@datagrok/sequence-translator 1.0.3 → 1.0.6

package/src/package.ts

@@ -1,27 +1,13 @@
-/* Do not change these import lines. Datagrok will import API library in exactly the same manner */
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import * as OCL from 'openchemlib/full.js';
-import $ from 'cash-dom';
-import {defineAxolabsPattern} from './defineAxolabsPattern';
+import {autostartOligoSdFileSubscription} from './autostart/registration';
+import {defineAxolabsPattern} from './axolabs/define-pattern';
 import {saveSenseAntiSense} from './structures-works/save-sense-antisense';
-import {sequenceToSmiles, sequenceToMolV3000} from './structures-works/from-monomers';
-import {convertSequence, undefinedInputSequence, isValidSequence, getFormat} from
-  './structures-works/sequence-codes-tools';
-import {map, COL_NAMES, MODIFICATIONS} from './structures-works/map';
-import {siRnaAxolabsToGcrs} from './structures-works/converters';
-import {SALTS_CSV} from './salts';
-import {USERS_CSV} from './users';
-import {ICDS} from './ICDs';
-import {SOURCES} from './sources';
-import {IDPS} from './IDPs';
+import {mainView} from './main/main-view';
 
 export const _package = new DG.Package();
 
-const defaultInput = 'fAmCmGmAmCpsmU';
-const sequenceWasCopied = 'Copied';
-const tooltipSequence = 'Copy sequence';
 
 //name: Sequence Translator
 //tags: app
@@ -31,380 +17,15 @@ export function sequenceTranslator(): void {
   windows.showToolbox = false;
   windows.showHelp = false;
 
-  function updateTableAndMolecule(sequence: string, inputFormat: string, isSet: boolean): void {
-    moleculeSvgDiv.innerHTML = '';
-    outputTableDiv.innerHTML = '';
-    const pi = DG.TaskBarProgressIndicator.create('Rendering table and molecule...');
-    let errorsExist = false;
-    try {
-      sequence = sequence.replace(/\s/g, '');
-      const output = isValidSequence(sequence, null);
-      if (isSet)
-        output.synthesizer = [inputFormat];
-      inputFormatChoiceInput.value = output.synthesizer![0];
-      const outputSequenceObj = convertSequence(sequence, output);
-      const tableRows = [];
-
-      for (const key of Object.keys(outputSequenceObj).slice(1)) {
-        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,
-          'value': ('indexOfFirstNotValidChar' in outputSequenceObj) ?
-            ui.divH([
-              ui.divText(sequence.slice(0, indexOfFirstNotValidChar), {style: {color: 'grey'}}),
-              ui.tooltip.bind(
-                ui.divText(sequence.slice(indexOfFirstNotValidChar), {style: {color: 'red'}}),
-                'Expected format: ' + JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).synthesizer +
-                '. See tables with valid codes on the right',
-              ),
-            ]) : //@ts-ignore
-            ui.link(outputSequenceObj[key], () => navigator.clipboard.writeText(outputSequenceObj[key])
-              .then(() => grok.shell.info(sequenceWasCopied)), tooltipSequence, ''),
-        });
-      }
-
-      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; }) =>
-            [item.key, item.value], ['Code', 'Sequence']).root,
-        ]),
-      );
-
-      if (outputSequenceObj.type != undefinedInputSequence && outputSequenceObj.Error != undefinedInputSequence) {
-        const canvas = ui.canvas(300, 170);
-        canvas.addEventListener('click', () => {
-          const canv = ui.canvas($(window).width(), $(window).height());
-          const mol = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, true,
-          output.synthesizer![0]);
-          // @ts-ignore
-          OCL.StructureView.drawMolecule(canv, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
-          ui.dialog('Molecule: ' + inputSequenceField.value)
-            .add(canv)
-            .showModal(true);
-        });
-        $(canvas).on('mouseover', () => $(canvas).css('cursor', 'zoom-in'));
-        $(canvas).on('mouseout', () => $(canvas).css('cursor', 'default'));
-        const mol = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, true,
-        output.synthesizer![0]);
-        // @ts-ignore
-        OCL.StructureView.drawMolecule(canvas, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
-        moleculeSvgDiv.append(canvas);
-      } else
-        moleculeSvgDiv.innerHTML = '';
-    } finally {
-      pi.close();
-    }
-  }
-
-  const inputFormatChoiceInput = ui.choiceInput(
-    'Input format: ', 'Janssen GCRS Codes', Object.keys(map), (format: string) => {
-      updateTableAndMolecule(inputSequenceField.value.replace(/\s/g, ''), format, true);
-    });
-  const moleculeSvgDiv = ui.block([]);
-  const outputTableDiv = ui.div([]);
-  const inputSequenceField = ui.textInput('', defaultInput, (sequence: string) => updateTableAndMolecule(sequence,
-    inputFormatChoiceInput.value!, false));
-
-  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 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},
-  );
-
-  const overhangModificationsGrid = DG.Viewer.grid(
-    DG.DataFrame.fromColumns([
-      DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
-    ])!, {showRowHeader: false, showCellTooltip: false},
-  );
-  updateTableAndMolecule(defaultInput, inputFormatChoiceInput.value!, true);
-
-  const appMainDescription = ui.info([
-    ui.divText('How to convert one sequence:', {style: {'font-weight': 'bolder'}}),
-    ui.divText('Paste sequence into the text field below'),
-    ui.divText('\n How to convert many sequences:', {style: {'font-weight': 'bolder'}}),
-    ui.divText('1. Drag & drop an Excel or CSV file with sequences into Datagrok'),
-    ui.divText('2. Right-click on the column header, then see the \'Convert\' menu'),
-    ui.divText('This will add the result column to the right of the table'),
-  ], 'Convert oligonucleotide sequences between Nucleotides, BioSpring, Axolabs, Mermade 12 and GCRS representations.');
-
-  const codesTablesDiv = ui.splitV([
-    ui.box(ui.h2('ASO Gapmers'), {style: {maxHeight: '40px'}}),
-    asoGapmersGrid.root,
-    ui.box(ui.h2('2\'-OMe and 2\'-F siRNA'), {style: {maxHeight: '40px'}}),
-    omeAndFluoroGrid.root,
-    ui.box(ui.h2('Overhang modifications'), {style: {maxHeight: '40px'}}),
-    overhangModificationsGrid.root,
-  ], {style: {maxWidth: '350px'}});
-
-  const tabControl = ui.tabControl({
-    'MAIN': ui.box(
-      ui.splitH([
-        ui.splitV([
-          ui.panel([
-            appMainDescription,
-            ui.div([
-              ui.h1('Input sequence'),
-              ui.div([
-                inputSequenceField.root,
-              ], 'input-base'),
-            ], 'inputSequence'),
-            ui.div([inputFormatChoiceInput], {style: {padding: '5px 0'}}),
-            ui.block([
-              ui.h1('Output'),
-              outputTableDiv,
-            ]),
-            moleculeSvgDiv,
-          ], 'sequence'),
-        ]),
-        codesTablesDiv,
-      ], {style: {height: '100%', width: '100%'}}),
-    ),
-    'AXOLABS': defineAxolabsPattern(),
-    'SDF': saveSenseAntiSense(),
-  });
-
-  $(codesTablesDiv).hide();
-
-  const v = grok.shell.newView('Sequence Translator', [tabControl]);
+  const v = grok.shell.newView('Sequence Translator', [
+    ui.tabControl({
+      'MAIN': mainView(),
+      'AXOLABS': defineAxolabsPattern(),
+      'SDF': saveSenseAntiSense(),
+    }),
+  ]);
   v.box = true;
-
-  const switchInput = ui.switchInput('Codes', false, (v: boolean) => (v) ?
-    $(codesTablesDiv).show() :
-    $(codesTablesDiv).hide(),
-  );
-
-  const topPanel = [
-    ui.iconFA('download', () => {
-      const result = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, false,
-        inputFormatChoiceInput.value!);
-      const element = document.createElement('a');
-      element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
-      element.setAttribute('download', inputSequenceField.value.replace(/\s/g, '') + '.mol');
-      element.click();
-    }, 'Save .mol file'),
-    ui.iconFA('copy', () => {
-      navigator.clipboard.writeText(
-        sequenceToSmiles(inputSequenceField.value.replace(/\s/g, ''), false, inputFormatChoiceInput.value!))
-        .then(() => grok.shell.info(sequenceWasCopied));
-    }, 'Copy SMILES'),
-    switchInput.root,
-  ];
-
-  tabControl.onTabChanged.subscribe((_) =>
-    v.setRibbonPanels([(tabControl.currentPane.name == 'MAIN') ? topPanel : []]));
-  v.setRibbonPanels([topPanel]);
-}
-
-async function saveTableAsSdFile(table: DG.DataFrame) {
-  if (!table.columns.contains('Compound Name')) {
-    grok.shell.warning(
-      'File saved without columns \'' +
-      [COL_NAMES.COMPOUND_NAME, COL_NAMES.COMPOUND_COMMENTS, COL_NAMES.CPD_MW,
-        COL_NAMES.SALT_MASS, COL_NAMES.BATCH_MW].join('\', \''),
-    );
-  }
-  const structureColumn = table.col(COL_NAMES.SEQUENCE)!;
-  const typeColumn = table.col(COL_NAMES.TYPE)!;
-  let result = '';
-  for (let i = 0; i < table.rowCount; i++) {
-    const format = getFormat(structureColumn.get(i));
-    result += (typeColumn.get(i) == 'SS') ?
-      sequenceToMolV3000(structureColumn.get(i), false, true, format!) + '\n' + `>  <Sequence>\nSense Strand\n\n` :
-      sequenceToMolV3000(structureColumn.get(i), true, true, format!) + '\n' + `>  <Sequence>\nAnti Sense\n\n`;
-    for (const col of table.columns) {
-      if (col.name != COL_NAMES.SEQUENCE)
-        result += `>  <${col.name}>\n${col.get(i)}\n\n`;
-    }
-    result += '$$$$\n\n';
-  }
-  const element = document.createElement('a');
-  element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
-  element.setAttribute('download', table.name + '.sdf');
-  element.click();
-}
-
-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;
-
-function sortByStringLengthInDescendingOrder(array: string[]): string[] {
-  return array.sort(function(a, b) {return b.length - a.length;});
-}
-
-function stringifyItems(items: string[]): string {
-  return '["' + items.join('", "') + '"]';
-}
-
-function molecularWeight(sequence: string, weightsObj: {[index: string]: number}): number {
-  const codes = sortByStringLengthInDescendingOrder(Object.keys(weightsObj)).concat(Object.keys(MODIFICATIONS));
-  let weight = 0;
-  let i = 0;
-  while (i < sequence.length) {
-    const matchedCode = codes.find((s) => s == sequence.slice(i, i + s.length))!;
-    weight += weightsObj[sequence.slice(i, i + matchedCode.length)];
-    i += matchedCode!.length;
-  }
-  return weight - 61.97;
 }
 
 //tags: autostart
-export function autostartOligoSdFileSubscription() {
-  let alreadyAdded = false;
-  grok.events.onViewAdded.subscribe((v: any) => {
-    if (v.type == 'TableView') {
-      if (v.dataFrame.columns.contains(COL_NAMES.TYPE))
-        oligoSdFile(v.dataFrame);
-      grok.events.onContextMenu.subscribe((args) => {
-        for (const col of v.dataFrame.columns) {
-          if (!alreadyAdded && DG.Detector.sampleCategories(col, (s) => /^[fsACGUacgu]{6,}$/.test(s))) {
-            alreadyAdded = true;
-            args.args.menu.item('Convert to GCRS', () => {
-              const seqCol = args.args.context.table.currentCol;
-              args.args.context.table.columns.addNewString(seqCol.name + ' to GCRS').init((i: number) => {
-                return siRnaAxolabsToGcrs(seqCol.get(i));
-              });
-            });
-            break;
-          };
-        }
-      });
-    }
-  });
-}
-
-export function oligoSdFile(table: DG.DataFrame) {
-  const saltsDf = DG.DataFrame.fromCsv(SALTS_CSV);
-  const usersDf = DG.DataFrame.fromCsv(USERS_CSV);
-  const sourcesDf = DG.DataFrame.fromCsv(SOURCES);
-  const icdsDf = DG.DataFrame.fromCsv(ICDS);
-  const idpsDf = DG.DataFrame.fromCsv(IDPS);
-
-  function addColumns(t: DG.DataFrame, saltsDf: DG.DataFrame) {
-    if (t.columns.contains(COL_NAMES.COMPOUND_NAME))
-      return grok.shell.error('Columns already exist!');
-
-    const sequence = t.col(COL_NAMES.SEQUENCE)!;
-    const salt = t.col(COL_NAMES.SALT)!;
-    const equivalents = t.col(COL_NAMES.EQUIVALENTS)!;
-
-    t.columns.addNewString(COL_NAMES.COMPOUND_NAME).init((i: number) => sequence.get(i));
-    t.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => (i > 0 && i % 2 == 0) ?
-      sequence.getString(i) + '; duplex of SS: ' + sequence.getString(i - 2) + ' and AS: ' + sequence.getString(i - 1) :
-      sequence.getString(i),
-    );
-    const molWeightCol = saltsDf.col('MOLWEIGHT')!;
-    const saltNamesList = saltsDf.col('DISPLAY')!.toList();
-    t.columns.addNewFloat(COL_NAMES.CPD_MW)
-      .init((i: number) => molecularWeight(sequence.get(i), weightsObj));
-    t.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) => {
-      const saltRowIndex = saltNamesList.indexOf(salt.get(i));
-      const mw = molWeightCol.get(saltRowIndex);
-      return mw * equivalents.get(i);
-    });
-    t.columns.addNewCalculated(COL_NAMES.BATCH_MW,
-      '${' + COL_NAMES.CPD_MW + '} + ${' + COL_NAMES.SALT_MASS + '}', DG.COLUMN_TYPE.FLOAT, false,
-    );
-
-    addColumnsPressed = true;
-    return newDf = t;
-  }
-
-  let newDf: DG.DataFrame;
-  let addColumnsPressed = false;
-
-  const d = ui.div([
-    ui.icons.edit(() => {
-      d.innerHTML = '';
-      if (table.col(COL_NAMES.IDP)!.type != DG.COLUMN_TYPE.STRING)
-        table.changeColumnType(COL_NAMES.IDP, DG.COLUMN_TYPE.STRING);
-      d.append(
-        ui.link('Add Columns', () => {
-          addColumns(table, saltsDf);
-          grok.shell.tableView(table.name).grid.columns.setOrder(Object.values(COL_NAMES));
-        }, 'Add columns: \'' + [COL_NAMES.COMPOUND_NAME, COL_NAMES.COMPOUND_COMMENTS, COL_NAMES.CPD_MW,
-          COL_NAMES.SALT_MASS, COL_NAMES.BATCH_MW].join('\', \''), ''),
-        ui.button('Save SD file', () => saveTableAsSdFile(addColumnsPressed ? newDf : table)),
-      );
-
-      const view = grok.shell.getTableView(table.name);
-
-      view.table!.col(COL_NAMES.TYPE)!.setTag(DG.TAGS.CHOICES, '["AS", "SS", "Duplex"]');
-      view.table!.col(COL_NAMES.OWNER)!.setTag(DG.TAGS.CHOICES, stringifyItems(usersDf.columns.byIndex(0).toList()));
-      view.table!.col(COL_NAMES.SALT)!.setTag(DG.TAGS.CHOICES, stringifyItems(saltsDf.columns.byIndex(0).toList()));
-      view.table!.col(COL_NAMES.SOURCE)!.setTag(DG.TAGS.CHOICES, stringifyItems(sourcesDf.columns.byIndex(0).toList()));
-      view.table!.col(COL_NAMES.ICD)!.setTag(DG.TAGS.CHOICES, stringifyItems(icdsDf.columns.byIndex(0).toList()));
-      view.table!.col(COL_NAMES.IDP)!.setTag(DG.TAGS.CHOICES, stringifyItems(idpsDf.columns.byIndex(0).toList()));
-
-      grok.events.onContextMenu.subscribe((args) => {
-        if ([COL_NAMES.TYPE, COL_NAMES.OWNER, COL_NAMES.SALT, COL_NAMES.SOURCE, COL_NAMES.ICD, COL_NAMES.IDP]
-          .includes(args.args.context.table.currentCol.name)) {
-          args.args.menu.item('Fill Column With Value', () => {
-            const v = args.args.context.table.currentCell.value;
-            args.args.context.table.currentCell.column.init(v);
-          });
-        }
-      });
-    }),
-  ]);
-  grok.shell.v.setRibbonPanels([[d]]);
-}
+autostartOligoSdFileSubscription();

package/src/structures-works/converters.ts

@@ -15,7 +15,10 @@ export function gcrsToLcms(sequence: string): string {
     arr1[i] = arr1[i].replace(')', '\\)');
   }
   const regExp = new RegExp('(' + arr1.join('|') + ')', 'g');
-  return sequence.replace(regExp, function(code) {return obj[code];});
+  let r1 = sequence.replace(regExp, function(code) {return obj[code];});
+  while (r1.indexOf('//') != -1)
+    r1 = r1.replace('//', '/');
+  return r1;
 }
 
 //name: asoGapmersNucleotidesToBioSpring

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

@@ -1,4 +1,4 @@
-import {map, stadardPhosphateLinkSmiles, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS} from './map';
+import {map, stadardPhosphateLinkSmiles, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, delimiter} from './map';
 import {isValidSequence} from './sequence-codes-tools';
 import {getNucleotidesMol} from './mol-transformations';
 
@@ -12,7 +12,7 @@ export function sequenceToMolV3000(sequence: string, inverted: boolean = false,
   const links = ['s', 'ps', '*'];
   const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
   const dropdowns = Object.keys(MODIFICATIONS);
-  codes = codes.concat(dropdowns);
+  codes = codes.concat(dropdowns).concat(delimiter);
   while (i < sequence.length) {
     const code = codes.find((s: string) => s == sequence.slice(i, i + s.length))!;
     i += code.length;
@@ -36,7 +36,7 @@ export function sequenceToMolV3000(sequence: string, inverted: boolean = false,
     }
   }
 
-  return getNucleotidesMol(smilesCodes, oclRender);
+  return getNucleotidesMol(smilesCodes);
 }
 
 export function sequenceToSmiles(sequence: string, inverted: boolean = false, format: string): string {
@@ -48,7 +48,7 @@ export function sequenceToSmiles(sequence: string, inverted: boolean = false, fo
   const links = ['s', 'ps', '*'];
   const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
   const dropdowns = Object.keys(MODIFICATIONS);
-  codes = codes.concat(dropdowns);
+  codes = codes.concat(dropdowns).concat(delimiter);
   while (i < sequence.length) {
     const code = codes.find((s: string) => s == sequence.slice(i, i + s.length))!;
     i += code.length;
@@ -98,6 +98,7 @@ function getObjectWithCodesAndSmiles(sequence: string, format: string) {
         obj[code] = map[format][technology][code].SMILES;
     }
   }
+  obj[delimiter] = '';
   // TODO: create object based from synthesizer type to avoid key(codes) duplicates
   const output = isValidSequence(sequence, format);
   if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12))

package/src/structures-works/map.ts

@@ -1,6 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import {getAllCodesOfSynthesizer} from './sequence-codes-tools';
 
+export const delimiter = ';';
 export const SYNTHESIZERS = {
   RAW_NUCLEOTIDES: 'Raw Nucleotides',
   BIOSPRING: 'BioSpring Codes',
@@ -339,6 +340,12 @@ export const map: {[synthesizer: string]:
             'normalized': '',
             'SMILES': 'OP(=O)(S)O',
           },
+          's': {
+            'name': 'ps linkage',
+            'weight': 16.07,
+            'normalized': '',
+            'SMILES': 'OP(=O)(S)O',
+          },
           'A': {
             'name': 'Adenine',
             'weight': 313.21,

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

@@ -1,5 +1,3 @@
-import * as OCL from 'openchemlib/full.js';
-
 const PHOSHATE = `
 Datagrok monomer library Nucleotides
 
@@ -80,7 +78,7 @@ M  V30 END COLLECTION
 M  V30 END CTAB
 M  END`;
 
-export function getNucleotidesMol(smilesCodes: string[], oclRender: boolean = false) {
+export function getNucleotidesMol(smilesCodes: string[]) {
   const molBlocks: string[] = [];
 
   for (let i = 0; i < smilesCodes.length - 1; i++) {
@@ -90,10 +88,10 @@ export function getNucleotidesMol(smilesCodes: string[], oclRender: boolean = fa
           molBlocks.push(rotateNucleotidesV3000(smilesCodes[i]));
   }
 
-  return linkV3000(molBlocks, false, oclRender);
+  return linkV3000(molBlocks, false);
 }
 
-export function linkV3000(molBlocks: string[], twoChains: boolean = false, oclRender: boolean = false) {
+export function linkV3000(molBlocks: string[], twoChains: boolean = false, 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';
@@ -215,14 +213,14 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, oclRe
   const entries = 4;
   const collNumber = Math.ceil(collection.length / entries);
 
-  if (oclRender) {
-    collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length;
+  //if (oclRender) {
+    // 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';
-  } else {
+    // collectionBlock += ')\n';
+  //} else {
     collectionBlock += 'M  V30 MDLV30/STEABS ATOMS=(' + collection.length + ' -\n';
     for (let i = 0; i < collNumber; i++) {
       collectionBlock += 'M  V30 ';
@@ -233,7 +231,7 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, oclRe
           collection[entries*i + j] + ' ';
       }
     }
-  }
+  //}
 
   //generate file
   twoChains? natom : natom++;
@@ -244,9 +242,13 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, oclRe
   macroMolBlock += 'M  V30 BEGIN BOND\n';
   macroMolBlock += bondBlock;
   macroMolBlock += 'M  V30 END BOND\n';
-  macroMolBlock += 'M  V30 BEGIN COLLECTION\n';
-  macroMolBlock += collectionBlock;
-  macroMolBlock += 'M  V30 END COLLECTION\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\n';
 
@@ -254,6 +256,7 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, oclRe
 }
 
 function rotateNucleotidesV3000(molecule: string) {
+  // @ts-ignore
   let molBlock = molecule.includes('M  END') ? molecule : OCL.Molecule.fromSmiles(molecule).toMolfileV3();
   const coordinates = extractAtomDataV3000(molBlock);
   const natom = coordinates.atomIndex.length;
@@ -320,6 +323,7 @@ function rotateNucleotidesV3000(molecule: string) {
 }
 
 function invertNucleotidesV3000(molecule: string) {
+  // @ts-ignore
   let molBlock = molecule.includes('M  END') ? molecule : OCL.Molecule.fromSmiles(molecule).toMolfileV3();
   const coordinates = extractAtomDataV3000(molBlock);
   const natom = coordinates.atomIndex.length;

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

@@ -3,14 +3,14 @@ import {sequenceToMolV3000} from '../structures-works/from-monomers';
 import {linkV3000} from '../structures-works/mol-transformations';
 import {getFormat} from '../structures-works/sequence-codes-tools';
 
-export function saveSdf(as: string, ss: string, oneEntity: boolean, fit3dx: boolean) {
+export function saveSdf(as: string, ss: string, oneEntity: boolean, useChirality: boolean, invertSS: boolean, invertAS: boolean) {
   const formatAs = getFormat(as);
   const formatSs = getFormat(ss);
-  const molSS = sequenceToMolV3000(ss, false, false, formatSs!);
-  const molAS = sequenceToMolV3000(as, true, false, formatAs!);
+  const molSS = sequenceToMolV3000(ss, invertSS, false, formatSs!);
+  const molAS = sequenceToMolV3000(as, invertAS, false, formatAs!);
   let result: string;
   if (oneEntity)
-    result = linkV3000([molSS, molAS], true, !fit3dx) + '\n\n$$$$\n';
+    result = linkV3000([molSS, molAS], true, useChirality) + '\n\n$$$$\n';
   else {
     result =
     molSS + '\n' +
@@ -27,22 +27,35 @@ export function saveSdf(as: string, ss: string, oneEntity: boolean, fit3dx: bool
 
 export function saveSenseAntiSense() {
   const moleculeSvgDiv = ui.block([]);
-  const ssInput = ui.textInput('Sense Strand 5\' ->3\'', '');
-  const asInput = ui.textInput('Anti Sense 3\' ->5\'', '');
+  const ssInput = ui.textInput('Sense Strand', '');
+  const asInput = ui.textInput('Anti Sense', '');
+  const straight = '5\' ->3\'';
+  const inverse = '3\' ->5\'';
+  let ssInverse = false;
+  let asInverse = 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 saveOption = ui.switchInput('Save as one entity', true);
-  const save3dx = ui.switchInput('Save 3dx', true);
+  const chirality = ui.switchInput('Use chiral', true);
   const saveBtn = ui.button('Save SDF', () =>
-    saveSdf(asInput.value, ssInput.value, saveOption.value, save3dx.value));
+    saveSdf(asInput.value, ssInput.value, saveOption.value, chirality.value, ssInverse, asInverse));
 
   const saveSection = ui.panel([
     ui.div([
       ui.div([
         ui.divH([ui.h1('Inputs')]),
         ui.divV([
-          ui.div([ssInput.root]),
-          ui.div([asInput.root]),
+          ssInput,
+          asInput,
+          ui.div([changeSense], {style: {width: '40'}}),
+          changeSense,
+          changeAntiSense,
           saveOption,
-          save3dx,
+          chirality,
           ui.buttonsInput([saveBtn]),
         ], 'ui-form'),
       ], 'ui-form'),