@datagrok/sequence-translator 1.0.11 → 1.0.13

package/src/helpers.ts

@@ -0,0 +1,28 @@
+import * as DG from 'datagrok-api/dg';
+
+export function sortByStringLengthInDescendingOrder(array: string[]): string[] {
+  return array.sort(function(a, b) {return b.length - a.length;});
+}
+  
+export function stringify(items: string[]): string {
+  return '["' + items.join('", "') + '"]';
+}
+
+export function download(name: string, href: string): void {
+  const element = document.createElement('a');
+  element.setAttribute('href', 'data:text/plain;charset=utf-8,' + href);
+  element.setAttribute('download', name);
+  element.click();
+}
+
+export function removeEmptyRows(t: DG.DataFrame, colToCheck: DG.Column): DG.DataFrame {
+  for (let i = t.rowCount - 1; i > -1; i--) {
+    if (colToCheck.getString(i) == '')
+      t.rows.removeAt(i, 1, false);
+  }
+  return t;
+}
+
+export function differenceOfTwoArrays(a: string[], b: string[]): string[] {
+  return a.filter((x) => !b.includes(x));
+}

package/src/main/main-view.ts

@@ -5,6 +5,7 @@ import {convertSequence, undefinedInputSequence, isValidSequence} from '../struc
 import {map, MODIFICATIONS} from '../structures-works/map';
 import {sequenceToSmiles, sequenceToMolV3000} from '../structures-works/from-monomers';
 import $ from 'cash-dom';
+import {download} from '../helpers';
 
 const defaultInput = 'fAmCmGmAmCpsmU';
 const sequenceWasCopied = 'Copied';
@@ -15,7 +16,6 @@ export function mainView() {
     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);
@@ -27,13 +27,6 @@ export function mainView() {
         const indexOfFirstNotValidChar = ('indexOfFirstNotValidChar' in outputSequenceObj) ?
           JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).indexOfFirstNotValidChar :
           -1;
-        if ('indexOfFirstNotValidChar' in outputSequenceObj) {
-          const indexOfFirstNotValidChar = ('indexOfFirstNotValidChar' in outputSequenceObj) ?
-            JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).indexOfFirstNotValidChar :
-            -1;
-          if (indexOfFirstNotValidChar != -1)
-            errorsExist = true;
-        }
 
         tableRows.push({
           'key': key,
@@ -51,20 +44,6 @@ export function mainView() {
         });
       }
 
-      if (errorsExist) {
-        const synthesizer = JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).synthesizer.slice(0, -6);
-        asoGapmersGrid.onCellPrepare(function(gc) {
-          gc.style.backColor = (gc.gridColumn.name == synthesizer) ? 0xFFF00000 : 0xFFFFFFFF;
-        });
-        omeAndFluoroGrid.onCellPrepare(function(gc) {
-          gc.style.backColor = (gc.gridColumn.name == synthesizer) ? 0xFFF00000 : 0xFFFFFFFF;
-        });
-        switchInput.enabled = true;
-      } else {
-        asoGapmersGrid.onCellPrepare(function(gc) {gc.style.backColor = 0xFFFFFFFF;});
-        omeAndFluoroGrid.onCellPrepare(function(gc) {gc.style.backColor = 0xFFFFFFFF;});
-      }
-
       outputTableDiv.append(
         ui.div([
           DG.HtmlTable.create(tableRows, (item: { key: string; value: string; }) =>
@@ -108,46 +87,43 @@ export function mainView() {
     updateTableAndMolecule(sequence, inputFormatChoiceInput.value!);
   });
 
-  const asoDf = DG.DataFrame.fromObjects([
-    {'Name': '2\'MOE-5Me-rU', 'BioSpring': '5', 'Janssen GCRS': 'moeT'},
-    {'Name': '2\'MOE-rA', 'BioSpring': '6', 'Janssen GCRS': 'moeA'},
-    {'Name': '2\'MOE-5Me-rC', 'BioSpring': '7', 'Janssen GCRS': 'moe5mC'},
-    {'Name': '2\'MOE-rG', 'BioSpring': '8', 'Janssen GCRS': 'moeG'},
-    {'Name': '5-Methyl-dC', 'BioSpring': '9', 'Janssen GCRS': '5mC'},
-    {'Name': 'ps linkage', 'BioSpring': '*', 'Janssen GCRS': 'ps'},
-    {'Name': 'dA', 'BioSpring': 'A', 'Janssen GCRS': 'A, dA'},
-    {'Name': 'dC', 'BioSpring': 'C', 'Janssen GCRS': 'C, dC'},
-    {'Name': 'dG', 'BioSpring': 'G', 'Janssen GCRS': 'G, dG'},
-    {'Name': 'dT', 'BioSpring': 'T', 'Janssen GCRS': 'T, dT'},
-    {'Name': 'rA', 'BioSpring': '', 'Janssen GCRS': 'rA'},
-    {'Name': 'rC', 'BioSpring': '', 'Janssen GCRS': 'rC'},
-    {'Name': 'rG', 'BioSpring': '', 'Janssen GCRS': 'rG'},
-    {'Name': 'rU', 'BioSpring': '', 'Janssen GCRS': 'rU'},
-  ])!;
-  const asoGapmersGrid = DG.Viewer.grid(asoDf, {showRowHeader: false, showCellTooltip: false});
-
-  asoDf.onCurrentCellChanged.subscribe((_) => {
-    navigator.clipboard.writeText(asoDf.currentCell.value).then(() => grok.shell.info('Copied'));
-  });
+  const asoGapmersGrid = DG.Viewer.grid(
+    DG.DataFrame.fromObjects([
+      {'Name': '2\'MOE-5Me-rU', 'BioSpring': '5', 'Janssen GCRS': 'moeT'},
+      {'Name': '2\'MOE-rA', 'BioSpring': '6', 'Janssen GCRS': 'moeA'},
+      {'Name': '2\'MOE-5Me-rC', 'BioSpring': '7', 'Janssen GCRS': 'moe5mC'},
+      {'Name': '2\'MOE-rG', 'BioSpring': '8', 'Janssen GCRS': 'moeG'},
+      {'Name': '5-Methyl-dC', 'BioSpring': '9', 'Janssen GCRS': '5mC'},
+      {'Name': 'ps linkage', 'BioSpring': '*', 'Janssen GCRS': 'ps'},
+      {'Name': 'dA', 'BioSpring': 'A', 'Janssen GCRS': 'A, dA'},
+      {'Name': 'dC', 'BioSpring': 'C', 'Janssen GCRS': 'C, dC'},
+      {'Name': 'dG', 'BioSpring': 'G', 'Janssen GCRS': 'G, dG'},
+      {'Name': 'dT', 'BioSpring': 'T', 'Janssen GCRS': 'T, dT'},
+      {'Name': 'rA', 'BioSpring': '', 'Janssen GCRS': 'rA'},
+      {'Name': 'rC', 'BioSpring': '', 'Janssen GCRS': 'rC'},
+      {'Name': 'rG', 'BioSpring': '', 'Janssen GCRS': 'rG'},
+      {'Name': 'rU', 'BioSpring': '', 'Janssen GCRS': 'rU'},
+    ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
+  );
 
   const omeAndFluoroGrid = DG.Viewer.grid(
-      DG.DataFrame.fromObjects([
-        {'Name': '2\'-fluoro-U', 'BioSpring': '1', 'Axolabs': 'Uf', 'Janssen GCRS': 'fU'},
-        {'Name': '2\'-fluoro-A', 'BioSpring': '2', 'Axolabs': 'Af', 'Janssen GCRS': 'fA'},
-        {'Name': '2\'-fluoro-C', 'BioSpring': '3', 'Axolabs': 'Cf', 'Janssen GCRS': 'fC'},
-        {'Name': '2\'-fluoro-G', 'BioSpring': '4', 'Axolabs': 'Gf', 'Janssen GCRS': 'fG'},
-        {'Name': '2\'OMe-rU', 'BioSpring': '5', 'Axolabs': 'u', 'Janssen GCRS': 'mU'},
-        {'Name': '2\'OMe-rA', 'BioSpring': '6', 'Axolabs': 'a', 'Janssen GCRS': 'mA'},
-        {'Name': '2\'OMe-rC', 'BioSpring': '7', 'Axolabs': 'c', 'Janssen GCRS': 'mC'},
-        {'Name': '2\'OMe-rG', 'BioSpring': '8', 'Axolabs': 'g', 'Janssen GCRS': 'mG'},
-        {'Name': 'ps linkage', 'BioSpring': '*', 'Axolabs': 's', 'Janssen GCRS': 'ps'},
-      ])!, {showRowHeader: false, showCellTooltip: false},
+    DG.DataFrame.fromObjects([
+      {'Name': '2\'-fluoro-U', 'BioSpring': '1', 'Axolabs': 'Uf', 'Janssen GCRS': 'fU'},
+      {'Name': '2\'-fluoro-A', 'BioSpring': '2', 'Axolabs': 'Af', 'Janssen GCRS': 'fA'},
+      {'Name': '2\'-fluoro-C', 'BioSpring': '3', 'Axolabs': 'Cf', 'Janssen GCRS': 'fC'},
+      {'Name': '2\'-fluoro-G', 'BioSpring': '4', 'Axolabs': 'Gf', 'Janssen GCRS': 'fG'},
+      {'Name': '2\'OMe-rU', 'BioSpring': '5', 'Axolabs': 'u', 'Janssen GCRS': 'mU'},
+      {'Name': '2\'OMe-rA', 'BioSpring': '6', 'Axolabs': 'a', 'Janssen GCRS': 'mA'},
+      {'Name': '2\'OMe-rC', 'BioSpring': '7', 'Axolabs': 'c', 'Janssen GCRS': 'mC'},
+      {'Name': '2\'OMe-rG', 'BioSpring': '8', 'Axolabs': 'g', 'Janssen GCRS': 'mG'},
+      {'Name': 'ps linkage', 'BioSpring': '*', 'Axolabs': 's', 'Janssen GCRS': 'ps'},
+    ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
   );
 
   const overhangModificationsGrid = DG.Viewer.grid(
       DG.DataFrame.fromColumns([
         DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
-      ])!, {showRowHeader: false, showCellTooltip: false},
+      ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
   );
   updateTableAndMolecule(defaultInput, inputFormatChoiceInput.value!);
 
@@ -175,27 +151,29 @@ export function mainView() {
     $(codesTablesDiv).hide(),
   );
 
+  const downloadMolFileIcon = ui.iconFA('download', () => {
+    const clearSequence = inputSequenceField.value.replace(/\s/g, '');
+    const result = sequenceToMolV3000(clearSequence, false, false, inputFormatChoiceInput.value!);
+    download(clearSequence + '.mol', encodeURIComponent(result));
+  }, 'Save .mol file');
+
+  const copySmilesIcon = ui.iconFA('copy', () => {
+    navigator.clipboard.writeText(
+      sequenceToSmiles(inputSequenceField.value.replace(/\s/g, ''), false, inputFormatChoiceInput.value!),
+    ).then(() => grok.shell.info(sequenceWasCopied));
+  }, 'Copy SMILES');
+
   const topPanel = [
-    ui.iconFA('download', () => {
-      const result = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, false,
-        inputFormatChoiceInput.value!);
-      const element = document.createElement('a');
-      element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
-      element.setAttribute('download', inputSequenceField.value.replace(/\s/g, '') + '.mol');
-      element.click();
-    }, 'Save .mol file'),
-    ui.iconFA('copy', () => {
-      navigator.clipboard.writeText(
-        sequenceToSmiles(inputSequenceField.value.replace(/\s/g, ''), false, inputFormatChoiceInput.value!))
-        .then(() => grok.shell.info(sequenceWasCopied));
-    }, 'Copy SMILES'),
+    downloadMolFileIcon,
+    copySmilesIcon,
     switchInput.root,
   ];
 
   const v = grok.shell.v;
   const tabControl = grok.shell.sidebar;
-  tabControl.onTabChanged.subscribe((_) =>
-    v.setRibbonPanels([(tabControl.currentPane.name == 'MAIN') ? topPanel : []]));
+  tabControl.onTabChanged.subscribe((_) => {
+    v.setRibbonPanels([(tabControl.currentPane.name == 'MAIN') ? topPanel : []]);
+  });
   v.setRibbonPanels([topPanel]);
 
   return ui.box(

package/src/package.ts

@@ -17,14 +17,13 @@ export function sequenceTranslator(): void {
   windows.showToolbox = false;
   windows.showHelp = false;
 
-  const v = grok.shell.newView('Sequence Translator', [
-    ui.tabControl({
-      'MAIN': mainView(),
-      'AXOLABS': defineAxolabsPattern(),
-      'SDF': saveSenseAntiSense(),
-    }),
-  ]);
+  const v = grok.shell.newView('Sequence Translator', []);
   v.box = true;
+  v.append(ui.tabControl({
+    'MAIN': mainView(),
+    'AXOLABS': defineAxolabsPattern(),
+    'SDF': saveSenseAntiSense(),
+  }));
 }
 
 //tags: autostart

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

@@ -1,6 +1,7 @@
 import {map, stadardPhosphateLinkSmiles, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, delimiter} from './map';
 import {isValidSequence} from './sequence-codes-tools';
 import {getNucleotidesMol} from './mol-transformations';
+import {sortByStringLengthInDescendingOrder} from '../helpers';
 
 export function sequenceToMolV3000(sequence: string, inverted: boolean = false, oclRender: boolean = false,
   format: string): string {
@@ -108,7 +109,3 @@ function getObjectWithCodesAndSmiles(sequence: string, format: string) {
     obj['g'] = map[SYNTHESIZERS.AXOLABS][TECHNOLOGIES.SI_RNA]['g'].SMILES;
   return obj;
 }
-
-function sortByStringLengthInDescendingOrder(array: string[]): string[] {
-  return array.sort(function(a: string, b: string) {return b.length - a.length;});
-}

package/src/structures-works/map.ts

@@ -1,5 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import {getAllCodesOfSynthesizer} from './sequence-codes-tools';
+import {differenceOfTwoArrays} from '../helpers';
 
 export const delimiter = ';';
 export const SYNTHESIZERS = {
@@ -16,29 +17,6 @@ export const TECHNOLOGIES = {
   ASO_GAPMERS: 'For ASO Gapmers',
   SI_RNA: 'For 2\'-OMe and 2\'-F modified siRNA',
 };
-export const COL_NAMES = {
-  CHEMISTRY: 'Chemistry',
-  NUMBER: 'Number',
-  TYPE: 'Type',
-  CHEMISTRY_NAME: 'Chemistry Name',
-  INTERNAL_COMPOUND_ID: 'Internal compound ID',
-  IDP: 'IDP',
-  SEQUENCE: 'Sequence',
-  COMPOUND_NAME: 'Compound Name',
-  COMPOUND_COMMENTS: 'Compound Comments',
-  SALT: 'Salt',
-  EQUIVALENTS: 'Equivalents',
-  PURITY: 'Purity',
-  CPD_MW: 'Cpd MW',
-  SALT_MOL_WEIGHT: 'Salt MW',
-  SALT_MASS: 'Salt mass',
-  BATCH_MW: 'Batch MW',
-  SOURCE: 'Source',
-  ICD: 'ICD',
-  OWNER: 'Owner',
-};
-// interface CODES {
-// }
 export const MODIFICATIONS: {[index: string]: {molecularWeight: number, left: string, right: string}} = {
   '(invabasic)': {
     molecularWeight: 118.13,
@@ -58,7 +36,7 @@ export const MODIFICATIONS: {[index: string]: {molecularWeight: number, left: st
 export const stadardPhosphateLinkSmiles = 'OP(=O)(O)O';
 export const map: {[synthesizer: string]:
   {[technology: string]: {[code: string]:
-    {'name'?: string, 'weight'?: number, 'normalized'?: string, 'SMILES': string}}}} = {
+    {'name': string, 'weight': number, 'normalized': string, 'SMILES': string}}}} = {
       'Raw Nucleotides': {
         'DNA': {
           'A': {
@@ -724,12 +702,20 @@ fU, fU
 /J-CbCS/, J-CbCS
 /J-MtCD/, J-MtCD`;
 
-function differenceOfTwoArrays(a: string[], b: string[]): string[] {
-  return a.filter((x) => !b.includes(x));
-}
 
 const codesWithSmiles = getAllCodesOfSynthesizer(SYNTHESIZERS.GCRS);
 const allGcrsCodes = DG.DataFrame.fromCsv(lcmsToGcrs).getCol('GCRS').toList();
 export const gcrsCodesWithoutSmiles = differenceOfTwoArrays(allGcrsCodes, codesWithSmiles);
 for (const e of gcrsCodesWithoutSmiles)
-  map[SYNTHESIZERS.GCRS]['Others'][e] = {'SMILES': ''};
+  map[SYNTHESIZERS.GCRS]['Others'][e] = {name: '', weight: 0, normalized: '', SMILES: ''};
+
+
+export const weightsObj: {[code: string]: number} = {};
+for (const synthesizer of Object.keys(map)) {
+  for (const technology of Object.keys(map[synthesizer])) {
+    for (const code of Object.keys(map[synthesizer][technology]))
+      weightsObj[code] = map[synthesizer][technology][code].weight;
+  }
+}
+for (const [key, value] of Object.entries(MODIFICATIONS))
+  weightsObj[key] = value.molecularWeight;

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

@@ -564,10 +564,10 @@ export function getNucleotidesMol(smilesCodes: string[]) {
           molBlocks.push(rotateNucleotidesV3000(smilesCodes[i]));
   }
 
-  return linkV3000(molBlocks, false);
+  return linkV3000(molBlocks);
 }
 
-export function linkV3000(molBlocks: string[], twoChains: boolean = false, 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';
@@ -579,18 +579,34 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
   let nbond = 0;
   let xShift = 0;
 
-  if (twoChains && molBlocks.length > 1)
-    molBlocks[1] = invertNucleotidesV3000(molBlocks[1]);
+  // if (twoChains && molBlocks.length > 1)
+  //   molBlocks[1] = invertNucleotidesV3000(molBlocks[1]);
+
+  if (strands.antiStrands.length > 0) {
+    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);
 
   for (let i = 0; i < molBlocks.length; i++) {
+
+    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]);
     const coordinates = extractAtomDataV3000(molBlocks[i]);
 
-    if (twoChains) {
-      const xShiftRight = Math.min(...coordinates.x);
-      const yShift = i == 0 ? Math.min(...coordinates.y) - 1 : Math.max(...coordinates.y) + 1;
+    if (inverted) {
+      const xShiftRight = Math.min(...coordinates.x) - xShift;
+      const yShift = !inverted ? Math.min(...coordinates.y) - 1 : Math.max(...coordinates.y) + 10;
       for (let j = 0; j < coordinates.x.length; j++)
         coordinates.x[j] -= xShiftRight;
       for (let j = 0; j < coordinates.y.length; j++)
@@ -603,7 +619,154 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
     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);
+      const atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
+
+      //rewrite coordinates
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      indexEnd = molBlocks[i].indexOf(' ', index);
+
+      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;
+      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;
+      molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
+
+      index = molBlocks[i].indexOf('\n', index) + 1;
+    }
+
+    const indexAtomsEnd = molBlocks[i].indexOf('M  V30 END ATOM');
+    atomBlock += molBlocks[i].substring(indexAtoms + 1, indexAtomsEnd);
+
+    let indexBonds = molBlocks[i].indexOf('M  V30 BEGIN BOND'); // V3000 index for bonds
+    indexBonds = molBlocks[i].indexOf('\n', indexBonds);
+    index = indexBonds;
+    indexEnd = indexBonds;
+
+    for (let j = 0; j < numbers.nbond; j++) {
+      //rewrite bond number
+      index = molBlocks[i].indexOf('V30', index) + 4;
+      indexEnd = molBlocks[i].indexOf(' ', index);
+      const bondNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + nbond;
+      molBlocks[i] = molBlocks[i].slice(0, index) + bondNumber + molBlocks[i].slice(indexEnd);
+
+      //rewrite atom pair in bond
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      indexEnd = molBlocks[i].indexOf(' ', index);
+      let atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
+      index = molBlocks[i].indexOf(' ', index) + 1;
+      indexEnd = Math.min(molBlocks[i].indexOf('\n', index), molBlocks[i].indexOf(' ', index));
+      atomNumber = parseInt(molBlocks[i].substring(index, indexEnd)) + natom;
+      molBlocks[i] = molBlocks[i].slice(0, index) + atomNumber + molBlocks[i].slice(indexEnd);
+
+      index = molBlocks[i].indexOf('\n', index) + 1;
+    }
+
+    const indexBondEnd = molBlocks[i].indexOf('M  V30 END BOND');
+    bondBlock += molBlocks[i].substring(indexBonds + 1, indexBondEnd);
+
+    let indexCollection = molBlocks[i].indexOf('M  V30 MDLV30/STEABS ATOMS=('); // V3000 index for collections
+
+    while (indexCollection != -1) {
+      indexCollection += 28;
+      const collectionEnd = molBlocks[i].indexOf(')', indexCollection);
+      const collectionEntries = molBlocks[i].substring(indexCollection, collectionEnd).split(' ').slice(1);
+      collectionEntries.forEach((e) => {
+        collection.push(parseInt(e) + natom);
+      });
+      indexCollection = collectionEnd;
+      indexCollection = molBlocks[i].indexOf('M  V30 MDLV30/STEABS ATOMS=(', indexCollection);
+    }
+
+    natom += true ? numbers.natom : numbers.natom - 1;
+    nbond += numbers.nbond;
+    xShift += Math.max(...coordinates.x) + 1;//twoChains ? 0 : coordinates.x[numbers.natom - 1] - coordinates.x[0];
+  }
+
+  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;
+      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++;
+  macroMolBlock += 'M  V30 COUNTS ' + natom + ' ' + nbond + ' 0 0 0\n';
+  macroMolBlock += 'M  V30 BEGIN ATOM\n';
+  macroMolBlock += atomBlock;
+  macroMolBlock += 'M  V30 END ATOM\n';
+  macroMolBlock += 'M  V30 BEGIN BOND\n';
+  macroMolBlock += bondBlock;
+  macroMolBlock += 'M  V30 END BOND\n';
+  if(useChirality){
+    macroMolBlock += 'M  V30 BEGIN COLLECTION\n';
+    macroMolBlock += collectionBlock;
+    macroMolBlock += 'M  V30 END COLLECTION\n';
+  } else
+    macroMolBlock = macroMolBlock.replace(/ CFG=\d/g, ' ');
+
+  macroMolBlock += 'M  V30 END CTAB\n';
+  macroMolBlock += 'M  END';
+
+  return macroMolBlock;
+}
+
+export function linkV3000(molBlocks: 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';
+  let atomBlock = '';
+  let bondBlock = '';
+  let collectionBlock = '';
+  const collection: number [] = [];
+  let natom = 0;
+  let nbond = 0;
+  let xShift = 0;
+
+  for (let i = 0; i < molBlocks.length; i++) {
+    molBlocks[i] = molBlocks[i].replaceAll('(-\nM  V30 ', '(')
+      .replaceAll('-\nM  V30 ', '').replaceAll(' )', ')');
+    const numbers = extractAtomsBondsNumbersV3000(molBlocks[i]);
+    const coordinates = extractAtomDataV3000(molBlocks[i]);
+
+    let indexAtoms = molBlocks[i].indexOf('M  V30 BEGIN ATOM'); // V3000 index for atoms coordinates
+    indexAtoms = molBlocks[i].indexOf('\n', indexAtoms);
+    let index = indexAtoms;
+    let indexEnd = indexAtoms;
+
+    for (let j = 0; j < numbers.natom; j++) {
+      if (coordinates.atomIndex[j] != 1 || i == 0) {
         //rewrite atom number
         index = molBlocks[i].indexOf('V30', index) + 4;
         indexEnd = molBlocks[i].indexOf(' ', index);
@@ -615,16 +778,14 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
         index = molBlocks[i].indexOf(' ', index) + 1;
         indexEnd = molBlocks[i].indexOf(' ', index);
 
-        const totalShift = twoChains ? 0 : xShift - coordinates.x[0];
-        let coordinate = twoChains ?
-          Math.round(10000*coordinates.x[j])/10000 :
+        const totalShift = xShift - coordinates.x[0];
+        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 = twoChains ?
-          Math.round(10000*coordinates.y[j])/10000 :
+        coordinate = 
           Math.round(10000*(parseFloat(molBlocks[i].substring(index, indexEnd))))/10000;
         molBlocks[i] = molBlocks[i].slice(0, index) + coordinate + molBlocks[i].slice(indexEnd);
 
@@ -681,9 +842,9 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
       indexCollection = molBlocks[i].indexOf('M  V30 MDLV30/STEABS ATOMS=(', indexCollection);
     }
 
-    natom += twoChains ? numbers.natom : numbers.natom - 1;
+    natom += numbers.natom - 1;
     nbond += numbers.nbond;
-    xShift += twoChains ? 0 : coordinates.x[numbers.natom - 1] - coordinates.x[0];
+    xShift += coordinates.x[numbers.natom - 1] - coordinates.x[0];
   }
 
   const entries = 4;
@@ -710,7 +871,7 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, useCh
   //}
 
   //generate file
-  twoChains? natom : natom++;
+  natom++;
   macroMolBlock += 'M  V30 COUNTS ' + natom + ' ' + nbond + ' 0 0 0\n';
   macroMolBlock += 'M  V30 BEGIN ATOM\n';
   macroMolBlock += atomBlock;

package/src/structures-works/save-sense-antisense.ts

@@ -1,48 +1,67 @@
 import * as ui from 'datagrok-api/ui';
+import {download} from '../helpers';
 import {sequenceToMolV3000} from '../structures-works/from-monomers';
-import {linkV3000} from '../structures-works/mol-transformations';
+import {linkStrandsV3000} from '../structures-works/mol-transformations';
 import {getFormat} from '../structures-works/sequence-codes-tools';
 
-export function saveSdf(as: string, ss: string, oneEntity: boolean, useChirality: boolean, invertSS: boolean, invertAS: boolean) {
+export function saveSdf(as: string, ss: string, 
+                        oneEntity: boolean, useChirality: boolean, 
+                        invertSS: boolean, invertAS: boolean,
+                        as2: string | null = null, invertAS2: boolean | null) {
   const formatAs = getFormat(as);
   const formatSs = getFormat(ss);
+  let formatAs2: string | null = null;
+  let molAS2: string | null = null;
+
   const molSS = sequenceToMolV3000(ss, invertSS, false, formatSs!);
   const molAS = sequenceToMolV3000(as, invertAS, false, formatAs!);
+
+  if (as2 != null && as2 != '') {
+    formatAs2 = getFormat(as2!);
+    molAS2 = sequenceToMolV3000(as2, invertAS2!, false, formatAs2!);
+  }
+
   let result: string;
-  if (oneEntity)
-    result = linkV3000([molSS, molAS], true, useChirality) + '\n$$$$\n';
-  else {
+  if (oneEntity) {
+    const antiStrands = molAS2 == null ? [molAS] : [molAS, molAS2];
+    result = linkStrandsV3000({senseStrands: [molSS], antiStrands: antiStrands}, useChirality) + '\n$$$$\n';
+  
+  } else {
     result =
     molSS + '\n' +
     `> <Sequence>\nSense Strand\n$$$$\n` +
     molAS + '\n' +
     `> <Sequence>\nAnti Sense\n$$$$\n`;
-  }
 
-  const element = document.createElement('a');
-  element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
-  element.setAttribute('download', ss.replace(/\s/g, '') + '.sdf');
-  element.click();
+    if (molAS2)
+      result += molAS2+ '\n' +
+      `> <Sequence>\nAnti Sense 2\n$$$$\n`;
+  }
+  download(ss.replace(/\s/g, '') + '.sdf', encodeURIComponent(result));
 }
 
 export function saveSenseAntiSense() {
   const moleculeSvgDiv = ui.block([]);
   const ssInput = ui.textInput('Sense Strand', '');
   const asInput = ui.textInput('Anti Sense', '');
+  const asInput2 = ui.textInput('Anti Sense 2', '');
   const straight = "5 prime -> 3 prime";
   const inverse = "3 prime -> 5 prime";
   let ssInverse = false;
   let asInverse = false;
+  let as2Inverse = false;
 
   const changeSense = ui.choiceInput('SS direction', straight, [straight, inverse]);
   changeSense.onChanged(() => {ssInverse = changeSense.value == inverse;});
   const changeAntiSense = ui.choiceInput('AS direction', straight, [straight, inverse]);
   changeAntiSense.onChanged(() => {asInverse = changeAntiSense.value == inverse;});
+  const changeAntiSense2 = ui.choiceInput('AS 2 direction', straight, [straight, inverse]);
+  changeAntiSense2.onChanged(() => {asInverse = changeAntiSense.value == inverse;});
 
   const saveOption = ui.switchInput('Save as one entity', true);
   const chirality = ui.switchInput('Use chiral', true);
   const saveBtn = ui.button('Save SDF', () =>
-    saveSdf(asInput.value, ssInput.value, saveOption.value, chirality.value, ssInverse, asInverse));
+    saveSdf(asInput.value, ssInput.value, saveOption.value, chirality.value, ssInverse, asInverse, asInput2.value, as2Inverse));
 
   const saveSection = ui.panel([
     ui.div([
@@ -51,9 +70,11 @@ export function saveSenseAntiSense() {
         ui.divV([
           ssInput,
           asInput,
+          asInput2,
           ui.div([changeSense], {style: {width: '40'}}),
           changeSense,
           changeAntiSense,
+          changeAntiSense2,
           saveOption,
           chirality,
           ui.buttonsInput([saveBtn]),