@datagrok/sequence-translator 1.0.15 → 1.0.17

package/src/utils/sdf-add-columns.ts

@@ -0,0 +1,118 @@
+import * as DG from 'datagrok-api/dg';
+import {COL_NAMES, GENERATED_COL_NAMES, SEQUENCE_TYPES} from '../autostart/constants';
+import * as grok from 'datagrok-api/grok';
+import {removeEmptyRows} from '../utils/helpers';
+import {parseStrandsFromDuplexCell, parseStrandsFromTriplexOrDimerCell} from './parse';
+import {isValidSequence} from '../sdf-tab/sequence-codes-tools';
+import {batchMolWeight, molecularWeight, saltMass, saltMolWeigth} from '../autostart/calculations';
+import {weightsObj} from '../hardcode-to-be-eliminated/map';
+
+export class SdfColumnsExistsError extends Error {
+  constructor(message: string) {
+    super();
+  }
+}
+
+export function sdfAddColumns(
+  df: DG.DataFrame, saltNamesList: string[], saltsMolWeightList: number[], onError: (rowI: number, err: any) => void
+): DG.DataFrame {
+  const sequenceCol = df.getCol(COL_NAMES.SEQUENCE);
+  const saltCol = df.getCol(COL_NAMES.SALT);
+  const equivalentsCol = df.getCol(COL_NAMES.EQUIVALENTS);
+  const typeCol = df.getCol(COL_NAMES.TYPE);
+  const chemistryNameCol = df.getCol(COL_NAMES.CHEMISTRY_NAME);
+
+  if (GENERATED_COL_NAMES.some((colName) => df.columns.contains(colName)))
+    throw new SdfColumnsExistsError('Columns already exist');
+
+  df = removeEmptyRows(df, sequenceCol);
+
+  df.columns.addNewString(COL_NAMES.COMPOUND_NAME).init((i: number) => {
+    let res: string = '';
+    try {
+      res = ([SEQUENCE_TYPES.DUPLEX, SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) ?
+        chemistryNameCol.get(i) :
+        sequenceCol.get(i);
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  df.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => {
+    let res: string = '';
+    try {
+      if ([SEQUENCE_TYPES.SENSE_STRAND, SEQUENCE_TYPES.ANTISENSE_STRAND].includes(typeCol.get(i))) {
+        res = sequenceCol.get(i);
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        res = `${chemistryNameCol.get(i)}; duplex of SS: ${obj.SS} and AS: ${obj.AS}`;
+      } else if ([SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) {
+        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+        res = `${chemistryNameCol.get(i)}; duplex of SS: ${obj.SS} and AS1: ${obj.AS1} and AS2: ${obj.AS2}`;
+      }
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  df.columns.addNewFloat(COL_NAMES.COMPOUND_MOL_WEIGHT).init((i: number) => {
+    let res: number = Number.NaN;
+    try {
+      if ([SEQUENCE_TYPES.SENSE_STRAND, SEQUENCE_TYPES.ANTISENSE_STRAND].includes(typeCol.get(i))) {
+        res = (isValidSequence(sequenceCol.get(i), null).indexOfFirstNotValidChar == -1) ?
+          molecularWeight(sequenceCol.get(i), weightsObj) :
+          DG.FLOAT_NULL;
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        res = (Object.values(obj).every((seq) => isValidSequence(seq, null).indexOfFirstNotValidChar == -1)) ?
+          molecularWeight(obj.SS, weightsObj) + molecularWeight(obj.AS, weightsObj) :
+          DG.FLOAT_NULL;
+      } else if ([SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) {
+        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+        res = (Object.values(obj).every((seq) => isValidSequence(seq, null).indexOfFirstNotValidChar == -1)) ?
+          molecularWeight(obj.SS, weightsObj) + molecularWeight(obj.AS1, weightsObj) +
+          molecularWeight(obj.AS2, weightsObj) :
+          DG.FLOAT_NULL;
+      }
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  df.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) => {
+    let res: number = Number.NaN;
+    try {
+      res = saltMass(saltNamesList, saltsMolWeightList, equivalentsCol, i, saltCol);
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  df.columns.addNewFloat(COL_NAMES.SALT_MOL_WEIGHT).init((i: number) => {
+    let res: number = Number.NaN;
+    try {
+      res = saltMolWeigth(saltNamesList, saltCol, saltsMolWeightList, i);
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  const compoundMolWeightCol = df.getCol(COL_NAMES.COMPOUND_MOL_WEIGHT);
+  const saltMassCol = df.getCol(COL_NAMES.SALT_MASS);
+  df.columns.addNewFloat(COL_NAMES.BATCH_MOL_WEIGHT).init((i: number) => {
+    let res: number = Number.NaN;
+    try {
+      res = batchMolWeight(compoundMolWeightCol, saltMassCol, i);
+    } catch (err) {
+      onError(i, err);
+    }
+    return res;
+  });
+
+  return df;
+}

package/src/utils/sdf-save-table.ts

@@ -0,0 +1,56 @@
+import * as DG from 'datagrok-api/dg';
+import {COL_NAMES, GENERATED_COL_NAMES, SEQUENCE_TYPES} from '../autostart/constants';
+import {differenceOfTwoArrays, download} from '../utils/helpers';
+import * as grok from 'datagrok-api/grok';
+import {SYNTHESIZERS} from '../hardcode-to-be-eliminated/map';
+import {sequenceToMolV3000} from '../utils/structures-works/from-monomers';
+import {parseStrandsFromDuplexCell, parseStrandsFromTriplexOrDimerCell} from './parse';
+import {linkStrandsV3000} from '../utils/structures-works/mol-transformations';
+
+export async function sdfSaveTable(table: DG.DataFrame, onError: (rowI: number, err: any) => void) {
+  if (GENERATED_COL_NAMES.some((colName) => !table.columns.contains(colName))) {
+    const absentColNames = differenceOfTwoArrays(GENERATED_COL_NAMES, table.columns.names()).join(`', '`);
+    grok.shell.warning(`File saved without columns '${absentColNames}'`);
+  }
+
+  const sequenceCol = table.getCol(COL_NAMES.SEQUENCE);
+  const typeCol = table.getCol(COL_NAMES.TYPE);
+
+  let resultStr = '';
+  const rowCount = table.rowCount;
+  for (let i = 0; i < rowCount; i++) {
+    try {
+      let rowStr = '';
+      const format = SYNTHESIZERS.GCRS; //getFormat(sequenceCol.get(i))!;
+      if (typeCol.get(i) == SEQUENCE_TYPES.SENSE_STRAND) {
+        rowStr += `${sequenceToMolV3000(sequenceCol.get(i), false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.ANTISENSE_STRAND) {
+        rowStr += `${sequenceToMolV3000(sequenceCol.get(i), true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        const as = `${sequenceToMolV3000(obj.AS, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+        const ss = `${sequenceToMolV3000(obj.SS, false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+        rowStr += `${linkStrandsV3000({senseStrands: [ss], antiStrands: [as]}, true)}\n\n`;
+      } else if ([SEQUENCE_TYPES.TRIPLEX, SEQUENCE_TYPES.DIMER].includes(typeCol.get(i))) {
+        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+        const as1 = `${sequenceToMolV3000(obj.AS1, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+        const as2 = `${sequenceToMolV3000(obj.AS2, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+        const ss = `${sequenceToMolV3000(obj.SS, false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+        rowStr += `${linkStrandsV3000({senseStrands: [ss], antiStrands: [as1, as2]}, true)}\n\n`;
+      }
+
+      for (const col of table.columns) {
+        if (col.name != COL_NAMES.SEQUENCE)
+          rowStr += `> <${col.name}>\n${col.get(i)}\n\n`;
+      }
+
+      rowStr += '$$$$\n';
+
+      resultStr += rowStr;
+    } catch (err: any) {
+      onError(i, err);
+    }
+  }
+
+  download(`${table.name}.sdf`, encodeURIComponent(resultStr));
+}

package/src/utils/structures-works/draw-molecule.ts

@@ -0,0 +1,84 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
+
+import $ from 'cash-dom';
+
+import {extractAtomDataV3000} from './mol-transformations';
+
+/** Draw molecule on the canvas and append it to the specified div, with the
+ * option of zoom-in */
+export async function drawMolecule(
+  moleculeImgDiv: HTMLDivElement,
+  canvasWidth: number, canvasHeight: number,
+  molfile: string
+): Promise<void> {
+  // clear the div's content if any
+  async function drawMolfileOnCanvas(canvas: HTMLCanvasElement): Promise<void> {
+    await grok.functions.call('Chem:canvasMol', {
+      x: 0, y: 0, w: canvas.width, h: canvas.height, canvas: canvas,
+      molString: molfile, scaffoldMolString: '',
+      options: {normalizeDepiction: false, straightenDepiction: false}
+    });
+  };
+
+  async function drawZoomedInMolecule(): Promise<void> {
+    try {
+      const dialogDivStyle = {
+        overflowX: 'scroll',
+      };
+      const dialogDiv = ui.div([], {style: dialogDivStyle});
+
+      // dialogDiv size required, but now available before dialog show()
+      const atomCoordinates = extractAtomDataV3000(molfile);
+      // const cw: number = $(window).width() * 0.80; // dialogDiv.clientWidth
+      const clientHeight: number = $(window).height() * 0.70; // dialogDiv.clientHeight
+      const molWidth: number = Math.max(...atomCoordinates.x) - Math.min(...atomCoordinates.x);
+      const molHeight: number = Math.max(...atomCoordinates.y) - Math.min(...atomCoordinates.y);
+
+      // const wR: number = cw / molWidth;
+      const hR: number = clientHeight / molHeight;
+      const r: number = hR; // Math.max(wR, hR);
+      const dialogCanvasWidth = r * molWidth;
+      const dialogCanvasHeight = r * molHeight;
+
+      const dialogCanvas = ui.canvas(
+        dialogCanvasWidth * window.devicePixelRatio, dialogCanvasHeight * window.devicePixelRatio
+      );
+      dialogCanvas.style.width = `${dialogCanvasWidth}px`;
+      dialogCanvas.style.height = `${dialogCanvasHeight}px`;
+      await drawMolfileOnCanvas(dialogCanvas);
+
+      dialogDiv.appendChild(dialogCanvas);
+      ui.dialog('Molecule')
+        .add(dialogDiv)
+        .showModal(true);
+    } catch (err) {
+      const errStr = errorToConsole(err);
+      console.error(errStr);
+    }
+  };
+
+  // clear div's content if any
+  moleculeImgDiv.innerHTML = '';
+
+  if (molfile !== '') {
+    const canvas = ui.canvas(canvasWidth * window.devicePixelRatio, canvasHeight * window.devicePixelRatio);
+
+    // Draw zoomed-out molecule
+    canvas.style.width = `${canvasWidth}px`;
+    canvas.style.height = `${canvasHeight}px`;
+    canvas.style.borderStyle = 'solid';
+    canvas.style.borderColor = 'blue';
+    drawMolfileOnCanvas(canvas);
+
+    // Dialog with zoomed-in molecule
+    $(canvas).on('click', drawZoomedInMolecule);
+    $(canvas).on('mouseover', () => $(canvas).css('cursor', 'grab')); // for some reason 'zoom-in' value wouldn't work
+    $(canvas).on('mouseout', () => $(canvas).css('cursor', 'default'));
+
+    moleculeImgDiv.append(canvas);
+  }
+}

package/src/{structures-works → utils/structures-works}/from-monomers.ts

@@ -1,12 +1,12 @@
 // import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, DELIMITER} from './map';
-import {map, SYNTHESIZERS, TECHNOLOGIES, DELIMITER} from './map';
-import {isValidSequence} from './sequence-codes-tools';
+import {map, SYNTHESIZERS, TECHNOLOGIES, DELIMITER} from '../../hardcode-to-be-eliminated/map';
+import {isValidSequence} from '../../sdf-tab/sequence-codes-tools';
 import {sortByStringLengthInDescendingOrder} from '../helpers';
-import {getMonomerWorks} from '../package';
+import {getMonomerWorks} from '../../package';
 import {getNucleotidesMol} from './mol-transformations';
 
-import {standardPhosphateLinkSmiles, MODIFICATIONS} from './const';
-import {getMonomerLib} from '../package';
+import {standardPhosphateLinkSmiles, MODIFICATIONS} from '../../hardcode-to-be-eliminated/const';
+import {getMonomerLib} from '../../package';
 // todo: remove
 // const NAME = 'name';
 const CODES = 'codes';
@@ -15,7 +15,7 @@ const MOL = 'molfile';
 
 export function sequenceToMolV3000(
   sequence: string, inverted: boolean = false, oclRender: boolean = false,
-  format: string,
+  format: string
 ): string {
   const monomerNameFromCode = getCodeToNameMap(sequence, format);
   let codes = sortByStringLengthInDescendingOrder(Object.keys(monomerNameFromCode));
@@ -38,25 +38,24 @@ export function sequenceToMolV3000(
       includesStandardLinkAlready.includes(codesList[i]) ||
       (i < codesList.length - 1 && links.includes(codesList[i + 1]))
     ) {
-      let aa = monomerNameFromCode[codesList[i]];
-      if(aa !== undefined)
+      const aa = monomerNameFromCode[codesList[i]];
+      if (aa !== undefined)
+        monomers.push(aa);
+      else
+        monomers.push(codesList[i]);
+    } else {
+      const 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++) {
+  for (let i = 0; i < monomers.length; i++) {
     const mnmr = lib?.getMonomer('RNA', monomers[i]);
     mols.push(mnmr?.molfile!);
   }

package/src/{structures-works → utils/structures-works}/mol-transformations.ts

@@ -1,30 +1,23 @@
 export function getNucleotidesMol(codes: string[]) {
   const molBlocks: string[] = [];
 
-  // for (let i = 0; i < smilesCodes.length - 1; i++) {
-  //   smilesCodes[i] == 'OP(=O)(O)O' ? molBlocks.push(PHOSHATE) :
-  //     smilesCodes[i] == 'OP(=O)(S)O' ? molBlocks.push(THIOPHOSHATE) :
-  //       smilesCodes[i] == 'O[C@@H]1C[C@@H]O[C@H]1CO' ? molBlocks.push(rotateNucleotidesV3000(INVABASIC)) :
-  //         smilesCodes[i] == 'OCC(O)CNC(=O)CCCC(=O)NC(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)' ? molBlocks.push(GALNAC) :
-  //           smilesCodes[i] == 'C(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)NC(=O)CCCC(=O)NCC(O)CO' ? molBlocks.push(GALNACPRIME) :
-  //         molBlocks.push(rotateNucleotidesV3000(smilesCodes[i]));
-  // }
-
   for (let i = 0; i < codes.length - 1; i++) {
     if (codes[i].includes('MODIFICATION')) {
-      if (i == 0)
+      if (i === 0)
         molBlocks.push(reflect(codes[i]));
       else
         molBlocks.push(codes[i]);
-    }
-    else
+    } else {
       molBlocks.push(rotateNucleotidesV3000(codes[i]));
+    }
   }
 
   return linkV3000(molBlocks);
 }
 
-export function linkStrandsV3000(strands: { senseStrands: string[], antiStrands: string[] }, useChirality: boolean = true) {
+export function linkStrandsV3000(
+  strands: { senseStrands: string[], antiStrands: string[] }, useChirality: boolean = true
+): string {
   let macroMolBlock = '\nDatagrok macromolecule handler\n\n';
   macroMolBlock += '  0  0  0  0  0  0            999 V3000\n';
   macroMolBlock += 'M  V30 BEGIN CTAB\n';
@@ -40,22 +33,19 @@ export function linkStrandsV3000(strands: { senseStrands: string[], antiStrands:
   //   molBlocks[1] = invertNucleotidesV3000(molBlocks[1]);
 
   if (strands.antiStrands.length > 0) {
-    for (let i = 0; i < strands.antiStrands.length; i++) {
+    for (let i = 0; i < strands.antiStrands.length; i++)
       strands.antiStrands[i] = invertNucleotidesV3000(strands.antiStrands[i]);
-    }
   }
 
   let inverted = false;
-  let molBlocks = strands.senseStrands.concat(strands.antiStrands);
+  const molBlocks = strands.senseStrands.concat(strands.antiStrands);
 
   for (let i = 0; i < molBlocks.length; i++) {
-
-    if (i >= strands.senseStrands.length && inverted == false) {
+    if (i >= strands.senseStrands.length && inverted === false) {
       inverted = true;
       xShift = 0;
     }
 
-
     molBlocks[i] = molBlocks[i].replaceAll('(-\nM  V30 ', '(')
       .replaceAll('-\nM  V30 ', '').replaceAll(' )', ')');
     const numbers = extractAtomsBondsNumbersV3000(molBlocks[i]);
@@ -63,7 +53,7 @@ export function linkStrandsV3000(strands: { senseStrands: string[], antiStrands:
 
     if (inverted) {
       const xShiftRight = Math.min(...coordinates.x) - xShift;
-      const yShift = !inverted ? Math.min(...coordinates.y) - 1 : Math.max(...coordinates.y) + 10;
+      const yShift = !inverted ? Math.min(...coordinates.y) - 1 : Math.max(...coordinates.y) + 15;
       for (let j = 0; j < coordinates.x.length; j++)
         coordinates.x[j] -= xShiftRight;
       for (let j = 0; j < coordinates.y.length; j++)
@@ -76,7 +66,7 @@ export function linkStrandsV3000(strands: { senseStrands: string[], antiStrands:
     let indexEnd = indexAtoms;
 
     for (let j = 0; j < numbers.natom; j++) {
-      // if (coordinates.atomIndex[j] != 1 || i == 0 || twoChains) {
+      // if (coordinates.atomIndex[j] !== 1 || i === 0 || twoChains) {
       //rewrite atom number
       index = molBlocks[i].indexOf('V30', index) + 4;
       indexEnd = molBlocks[i].indexOf(' ', index);
@@ -138,7 +128,7 @@ export function linkStrandsV3000(strands: { senseStrands: string[], antiStrands:
 
     let indexCollection = molBlocks[i].indexOf('M  V30 MDLV30/STEABS ATOMS=('); // V3000 index for collections
 
-    while (indexCollection != -1) {
+    while (indexCollection !== -1) {
       indexCollection += 28;
       const collectionEnd = molBlocks[i].indexOf(')', indexCollection);
       const collectionEntries = molBlocks[i].substring(indexCollection, collectionEnd).split(' ').slice(1);
@@ -157,25 +147,16 @@ export function linkStrandsV3000(strands: { senseStrands: string[], antiStrands:
   const entries = 4;
   const collNumber = Math.ceil(collection.length / entries);
 
-  //if (oclRender) {
-  // collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length;
-
-  // for (let j = 0; j < collection.length; j++)
-  //   collectionBlock += ' ' + collection[j];
-
-  // collectionBlock += ')\n';
-  //} else {
   collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length + ' -\n';
   for (let i = 0; i < collNumber; i++) {
     collectionBlock += 'M  V30 ';
-    const entriesCurrent = i + 1 == collNumber ? collection.length - (collNumber - 1) * entries : entries;
+    const entriesCurrent = i + 1 === collNumber ? collection.length - (collNumber - 1) * entries : entries;
     for (let j = 0; j < entriesCurrent; j++) {
-      collectionBlock += (j + 1 == entriesCurrent) ?
-        (i == collNumber - 1 ? collection[entries * i + j] + ')\n' : collection[entries * i + j] + ' -\n') :
+      collectionBlock += (j + 1 === entriesCurrent) ?
+        (i === collNumber - 1 ? collection[entries * i + j] + ')\n' : collection[entries * i + j] + ' -\n') :
         collection[entries * i + j] + ' ';
     }
   }
-  //}
 
   //generate file
   true ? natom : natom++;
@@ -190,8 +171,9 @@ export function linkStrandsV3000(strands: { senseStrands: string[], antiStrands:
     macroMolBlock += 'M  V30 BEGIN COLLECTION\n';
     macroMolBlock += collectionBlock;
     macroMolBlock += 'M  V30 END COLLECTION\n';
-  } else
+  } else {
     macroMolBlock = macroMolBlock.replace(/ CFG=\d/g, ' ');
+  }
 
   macroMolBlock += 'M  V30 END CTAB\n';
   macroMolBlock += 'M  END';
@@ -199,7 +181,7 @@ export function linkStrandsV3000(strands: { senseStrands: string[], antiStrands:
   return macroMolBlock;
 }
 
-export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
+export function linkV3000(molBlocks: string[], useChirality: boolean = true): string {
   let macroMolBlock = '\nDatagrok macromolecule handler\n\n';
   macroMolBlock += '  0  0  0  0  0  0            999 V3000\n';
   macroMolBlock += 'M  V30 BEGIN CTAB\n';
@@ -212,7 +194,7 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
   let xShift = 0;
 
   for (let i = 0; i < molBlocks.length; i++) {
-    const isBoundary = molBlocks[i].includes('MODIFICATION') && i == 0;
+    const isBoundary = molBlocks[i].includes('MODIFICATION') && i === 0;
     let specLength = 0;
     if (isBoundary) {
       const coordinates = extractAtomDataV3000(molBlocks[i]);
@@ -231,16 +213,16 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
     let indexEnd = indexAtoms;
 
     for (let j = 0; j < numbers.natom; j++) {
-      if (coordinates.atomIndex[j] != 1 || i == 0) {
+      if (coordinates.atomIndex[j] !== 1 || i === 0) {
         //rewrite atom number
         index = molBlocks[i].indexOf('V30', index) + 4;
         indexEnd = molBlocks[i].indexOf(' ', index);
         let atomNumber = 0;
         if (isBoundary) {
           atomNumber = parseInt(molBlocks[i].substring(index, indexEnd))
-          if (atomNumber == 1)
+          if (atomNumber === 1)
             atomNumber = specLength;
-          else if (atomNumber == specLength)
+          else if (atomNumber === specLength)
             atomNumber = 1;
           atomNumber += natom;
         } else {
@@ -294,9 +276,9 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
       let atomNumber = 0;
       if (isBoundary) {
         atomNumber = parseInt(molBlocks[i].substring(index, indexEnd))
-        if (atomNumber == 1)
+        if (atomNumber === 1)
           atomNumber = specLength;
-        else if (atomNumber == specLength)
+        else if (atomNumber === specLength)
           atomNumber = 1;
         atomNumber += natom;
       } else {
@@ -309,9 +291,9 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
       atomNumber = 0;
       if (isBoundary) {
         atomNumber = parseInt(molBlocks[i].substring(index, indexEnd))
-        if (atomNumber == 1)
+        if (atomNumber === 1)
           atomNumber = specLength;
-        else if (atomNumber == specLength)
+        else if (atomNumber === specLength)
           atomNumber = 1;
         atomNumber += natom;
       } else {
@@ -327,7 +309,7 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
 
     let indexCollection = molBlocks[i].indexOf('M  V30 MDLV30/STEABS ATOMS=('); // V3000 index for collections
 
-    while (indexCollection != -1) {
+    while (indexCollection !== -1) {
       indexCollection += 28;
       const collectionEnd = molBlocks[i].indexOf(')', indexCollection);
       const collectionEntries = molBlocks[i].substring(indexCollection, collectionEnd).split(' ').slice(1);
@@ -360,10 +342,10 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
   collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length + ' -\n';
   for (let i = 0; i < collNumber; i++) {
     collectionBlock += 'M  V30 ';
-    const entriesCurrent = i + 1 == collNumber ? collection.length - (collNumber - 1) * entries : entries;
+    const entriesCurrent = i + 1 === collNumber ? collection.length - (collNumber - 1) * entries : entries;
     for (let j = 0; j < entriesCurrent; j++) {
-      collectionBlock += (j + 1 == entriesCurrent) ?
-        (i == collNumber - 1 ? collection[entries * i + j] + ')\n' : collection[entries * i + j] + ' -\n') :
+      collectionBlock += (j + 1 === entriesCurrent) ?
+        (i === collNumber - 1 ? collection[entries * i + j] + ')\n' : collection[entries * i + j] + ' -\n') :
         collection[entries * i + j] + ' ';
     }
   }
@@ -391,7 +373,7 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
   return macroMolBlock;
 }
 
-function rotateNucleotidesV3000(molecule: string) {
+function rotateNucleotidesV3000(molecule: string): string {
   // @ts-ignore
   let molBlock = molecule.includes('M  END') ? molecule : OCL.Molecule.fromSmiles(molecule).toMolfileV3();
   const coordinates = extractAtomDataV3000(molBlock);
@@ -414,9 +396,9 @@ function rotateNucleotidesV3000(molecule: string) {
   }
 
   let angle = 0;
-  if (coordinates.x[indexFivePrime] == 0)
+  if (coordinates.x[indexFivePrime] === 0)
     angle = coordinates.y[indexFivePrime] > coordinates.y[indexThreePrime] ? Math.PI / 2 : 3 * Math.PI / 2;
-  else if (coordinates.y[indexFivePrime] == 0)
+  else if (coordinates.y[indexFivePrime] === 0)
     angle = coordinates.x[indexFivePrime] > coordinates.x[indexThreePrime] ? Math.PI : 0;
   else {
     const derivative = coordinates.y[indexFivePrime] / coordinates.x[indexFivePrime];
@@ -460,7 +442,7 @@ function rotateNucleotidesV3000(molecule: string) {
   return molBlock;
 }
 
-function reflect(molecule: string) {
+function reflect(molecule: string): string {
   // @ts-ignore
   let molBlock = molecule.includes('M  END') ? molecule : OCL.Molecule.fromSmiles(molecule).toMolfileV3();
   const coordinates = extractAtomDataV3000(molBlock);

package/{test-SequenceTranslator-91c83d8913ff-f94596bc.html → test-SequenceTranslator-6288c2fbe346-695b7b55.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=91c83d8913ff. Commit f94596bc.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=6288c2fbe346. Commit 695b7b55.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,31 +229,31 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=91c83d8913ff. Commit f94596bc.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-29 11:55:21</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">18.993s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">5.501s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=6288c2fbe346. Commit 695b7b55.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-12-19 15:46:37</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">15.201s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">4.324s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:40:11
     at Generator.next (&lt;anonymous&gt;)
-    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:31:71
+    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:34:71
     at new Promise (&lt;anonymous&gt;)
-    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:27:12)
+    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:30:12)
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:38:23)
     at Promise.then.completed (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/jest-circus/build/utils.js:391:28)
     at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing SequenceTranslator package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:72:11
     at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
+    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:31:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 2 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
 Test result : Success : 1 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu : OK
 Test result : Success : 1 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.acacacsacsac : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.cccgggusug : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.cccgggusug : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.UfAfCfGfGfCfAfUf : OK
 Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
+Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
 Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
 </pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:74:11
     at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:28:58)
+    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:31:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message"/></div></div></div></div></body></html>