@datagrok/sequence-translator 1.0.14 → 1.0.16

package/src/structures-works/mol-transformations.ts

@@ -11,8 +11,8 @@ export function getNucleotidesMol(codes: string[]) {
   // }
 
   for (let i = 0; i < codes.length - 1; i++) {
-    if(codes[i].includes('MODIFICATION')) {
-      if(i == 0)
+    if (codes[i].includes('MODIFICATION')) {
+      if (i == 0)
         molBlocks.push(reflect(codes[i]));
       else
         molBlocks.push(codes[i]);
@@ -24,7 +24,7 @@ export function getNucleotidesMol(codes: string[]) {
   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) {
   let macroMolBlock = '\nDatagrok macromolecule handler\n\n';
   macroMolBlock += '  0  0  0  0  0  0            999 V3000\n';
   macroMolBlock += 'M  V30 BEGIN CTAB\n';
@@ -40,7 +40,7 @@ export function linkStrandsV3000(strands:{senseStrands: string[], antiStrands: s
   //   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]);
     }
   }
@@ -90,15 +90,15 @@ export function linkStrandsV3000(strands:{senseStrands: string[], antiStrands: s
 
       const totalShift = true ? 0 : xShift - coordinates.x[0];
       let coordinate = true ?
-        Math.round(10000*coordinates.x[j])/10000 :
-        Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd)) + totalShift))/10000;
+        Math.round(10000 * coordinates.x[j]) / 10000 :
+        Math.round(10000 * (parseFloat(molBlocks[i].substring(index, indexEnd)) + totalShift)) / 10000;
       molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
 
       index = molBlocks[i].indexOf(' ', index) + 1;
       indexEnd = molBlocks[i].indexOf(' ', index);
       coordinate = true ?
-        Math.round(10000*coordinates.y[j])/10000 :
-        Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd))))/10000;
+        Math.round(10000 * coordinates.y[j]) / 10000 :
+        Math.round(10000 * (parseFloat(molBlocks[i].substring(index, indexEnd)))) / 10000;
       molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
 
       index = molBlocks[i].indexOf('\n', index) + 1;
@@ -158,27 +158,27 @@ export function linkStrandsV3000(strands:{senseStrands: string[], antiStrands: s
   const collNumber = Math.ceil(collection.length / entries);
 
   //if (oclRender) {
-    // collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length;
+  // collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length;
 
-    // for (let j = 0; j < collection.length; j++)
-    //   collectionBlock += ' ' + collection[j];
+  // for (let j = 0; j < collection.length; j++)
+  //   collectionBlock += ' ' + collection[j];
 
-    // collectionBlock += ')\n';
+  // 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;
-      for (let j = 0; j < entriesCurrent; j++) {
-        collectionBlock += (j + 1 == entriesCurrent) ?
-          (i == collNumber - 1 ? collection[entries*i + j] + ')\n' : collection[entries*i + j] + ' -\n') :
-          collection[entries*i + j] + ' ';
-      }
+  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;
+    for (let j = 0; j < entriesCurrent; j++) {
+      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++;
+  true ? natom : natom++;
   macroMolBlock += 'M  V30 COUNTS ' + natom + ' ' + nbond + ' 0 0 0\n';
   macroMolBlock += 'M  V30 BEGIN ATOM\n';
   macroMolBlock += atomBlock;
@@ -186,7 +186,7 @@ export function linkStrandsV3000(strands:{senseStrands: string[], antiStrands: s
   macroMolBlock += 'M  V30 BEGIN BOND\n';
   macroMolBlock += bondBlock;
   macroMolBlock += 'M  V30 END BOND\n';
-  if(useChirality){
+  if (useChirality) {
     macroMolBlock += 'M  V30 BEGIN COLLECTION\n';
     macroMolBlock += collectionBlock;
     macroMolBlock += 'M  V30 END COLLECTION\n';
@@ -218,7 +218,7 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
       const coordinates = extractAtomDataV3000(molBlocks[i]);
       specLength = coordinates.atomIndex.length;
     }
-      
+
 
     molBlocks[i] = molBlocks[i].replaceAll('(-\nM  V30 ', '(')
       .replaceAll('-\nM  V30 ', '').replaceAll(' )', ')');
@@ -236,11 +236,11 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
         index = molBlocks[i].indexOf('V30', index) + 4;
         indexEnd = molBlocks[i].indexOf(' ', index);
         let atomNumber = 0;
-        if(isBoundary) {
+        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 {
@@ -254,14 +254,14 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
         indexEnd = molBlocks[i].indexOf(' ', index);
 
         const totalShift = xShift - coordinates.x[0];
-        let coordinate = 
-          Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd)) + totalShift))/10000;
+        let coordinate =
+          Math.round(10000 * (parseFloat(molBlocks[i].substring(index, indexEnd)) + totalShift)) / 10000;
         molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
 
         index = molBlocks[i].indexOf(' ', index) + 1;
         indexEnd = molBlocks[i].indexOf(' ', index);
-        coordinate = 
-          Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd))))/10000;
+        coordinate =
+          Math.round(10000 * (parseFloat(molBlocks[i].substring(index, indexEnd)))) / 10000;
         molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
 
         index = molBlocks[i].indexOf('\n', index) + 1;
@@ -292,11 +292,11 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
       index = molBlocks[i].indexOf(' ', index) + 1;
       indexEnd = molBlocks[i].indexOf(' ', index);
       let atomNumber = 0;
-      if(isBoundary) {
+      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 {
@@ -307,11 +307,11 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
       index = molBlocks[i].indexOf(' ', index) + 1;
       indexEnd = Math.min(molBlocks[i].indexOf('\n', index), molBlocks[i].indexOf(' ', index));
       atomNumber = 0;
-      if(isBoundary) {
+      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 {
@@ -340,7 +340,7 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
 
     natom += numbers.natom - 1;
     nbond += numbers.nbond;
-    if(isBoundary)
+    if (isBoundary)
       xShift += Math.max(...coordinates.x);
     else
       xShift += coordinates.x[numbers.natom - 1] - coordinates.x[0];
@@ -350,23 +350,23 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
   const collNumber = Math.ceil(collection.length / entries);
 
   //if (oclRender) {
-    // collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length;
+  // collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length;
 
-    // for (let j = 0; j < collection.length; j++)
-    //   collectionBlock += ' ' + collection[j];
+  // for (let j = 0; j < collection.length; j++)
+  //   collectionBlock += ' ' + collection[j];
 
-    // collectionBlock += ')\n';
+  // 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;
-      for (let j = 0; j < entriesCurrent; j++) {
-        collectionBlock += (j + 1 == entriesCurrent) ?
-          (i == collNumber - 1 ? collection[entries*i + j] + ')\n' : collection[entries*i + j] + ' -\n') :
-          collection[entries*i + j] + ' ';
-      }
+  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;
+    for (let j = 0; j < entriesCurrent; j++) {
+      collectionBlock += (j + 1 == entriesCurrent) ?
+        (i == collNumber - 1 ? collection[entries * i + j] + ')\n' : collection[entries * i + j] + ' -\n') :
+        collection[entries * i + j] + ' ';
     }
+  }
   //}
 
   //generate file
@@ -378,7 +378,7 @@ export function linkV3000(molBlocks: string[], useChirality: boolean = true) {
   macroMolBlock += 'M  V30 BEGIN BOND\n';
   macroMolBlock += bondBlock;
   macroMolBlock += 'M  V30 END BOND\n';
-  if(useChirality){
+  if (useChirality) {
     macroMolBlock += 'M  V30 BEGIN COLLECTION\n';
     macroMolBlock += collectionBlock;
     macroMolBlock += 'M  V30 END COLLECTION\n';
@@ -404,8 +404,8 @@ function rotateNucleotidesV3000(molecule: string) {
   if (natom > 8)
     fix5Prime(coordinates, indexFivePrime, indexThreePrime);
 
-  const xCenter = (coordinates.x[indexThreePrime] + coordinates.x[indexFivePrime])/2;
-  const yCenter = (coordinates.y[indexThreePrime] + coordinates.y[indexFivePrime])/2;
+  const xCenter = (coordinates.x[indexThreePrime] + coordinates.x[indexFivePrime]) / 2;
+  const yCenter = (coordinates.y[indexThreePrime] + coordinates.y[indexFivePrime]) / 2;
 
   //place to center
   for (let i = 0; i < natom; i++) {
@@ -415,16 +415,14 @@ function rotateNucleotidesV3000(molecule: string) {
 
   let angle = 0;
   if (coordinates.x[indexFivePrime] == 0)
-    angle = coordinates.y[indexFivePrime] > coordinates.y[indexThreePrime] ? Math.PI/2 : 3*Math.PI/2;
+    angle = coordinates.y[indexFivePrime] > coordinates.y[indexThreePrime] ? Math.PI / 2 : 3 * Math.PI / 2;
   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];
-    angle = derivative > 0 ? Math.PI - Math.atan(derivative) : 
-            (coordinates.x[indexFivePrime] < 0 ? 
-              Math.atan(derivative) : 
-              - Math.PI - Math.atan(derivative)
-            );
+    const derivative = coordinates.y[indexFivePrime] / coordinates.x[indexFivePrime];
+    angle = derivative > 0
+      ? (coordinates.x[indexFivePrime] > 0 ? Math.PI - Math.atan(derivative) : Math.PI * 2 - Math.atan(derivative))
+      : (coordinates.x[indexFivePrime] > 0 ? -Math.PI - Math.atan(derivative) : Math.atan(derivative));
   }
 
   const cos = Math.cos(angle);
@@ -432,8 +430,8 @@ function rotateNucleotidesV3000(molecule: string) {
 
   for (let i = 0; i < natom; i++) {
     const xAdd = coordinates.x[i];
-    coordinates.x[i] = xAdd*cos - coordinates.y[i]*sin;
-    coordinates.y[i] = xAdd*sin + coordinates.y[i]*cos;
+    coordinates.x[i] = xAdd * cos - coordinates.y[i] * sin;
+    coordinates.y[i] = xAdd * sin + coordinates.y[i] * cos;
   }
 
   //place to right
@@ -471,8 +469,8 @@ function reflect(molecule: string) {
   const indexFivePrime = coordinates.atomIndex.indexOf(1);
   const indexThreePrime = coordinates.atomIndex.indexOf(natom);
 
-  const xCenter = (coordinates.x[indexThreePrime] + coordinates.x[indexFivePrime])/2;
-  const yCenter = (coordinates.y[indexThreePrime] + coordinates.y[indexFivePrime])/2;
+  const xCenter = (coordinates.x[indexThreePrime] + coordinates.x[indexFivePrime]) / 2;
+  const yCenter = (coordinates.y[indexThreePrime] + coordinates.y[indexFivePrime]) / 2;
 
   //place to center
   for (let i = 0; i < natom; i++) {
@@ -517,8 +515,8 @@ function invertNucleotidesV3000(molecule: string) {
   const coordinates = extractAtomDataV3000(molBlock);
   const natom = coordinates.atomIndex.length;
 
-  const xCenter = (Math.max(...coordinates.x) + Math.min(...coordinates.x))/2;
-  const yCenter = (Math.max(...coordinates.y) + Math.min(...coordinates.y))/2;
+  const xCenter = (Math.max(...coordinates.x) + Math.min(...coordinates.x)) / 2;
+  const yCenter = (Math.max(...coordinates.y) + Math.min(...coordinates.y)) / 2;
 
   //place to center
   for (let i = 0; i < natom; i++) {
@@ -533,8 +531,8 @@ function invertNucleotidesV3000(molecule: string) {
 
   for (let i = 0; i < natom; i++) {
     const xAdd = coordinates.x[i];
-    coordinates.x[i] = xAdd*cos - coordinates.y[i]*sin;
-    coordinates.y[i] = xAdd*sin + coordinates.y[i]*cos;
+    coordinates.x[i] = xAdd * cos - coordinates.y[i] * sin;
+    coordinates.y[i] = xAdd * sin + coordinates.y[i] * cos;
   }
 
   //place back
@@ -565,7 +563,7 @@ function invertNucleotidesV3000(molecule: string) {
   return molBlock;
 }
 
-function fix5Prime(coordinates: {atomIndex: number[], atomType: string[], x: number[], y: number[]},
+function fix5Prime(coordinates: { atomIndex: number[], atomType: string[], x: number[], y: number[] },
   indexFivePrime: number, indexThreePrime: number) {
   const indexFivePrimeNeighbour = indexFivePrime + 1;
   const xShift = coordinates.x[indexFivePrimeNeighbour];
@@ -575,21 +573,21 @@ function fix5Prime(coordinates: {atomIndex: number[], atomType: string[], x: num
   const base5PrimeX = coordinates.x[indexFivePrime] - xShift;
   const base5PrimeY = coordinates.y[indexFivePrime] - yShift;
 
-  const rotated5PrimeX = base5PrimeX*Math.cos(Math.PI*2/3) - base5PrimeY*Math.sin(Math.PI*2/3);
-  const rotated5PrimeY = base5PrimeX*Math.sin(Math.PI*2/3) + base5PrimeY*Math.cos(Math.PI*2/3);
+  const rotated5PrimeX = base5PrimeX * Math.cos(Math.PI * 2 / 3) - base5PrimeY * Math.sin(Math.PI * 2 / 3);
+  const rotated5PrimeY = base5PrimeX * Math.sin(Math.PI * 2 / 3) + base5PrimeY * Math.cos(Math.PI * 2 / 3);
 
   const dx = base5PrimeX - base3PrimeX;
   const dy = base5PrimeY - base3PrimeY;
   const dxRotated = rotated5PrimeX - base3PrimeX;
   const dyRotated = rotated5PrimeY - base3PrimeY;
 
-  if (Math.sqrt(dyRotated*dyRotated + dxRotated*dxRotated) >= Math.sqrt(dy*dy + dx*dx)) {
+  if (Math.sqrt(dyRotated * dyRotated + dxRotated * dxRotated) >= Math.sqrt(dy * dy + dx * dx)) {
     coordinates.x[indexFivePrime] = rotated5PrimeX + xShift;
     coordinates.y[indexFivePrime] = rotated5PrimeY + yShift;
   }
 }
 
-function extractAtomsBondsNumbersV3000(molBlock: string): {natom: number, nbond: number} {
+function extractAtomsBondsNumbersV3000(molBlock: string): { natom: number, nbond: number } {
   molBlock = molBlock.replaceAll('\r', ''); //equalize old and new sdf standards
   let index = molBlock.indexOf('COUNTS') + 7; // V3000 index for atoms and bonds number
   let indexEnd = molBlock.indexOf(' ', index);
@@ -602,7 +600,7 @@ function extractAtomsBondsNumbersV3000(molBlock: string): {natom: number, nbond:
   return {natom: atomsNumber, nbond: bondsNumber};
 }
 
-function extractAtomDataV3000(molBlock: string) {
+export function extractAtomDataV3000(molBlock: string) {
   const numbers = extractAtomsBondsNumbersV3000(molBlock);
   let index = molBlock.indexOf('M  V30 BEGIN ATOM'); // V3000 index for atoms coordinates
   index = molBlock.indexOf('\n', index);

package/src/utils/parse.ts

@@ -0,0 +1,27 @@
+export const CELL_STRUCTURE = {
+  DUPLEX: {
+    BEFORE_SS: 'SS ',
+    BEFORE_AS: '\r\nAS ',
+  },
+  TRIPLEX_OR_DIMER: {
+    BEFORE_SS: 'SS ',
+    BEFORE_AS1: '\r\nAS1 ',
+    BEFORE_AS2: '\r\nAS2 ',
+  },
+};
+
+export function parseStrandsFromDuplexCell(s: string): { SS: string, AS: string } {
+  const arr = s
+    .slice(CELL_STRUCTURE.DUPLEX.BEFORE_SS.length)
+    .split(CELL_STRUCTURE.DUPLEX.BEFORE_AS);
+  return {SS: arr[0], AS: arr[1]};
+}
+
+export function parseStrandsFromTriplexOrDimerCell(s: string): { SS: string, AS1: string, AS2: string } {
+  const arr1 = s
+    .slice(CELL_STRUCTURE.TRIPLEX_OR_DIMER.BEFORE_SS.length)
+    .split(CELL_STRUCTURE.TRIPLEX_OR_DIMER.BEFORE_AS1);
+  const arr2 = arr1[1]
+    .split(CELL_STRUCTURE.TRIPLEX_OR_DIMER.BEFORE_AS2);
+  return {SS: arr1[0], AS1: arr2[0], AS2: arr2[1]};
+}

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 '../helpers';
+import {parseStrandsFromDuplexCell, parseStrandsFromTriplexOrDimerCell} from './parse';
+import {isValidSequence} from '../structures-works/sequence-codes-tools';
+import {batchMolWeight, molecularWeight, saltMass, saltMolWeigth} from '../autostart/calculations';
+import {weightsObj} from '../structures-works/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 '../helpers';
+import * as grok from 'datagrok-api/grok';
+import {SYNTHESIZERS} from '../structures-works/map';
+import {sequenceToMolV3000} from '../structures-works/from-monomers';
+import {parseStrandsFromDuplexCell, parseStrandsFromTriplexOrDimerCell} from './parse';
+import {linkStrandsV3000} from '../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/{test-SequenceTranslator-e8c06047b7e7-eb4db608.html → test-SequenceTranslator-6288c2fbe346-cce4ac1d.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=e8c06047b7e7. Commit eb4db608.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=6288c2fbe346. Commit cce4ac1d.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ 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=e8c06047b7e7. Commit eb4db608.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-11-22 12:28:58</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">15.587s</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">3.952s</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 cce4ac1d.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-12-12 14:55:37</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">21.067s</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">6.276s</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
@@ -242,17 +242,17 @@ header {
     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
+    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 : 0 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
+Test result : Success : 0 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu : OK
 Test result : Success : 0 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
 Test result : Success : 1 : SequenceTranslator.sequence-translator.acacacsacsac : 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 : 0 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : 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)