIONS));
+    const sortedCodes = sortByStringLengthInDescendingOrder(codes);
+    let i = 0;
+    let r1 = '';
+    while (i < sequence.length) {
+      const matchedCode = sortedCodes.find((c) => c == sequence.slice(i, i + c.length))!;
+      r1 += obj[sequence.slice(i, i + matchedCode.length)];
+      i += matchedCode.length;
+    }
+    while (r1.indexOf('//') != -1)
+      r1 = r1.replace('//', '/');
+    return r1;
+  } catch {
+    return '<error>';
   }
-  while (r1.indexOf('//') != -1)
-    r1 = r1.replace('//', '/');
-  return r1;
 }
 
 //name: asoGapmersNucleotidesToBioSpring
@@ -35,9 +37,9 @@ export function gcrsToLcms(sequence: string): string {
 //output: string result {semType: BioSpring / Gapmers}
 export function asoGapmersNucleotidesToBioSpring(nucleotides: string): string {
   let count: number = -1;
-  const objForEdges: {[index: string]: string} = {
+  const objForEdges: { [index: string]: string } = {
     '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': '5*', 'A': '6*', 'C': '7*', 'G': '8*'};
-  const objForCenter: {[index: string]: string} = {
+  const objForCenter: { [index: string]: string } = {
     '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': 'T*', 'A': 'A*', 'C': '9*', 'G': 'G*'};
   return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|T|C|G)/g, function(x: string) {
     count++;
@@ -51,7 +53,7 @@ export function asoGapmersNucleotidesToBioSpring(nucleotides: string): string {
 //output: string result {semType: GCRS / Gapmers}
 export function asoGapmersNucleotidesToGcrs(nucleotides: string): string {
   let count: number = -1;
-  const objForEdges: {[index: string]: string} = {
+  const objForEdges: { [index: string]: string } = {
     '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': 'moeUnps',
     'A': 'moeAnps', 'C': 'moe5mCnps', 'G': 'moeGnps'};
   const objForCenter: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',

package/src/structures-works/from-monomers.ts

@@ -1,44 +1,104 @@
-import {map, stadardPhosphateLinkSmiles, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, delimiter} from './map';
+// import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, DELIMITER} from './map';
+import {map, SYNTHESIZERS, TECHNOLOGIES, DELIMITER} from './map';
 import {isValidSequence} from './sequence-codes-tools';
-import {getNucleotidesMol} from './mol-transformations';
 import {sortByStringLengthInDescendingOrder} from '../helpers';
+import {getMonomerWorks} from '../package';
+import {getNucleotidesMol} from './mol-transformations';
 
-export function sequenceToMolV3000(sequence: string, inverted: boolean = false, oclRender: boolean = false,
-  format: string): string {
-  const obj = getObjectWithCodesAndSmiles(sequence, format);
-  let codes = sortByStringLengthInDescendingOrder(Object.keys(obj));
+import {standardPhosphateLinkSmiles, MODIFICATIONS} from './const';
+import {getMonomerLib} from '../package';
+// todo: remove
+// const NAME = 'name';
+const CODES = 'codes';
+// const SMILES = 'smiles';
+const MOL = 'molfile';
+
+export function sequenceToMolV3000(
+  sequence: string, inverted: boolean = false, oclRender: boolean = false,
+  format: string,
+): string {
+  const monomerNameFromCode = getCodeToNameMap(sequence, format);
+  let codes = sortByStringLengthInDescendingOrder(Object.keys(monomerNameFromCode));
   let i = 0;
-  const smilesCodes:string[] = [];
   const codesList = [];
   const links = ['s', 'ps', '*'];
   const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
   const dropdowns = Object.keys(MODIFICATIONS);
-  codes = codes.concat(dropdowns).concat(delimiter);
+  codes = codes.concat(dropdowns).concat(DELIMITER);
   while (i < sequence.length) {
-    const code = codes.find((s: string) => s == sequence.slice(i, i + s.length))!;
+    const code = codes.find((s: string) => s === sequence.slice(i, i + s.length))!;
     i += code.length;
     inverted ? codesList.unshift(code) : codesList.push(code);
   }
+
+  const monomers: string[] = [];
+
   for (let i = 0; i < codesList.length; i++) {
-    if (dropdowns.includes(codesList[i])) {
-      smilesCodes.push((i >= codesList.length / 2) ?
-        MODIFICATIONS[codesList[i]].right : MODIFICATIONS[codesList[i]].left);
-      if (!(i < codesList.length - 1 && links.includes(codesList[i + 1])))
-        smilesCodes.push(stadardPhosphateLinkSmiles);
-    } else {
-      if (links.includes(codesList[i]) ||
-        includesStandardLinkAlready.includes(codesList[i]) ||
-        (i < codesList.length - 1 && links.includes(codesList[i + 1]))
-      )
-        smilesCodes.push(obj[codesList[i]]);
-      else {
-        smilesCodes.push(obj[codesList[i]]);
-        smilesCodes.push(stadardPhosphateLinkSmiles);
-      }
+    if (links.includes(codesList[i]) ||
+      includesStandardLinkAlready.includes(codesList[i]) ||
+      (i < codesList.length - 1 && links.includes(codesList[i + 1]))
+    ) {
+      let aa = monomerNameFromCode[codesList[i]];
+      if(aa !== undefined)
+        monomers.push(aa);
+      else
+        monomers.push(codesList[i]);
+    }
+    else {
+      let aa = monomerNameFromCode[codesList[i]];
+      if(aa !== undefined)
+      monomers.push(aa);
+    else
+      monomers.push(codesList[i]);
+      monomers.push('p linkage');
+    }
+  }
+
+  const lib = getMonomerLib();
+  const mols: string [] = [];
+  for(let i = 0; i < monomers.length; i++) {
+    const mnmr = lib?.getMonomer('RNA', monomers[i]);
+    mols.push(mnmr?.molfile!);
+  }
+
+
+  return getNucleotidesMol(mols);
+  //return getMonomerWorks()?.getAtomicLevel(monomers, 'RNA')!;
+}
+
+export function sequenceToMolV3000_new(
+  sequence: string, inverted: boolean = false, oclRender: boolean = false,
+  format: string,
+): string {
+  const monomerNameFromCode = getCodeToNameMap(sequence, format);
+  let codes = sortByStringLengthInDescendingOrder(Object.keys(monomerNameFromCode));
+  let i = 0;
+  const codesList = [];
+  const links = ['s', 'ps', '*'];
+  const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
+  const dropdowns = Object.keys(MODIFICATIONS);
+  codes = codes.concat(dropdowns).concat(DELIMITER);
+  while (i < sequence.length) {
+    const code = codes.find((s: string) => s === sequence.slice(i, i + s.length))!;
+    i += code.length;
+    inverted ? codesList.unshift(code) : codesList.push(code);
+  }
+
+  const monomers: string[] = [];
+
+  for (let i = 0; i < codesList.length; i++) {
+    if (links.includes(codesList[i]) ||
+      includesStandardLinkAlready.includes(codesList[i]) ||
+      (i < codesList.length - 1 && links.includes(codesList[i + 1]))
+    )
+      monomers.push(monomerNameFromCode[codesList[i]]);
+    else {
+      monomers.push(monomerNameFromCode[codesList[i]]);
+      monomers.push('p linkage');
     }
   }
 
-  return getNucleotidesMol(smilesCodes);
+  return getMonomerWorks()?.getAtomicLevel(monomers, 'RNA')!;
 }
 
 export function sequenceToSmiles(sequence: string, inverted: boolean = false, format: string): string {
@@ -50,7 +110,7 @@ export function sequenceToSmiles(sequence: string, inverted: boolean = false, fo
   const links = ['s', 'ps', '*'];
   const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
   const dropdowns = Object.keys(MODIFICATIONS);
-  codes = codes.concat(dropdowns).concat(delimiter);
+  codes = codes.concat(dropdowns).concat(DELIMITER);
   while (i < sequence.length) {
     const code = codes.find((s: string) => s == sequence.slice(i, i + s.length))!;
     i += code.length;
@@ -59,8 +119,8 @@ export function sequenceToSmiles(sequence: string, inverted: boolean = false, fo
   for (let i = 0; i < codesList.length; i++) {
     if (dropdowns.includes(codesList[i])) {
       smiles += (i >= codesList.length / 2) ?
-        MODIFICATIONS[codesList[i]].right + stadardPhosphateLinkSmiles:
-        MODIFICATIONS[codesList[i]].left + stadardPhosphateLinkSmiles;
+        MODIFICATIONS[codesList[i]].right + standardPhosphateLinkSmiles :
+        MODIFICATIONS[codesList[i]].left + standardPhosphateLinkSmiles;
     } else {
       if (links.includes(codesList[i]) ||
         includesStandardLinkAlready.includes(codesList[i]) ||
@@ -68,7 +128,7 @@ export function sequenceToSmiles(sequence: string, inverted: boolean = false, fo
       )
         smiles += obj[codesList[i]];
       else
-        smiles += obj[codesList[i]] + stadardPhosphateLinkSmiles;
+        smiles += obj[codesList[i]] + standardPhosphateLinkSmiles;
     }
   }
   smiles = smiles.replace(/OO/g, 'O');
@@ -82,7 +142,34 @@ export function sequenceToSmiles(sequence: string, inverted: boolean = false, fo
     includesStandardLinkAlready.includes(codesList[codesList.length - 1])
   ) ?
     smiles :
-    smiles.slice(0, smiles.length - stadardPhosphateLinkSmiles.length + 1);
+    smiles.slice(0, smiles.length - standardPhosphateLinkSmiles.length + 1);
+}
+
+function getCodeToNameMap(sequence: string, format: string) {
+  const obj: { [code: string]: string } = {};
+  const NAME = 'name';
+  if (format == null) {
+    for (const synthesizer of Object.keys(map)) {
+      for (const technology of Object.keys(map[synthesizer])) {
+        for (const code of Object.keys(map[synthesizer][technology]))
+          obj[code] = map[synthesizer][technology][code][NAME]!;
+      }
+    }
+  } else {
+    for (const technology of Object.keys(map[format])) {
+      for (const code of Object.keys(map[format][technology]))
+        obj[code] = map[format][technology][code][NAME]!;
+      // obj[code] = map[format][technology][code].SMILES;
+    }
+  }
+  obj[DELIMITER] = '';
+  // TODO: create object based from synthesizer type to avoid key(codes) duplicates
+  const output = isValidSequence(sequence, format);
+  if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12))
+    obj['g'] = map[SYNTHESIZERS.MERMADE_12][TECHNOLOGIES.SI_RNA]['g'][NAME]!;
+  else if (output.synthesizer!.includes(SYNTHESIZERS.AXOLABS))
+    obj['g'] = map[SYNTHESIZERS.AXOLABS][TECHNOLOGIES.SI_RNA]['g'][NAME]!;
+  return obj;
 }
 
 function getObjectWithCodesAndSmiles(sequence: string, format: string) {
@@ -100,7 +187,7 @@ function getObjectWithCodesAndSmiles(sequence: string, format: string) {
         obj[code] = map[format][technology][code].SMILES;
     }
   }
-  obj[delimiter] = '';
+  obj[DELIMITER] = '';
   // TODO: create object based from synthesizer type to avoid key(codes) duplicates
   const output = isValidSequence(sequence, format);
   if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12))
@@ -109,3 +196,72 @@ function getObjectWithCodesAndSmiles(sequence: string, format: string) {
     obj['g'] = map[SYNTHESIZERS.AXOLABS][TECHNOLOGIES.SI_RNA]['g'].SMILES;
   return obj;
 }
+
+function getObjectWithCodesAndMolsFromFile(sequence: string, format: string, libFileContent: string) {
+  const obj: { [code: string]: string } = {};
+  // todo: type
+  const lib: any[] = JSON.parse(libFileContent); //consider using library
+
+  for (const item of lib) {
+    for (const synthesizer of Object.keys(item[CODES])) {
+      if (synthesizer === format) {
+        for (const technology of Object.keys(item[CODES][synthesizer])) {
+          const codes = item[CODES][synthesizer][technology];
+          let mol: string = item[MOL];
+          // todo: find another solution
+          mol = mol.replace(/ R /g, ' O ');
+
+          for (const code of codes)
+            obj[code] = mol;
+        }
+      }
+    }
+  }
+
+  obj[DELIMITER] = '';
+  // TODO: create object based on synthesizer type to avoid key(codes) duplicates
+  const output = isValidSequence(sequence, format);
+  if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12)) {
+    // todo: remove as quickfix, optimize access to 'g'
+    for (const item of lib) {
+      for (const synthesizer of Object.keys(item[CODES])) {
+        for (const technology of Object.keys(item[CODES][synthesizer])) {
+          const codes = item[CODES][synthesizer][technology];
+          for (const code of codes) {
+            const condition =
+              (code === 'g') &&
+              (synthesizer === SYNTHESIZERS.MERMADE_12) &&
+              (technology === TECHNOLOGIES.SI_RNA);
+            if (condition) {
+              let mol: string = item[MOL];
+              // todo: find another solution
+              mol = mol.replace(/ R /g, ' O ');
+              obj[code] = mol;
+            }
+          }
+        }
+      }
+    }
+  } else if (output.synthesizer!.includes(SYNTHESIZERS.AXOLABS)) {
+    for (const item of lib) {
+      for (const synthesizer of Object.keys(item[CODES])) {
+        for (const technology of Object.keys(item[CODES][synthesizer])) {
+          const codes = item[CODES][synthesizer][technology];
+          for (const code of codes) {
+            const condition =
+              (code === 'g') &&
+              (synthesizer === SYNTHESIZERS.AXOLABS) &&
+              (technology === TECHNOLOGIES.SI_RNA);
+            if (condition) {
+              let mol: string = item[MOL];
+              // todo: find another solution
+              mol = mol.replace(/ R /g, ' O ');
+              obj[code] = mol;
+            }
+          }
+        }
+      }
+    }
+  }
+  return obj;
+}

package/src/structures-works/map.ts

@@ -2,7 +2,8 @@ import * as DG from 'datagrok-api/dg';
 import {getAllCodesOfSynthesizer} from './sequence-codes-tools';
 import {differenceOfTwoArrays} from '../helpers';
 
-export const delimiter = ';';
+export const DELIMITER = ';';
+export const NUCLEOTIDES = ['A', 'G', 'C', 'U', 'T'];
 export const SYNTHESIZERS = {
   RAW_NUCLEOTIDES: 'Raw Nucleotides',
   BIOSPRING: 'BioSpring Codes',
@@ -46,7 +47,7 @@ export const map: {[synthesizer: string]:
             'SMILES': 'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[C@@H]1O',
           },
           'T': {
-            'name': 'Tyrosine',
+            'name': 'Thymine',
             'weight': 304.2,
             'normalized': 'dT',
             'SMILES': 'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O',
@@ -148,7 +149,7 @@ export const map: {[synthesizer: string]:
             'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'T': {
-            'name': 'Tyrosine',
+            'name': 'Thymine',
             'weight': 304.2,
             'normalized': 'dT',
             'SMILES': 'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O',
@@ -362,13 +363,13 @@ export const map: {[synthesizer: string]:
             'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'T': {
-            'name': 'Tyrosine',
+            'name': 'Thymine',
             'weight': 304.2,
             'normalized': 'dT',
             'SMILES': 'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O',
           },
           'dT': {
-            'name': 'Tyrosine',
+            'name': 'Thymine',
             'weight': 304.2,
             'normalized': 'dT',
             'SMILES': 'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1O',
@@ -550,8 +551,6 @@ export const map: {[synthesizer: string]:
           },
         },
       },
-      // 'LCMS': {
-      //   'For 2\'-OMe and 2\'-F modified siRNA': {
     };
 
 export const lcmsToGcrs = `LCMS, GCRS