@datagrok/sequence-translator 1.0.5 → 1.0.7

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.0.5",
+  "version": "1.0.7",
   "author": {
     "name": "Vadym Kovadlo",
     "email": "vkovadlo@datagrok.ai"
@@ -15,7 +15,7 @@
   "dependencies": {
     "@datagrok-libraries/utils": "^0.1.0",
     "@types/react": "^18.0.15",
-    "datagrok-api": "^1.1.7",
+    "datagrok-api": "^1.6.0",
     "datagrok-tools": "^4.1.2",
     "npm": "^8.11.0",
     "openchemlib": "6.0.1",
@@ -33,7 +33,7 @@
     "release-sequencetranslator-public": "grok publish public --release",
     "debug-sequencetranslator-local": "grok publish local",
     "release-sequencetranslator-local": "grok publish local --release",
-    "test": "set HOST=dev && jest",
+    "test": "jest",
     "test-dev": "set HOST=dev && jest",
     "test-local": "set HOST=localhost && jest"
   },
@@ -54,7 +54,11 @@
     "puppeteer": "^13.7.0",
     "ts-jest": "^27.0.0",
     "webpack": "^5.31.0",
-    "webpack-cli": "^4.6.0"
+    "webpack-cli": "^4.6.0",
+    "@types/js-yaml": "^4.0.5",
+    "js-yaml": "^4.1.0",
+    "@types/node-fetch": "^2.6.2",
+    "node-fetch": "^2.6.7"
   },
   "category": "Bioinformatics"
 }

package/src/__jest__/remote.test.ts

@@ -5,7 +5,7 @@
 import * as utils from './test-node';
 import puppeteer from 'puppeteer';
 
-const P_START_TIMEOUT: number = 100000;
+const P_START_TIMEOUT: number = 3600000;
 let browser: puppeteer.Browser;
 let page: puppeteer.Page;
 
@@ -42,19 +42,20 @@ it('TEST', async () => {
   let r = await page.evaluate((targetPackage):Promise<object> => {
     return new Promise<object>((resolve, reject) => {
       (<any>window).grok.functions.eval(targetPackage + ':test()').then((df: any) => {
-        let cStatus = df.columns.byName('success');
-        let cMessage = df.columns.byName('result');
-        let cCat = df.columns.byName('category');
-        let cName = df.columns.byName('name');
+        const cStatus = df.columns.byName('success');
+        const cMessage = df.columns.byName('result');
+        const cCat = df.columns.byName('category');
+        const cName = df.columns.byName('name');
+        const cTime = df.columns.byName('ms');
         let failed = false;
         let passReport = '';
         let failReport = '';
         for (let i = 0; i < df.rowCount; i++) {
           if (cStatus.get(i)) {
-            passReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+            passReport += `Test result : Success : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
           } else {
             failed = true;
-            failReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+            failReport += `Test result : Failed : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
           }
         }
         resolve({failReport, passReport, failed});
@@ -65,4 +66,4 @@ it('TEST', async () => {
   console.log(r.passReport);
   // @ts-ignore
   expect(r.failed).checkOutput(false, r.failReport);
-}, 100000);
+}, 3600000);

package/src/__jest__/test-node.ts

@@ -67,6 +67,7 @@ export async function getBrowserPage(puppeteer: any): Promise<{browser: any, pag
   });
 
   let page = await browser.newPage();
+  await page.setDefaultNavigationTimeout(0);
   await page.goto(`${url}/oauth/`);
   await page.setCookie({name: 'auth', value: token});
   await page.evaluate((token: any) => {
@@ -74,8 +75,8 @@ export async function getBrowserPage(puppeteer: any): Promise<{browser: any, pag
   }, token);
   await page.goto(url);
   try {
-    await page.waitForSelector('.grok-preloader');
-    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 100000});
+//    await page.waitForSelector('.grok-preloader', { timeout: 1800000 });
+    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 3600000});
   } catch (error) {
     throw error;
   }

package/src/autostart/registration.ts

@@ -4,7 +4,7 @@ import * as DG from 'datagrok-api/dg';
 import {siRnaAxolabsToGcrs, gcrsToNucleotides, asoGapmersBioSpringToGcrs, gcrsToMermade12,
 } from '../structures-works/converters';
 import {map, COL_NAMES, MODIFICATIONS} from '../structures-works/map';
-import {getFormat} from '../structures-works/sequence-codes-tools';
+import {isValidSequence} from '../structures-works/sequence-codes-tools';
 import {sequenceToMolV3000} from '../structures-works/from-monomers';
 
 import {SALTS_CSV} from '../salts';
@@ -13,16 +13,6 @@ import {ICDS} from '../ICDs';
 import {SOURCES} from '../sources';
 import {IDPS} from '../IDPs';
 
-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;});
@@ -56,15 +46,15 @@ async function saveTableAsSdFile(table: DG.DataFrame) {
   const typeColumn = table.getCol(COL_NAMES.TYPE);
   let result = '';
   for (let i = 0; i < table.rowCount; i++) {
-    const format = getFormat(structureColumn.get(i))!;
+    const format = 'Janssen GCRS Codes'; //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`;
+      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 += `> <${col.name}>\n${col.get(i)}\n\n`;
     }
-    result += '$$$$\n\n';
+    result += '$$$$\n';
   }
   const element = document.createElement('a');
   element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
@@ -78,14 +68,16 @@ export function autostartOligoSdFileSubscription() {
       if (v.dataFrame.columns.contains(COL_NAMES.TYPE))
         oligoSdFile(v.dataFrame);
       grok.events.onContextMenu.subscribe((args) => {
-        const seqCol = args.args.context.table.currentCol;
-        if (DG.Detector.sampleCategories(seqCol, (s) => /^[fsACGUacgu]{6,}$/.test(s))) {
+        const seqCol = args.args.context.table.currentCol; // /^[fsACGUacgu]{6,}$/
+        if (DG.Detector.sampleCategories(seqCol,
+          (s) => /(\(invabasic\)|\(GalNAc-2-JNJ\)|f|s|A|C|G|U|a|c|g|u){6,}$/.test(s))) {
           args.args.menu.item('Convert Axolabs to GCRS', () => {
             args.args.context.table.columns.addNewString(seqCol.name + ' to GCRS').init((i: number) => {
               return siRnaAxolabsToGcrs(seqCol.get(i));
             });
-          });
-        } else if (DG.Detector.sampleCategories(seqCol, (s) => /^[fmpsACGU]{6,}$/.test(s)) ||
+          }); // /^[fmpsACGU]{6,}$/
+        } else if (DG.Detector.sampleCategories(seqCol,
+          (s) => /(\(invabasic\)|\(GalNAc-2-JNJ\)|f|m|ps|A|C|G|U){6,}$/.test(s)) ||
         DG.Detector.sampleCategories(seqCol, (s) => /^(?=.*moe)(?=.*5mC)(?=.*ps){6,}/.test(s))) {
           args.args.menu.item('Convert GCRS to raw', () => {
             args.args.context.table.columns.addNewString(seqCol.name + ' to raw').init((i: number) => {
@@ -96,15 +88,17 @@ export function autostartOligoSdFileSubscription() {
             args.args.context.table.columns.addNewString(seqCol.name + ' to MM12').init((i: number) => {
               return gcrsToMermade12(seqCol.get(i));
             });
-          });
-        } else if (DG.Detector.sampleCategories(seqCol, (s) => /^[*56789ATGC]{6,}$/.test(s))) {
+          }); // /^[*56789ATGC]{6,}$/
+        } else if (DG.Detector.sampleCategories(seqCol,
+          (s) => /(\(invabasic\)|\(GalNAc-2-JNJ\)|\*|5|6|7|8|9|A|T|G|C){6,}$/.test(s))) {
           args.args.menu.item('Convert Biospring to GCRS', () => {
             const seqCol = args.args.context.table.currentCol;
             args.args.context.table.columns.addNewString(seqCol.name + ' to GCRS').init((i: number) => {
               return asoGapmersBioSpringToGcrs(seqCol.get(i));
             });
-          });
-        } else if (DG.Detector.sampleCategories(seqCol, (s) => /^[*1-8]{6,}$/.test(s))) {
+          }); // /^[*1-8]{6,}$/
+        } else if (DG.Detector.sampleCategories(seqCol,
+          (s) => /(\(invabasic\)|\(GalNAc-2-JNJ\)|\*|1|2|3|4|5|6|7|8){6,}$/.test(s))) {
           args.args.menu.item('Convert Biospring to GCRS', () => {
             args.args.context.table.columns.addNewString(seqCol.name + ' to GCRS').init((i: number) => {
               return siRnaAxolabsToGcrs(seqCol.get(i));
@@ -123,29 +117,54 @@ export function oligoSdFile(table: DG.DataFrame) {
   const icdsDf = DG.DataFrame.fromCsv(ICDS);
   const idpsDf = DG.DataFrame.fromCsv(IDPS);
 
-  function addColumns(t: DG.DataFrame, saltsDf: DG.DataFrame) {
+  async 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.getCol(COL_NAMES.SEQUENCE);
-    const salt = t.getCol(COL_NAMES.SALT);
-    const equivalents = t.getCol(COL_NAMES.EQUIVALENTS);
+    const sequenceCol = t.getCol(COL_NAMES.SEQUENCE);
+    const saltCol = t.getCol(COL_NAMES.SALT);
+    const equivalentsCol = t.getCol(COL_NAMES.EQUIVALENTS);
+
+    for (let i = t.rowCount - 1; i > -1; i--) {
+      if (sequenceCol.get(i) == '')
+        t.rows.removeAt(i, 1, false);
+    }
+
+    t.columns.addNewString(COL_NAMES.COMPOUND_NAME).init((i: number) => sequenceCol.get(i));
 
-    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),
+      sequenceCol.get(i) + '; duplex of SS: ' + sequenceCol.get(i - 2) + ' and AS: ' + sequenceCol.get(i - 1) :
+      sequenceCol.get(i),
     );
     const molWeightCol = saltsDf.getCol('MOLWEIGHT');
     const saltNamesList = saltsDf.getCol('DISPLAY').toList();
-    t.columns.addNewFloat(COL_NAMES.CPD_MW)
-      .init((i: number) => molecularWeight(sequence.get(i), weightsObj));
+    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;
+
+    t.columns.addNewFloat(COL_NAMES.CPD_MW).init((i: number) => {
+      return (isValidSequence(sequenceCol.get(i), null).indexOfFirstNotValidChar == -1) ?
+        molecularWeight(sequenceCol.get(i), weightsObj) :
+        DG.FLOAT_NULL;
+    });
+
     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);
+      const saltRowIndex = saltNamesList.indexOf(saltCol.get(i));
+      return (saltRowIndex == -1) ? DG.FLOAT_NULL : molWeightCol.get(saltRowIndex) * equivalentsCol.get(i);
+    });
+
+    t.columns.addNewFloat(COL_NAMES.SALT_MOL_WEIGHT).init((i: number) => {
+      const saltRowIndex = saltNamesList.indexOf(saltCol.get(i));
+      return (saltRowIndex == -1) ? DG.FLOAT_NULL : molWeightCol.get(saltRowIndex);
     });
-    t.columns.addNewCalculated(COL_NAMES.BATCH_MW,
+
+    await t.columns.addNewCalculated(COL_NAMES.BATCH_MW,
       '${' + COL_NAMES.CPD_MW + '} + ${' + COL_NAMES.SALT_MASS + '}', DG.COLUMN_TYPE.FLOAT, false,
     );
 
@@ -162,11 +181,12 @@ export function oligoSdFile(table: DG.DataFrame) {
       if (table.getCol(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));
+        ui.link('Add Columns', async () => {
+          await addColumns(table, saltsDf);
+          view.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('\', \''), ''),
+          COL_NAMES.SALT_MASS, COL_NAMES.BATCH_MW].join('\', \''), '',
+        ),
         ui.button('Save SD file', () => saveTableAsSdFile(addColumnsPressed ? newDf : table)),
       );
 

package/src/axolabs/define-pattern.ts

@@ -361,6 +361,11 @@ export function defineAxolabsPattern() {
         })
         .show();
     }
+    if (col.get(0) != ssLength.value) {
+      const d = ui.dialog('Length was updated by value to from imported file');
+      d.add(ui.divText('Latest modifications may not take effect during translation'))
+        .onOK(() => grok.shell.info('Lengths changed')).show();
+    }
     return allLengthsAreTheSame;
   }
 
@@ -513,7 +518,9 @@ export function defineAxolabsPattern() {
   let asPtoLinkages = Array(defaultSequenceLength).fill(ui.boolInput('', defaultPto));
 
   const ssLength = ui.intInput('SS Length', defaultSequenceLength, () => updateUiForNewSequenceLength());
+  ssLength.setTooltip('Length of sense strand, including overhangs');
   const asLength = ui.intInput('AS Length', defaultSequenceLength, () => updateUiForNewSequenceLength());
+  asLength.setTooltip('Length of sense strand, including overhangs');
   const asLengthDiv = ui.div([asLength.root]);
 
   function validateSsColumn(colName: string): void {
@@ -605,7 +612,9 @@ export function defineAxolabsPattern() {
   });
 
   const firstSsPto = ui.boolInput('First SS PTO', fullyPto.value!, () => updateSvgScheme());
+  firstSsPto.setTooltip('ps linkage before first nucleotide of sense strand');
   const firstAsPto = ui.boolInput('First AS PTO', fullyPto.value!, () => updateSvgScheme());
+  firstAsPto.setTooltip('ps linkage before first nucleotide of antisense strand');
   firstAsPtoDiv.append(firstAsPto.root);
 
   const createAsStrand = ui.boolInput('Create AS Strand', true, (v: boolean) => {
@@ -617,6 +626,7 @@ export function defineAxolabsPattern() {
     firstAsPtoDiv.hidden = (!v);
     updateSvgScheme();
   });
+  createAsStrand.setTooltip('Create antisense strand sections on SVG and table to the right');
 
   const saveAs = ui.textInput('Save As', 'Pattern Name', () => updateSvgScheme());
   saveAs.setTooltip('Name Of New Pattern');

package/src/main/main-view.ts

@@ -4,7 +4,6 @@ import * as DG from 'datagrok-api/dg';
 import {convertSequence, undefinedInputSequence, isValidSequence} from '../structures-works/sequence-codes-tools';
 import {map, MODIFICATIONS} from '../structures-works/map';
 import {sequenceToSmiles, sequenceToMolV3000} from '../structures-works/from-monomers';
-
 import $ from 'cash-dom';
 
 const defaultInput = 'fAmCmGmAmCpsmU';
@@ -12,7 +11,7 @@ const sequenceWasCopied = 'Copied';
 const tooltipSequence = 'Copy sequence';
 
 export function mainView() {
-  function updateTableAndMolecule(sequence: string, inputFormat: string, isSet: boolean): void {
+  function updateTableAndMolecule(sequence: string, inputFormat: string): void {
     moleculeSvgDiv.innerHTML = '';
     outputTableDiv.innerHTML = '';
     const pi = DG.TaskBarProgressIndicator.create('Rendering table and molecule...');
@@ -20,9 +19,8 @@ export function mainView() {
     try {
       sequence = sequence.replace(/\s/g, '');
       const output = isValidSequence(sequence, null);
-      if (isSet)
-        output.synthesizer = [inputFormat];
-      inputFormatChoiceInput.value = output.synthesizer![0];
+      output.synthesizer = [inputFormat];
+      // inputFormatChoiceInput.value = output.synthesizer![0];
       const outputSequenceObj = convertSequence(sequence, output);
       const tableRows = [];
 
@@ -101,14 +99,15 @@ export function mainView() {
     }
   }
 
-  const inputFormatChoiceInput = ui.choiceInput(
-    'Input format: ', 'Janssen GCRS Codes', Object.keys(map), (format: string) => {
-      updateTableAndMolecule(inputSequenceField.value.replace(/\s/g, ''), format, true);
-    });
+  const inputFormatChoiceInput = ui.choiceInput('Input format: ', 'Janssen GCRS Codes', Object.keys(map));
+  inputFormatChoiceInput.onInput((format: string) => {
+    updateTableAndMolecule(inputSequenceField.value.replace(/\s/g, ''), format);
+  });
   const moleculeSvgDiv = ui.block([]);
   const outputTableDiv = ui.div([]);
-  const inputSequenceField = ui.textInput('', defaultInput, (sequence: string) => updateTableAndMolecule(sequence,
-      inputFormatChoiceInput.value!, false));
+  const inputSequenceField = ui.textInput('', defaultInput, (sequence: string) => {
+    updateTableAndMolecule(sequence, inputFormatChoiceInput.value!);
+  });
 
   const asoDf = DG.DataFrame.fromObjects([
     {'Name': '2\'MOE-5Me-rU', 'BioSpring': '5', 'Janssen GCRS': 'moeT'},
@@ -151,7 +150,7 @@ export function mainView() {
         DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
       ])!, {showRowHeader: false, showCellTooltip: false},
   );
-  updateTableAndMolecule(defaultInput, inputFormatChoiceInput.value!, true);
+  updateTableAndMolecule(defaultInput, inputFormatChoiceInput.value!);
 
   const codesTablesDiv = ui.splitV([
     ui.box(ui.h2('ASO Gapmers'), {style: {maxHeight: '40px'}}),

package/src/structures-works/converters.ts

@@ -1,6 +1,6 @@
 import {lcmsToGcrs} from './map';
 import * as DG from 'datagrok-api/dg';
-
+import {delimiter} from './map';
 //name: gcrsToLcms
 //input: string nucleotides {semType: GCRS}
 //output: string result {semType: LCMS}
@@ -10,15 +10,24 @@ export function gcrsToLcms(sequence: string): string {
   const arr2 = df.getCol('LCMS').toList();
   const obj: {[i: string]: string} = {};
   arr1.forEach((element, index) => obj[element] = arr2[index]);
-  for (let i = 0; i < arr1.length; i++) {
-    arr1[i] = arr1[i].replace('(', '\\(');
-    arr1[i] = arr1[i].replace(')', '\\)');
+  obj[delimiter] = delimiter;
+  // for (let i = 0; i < arr1.length; i++) {
+  //   arr1[i] = arr1[i].replace('(', '\\(');
+  //   arr1[i] = arr1[i].replace(')', '\\)');
+  // }
+  // const regExp = new RegExp('(' + arr1.join('|') + ')', 'g');
+  // let r1 = sequence.replace(regExp, function(code) {return obj[code];});
+  const codes = arr1.concat(delimiter).sort(function(a, b) {return b.length - a.length;});
+  let i = 0;
+  let r1 = '';
+  while (i < sequence.length) {
+    const matchedCode = codes.find((c) => c == sequence.slice(i, i + c.length));
+    r1 += obj[sequence.slice(i, i + matchedCode.length)];
+    i += matchedCode.length;
   }
-  const regExp = new RegExp('(' + arr1.join('|') + ')', 'g');
-  let r1 = sequence.replace(regExp, function(code) {return obj[code];});
-  r1 = r1.replace('//', '/');
-  r1 = r1.replace('//', '/');
-  return r1.replace('//', '/');
+  while (r1.indexOf('//') != -1)
+    r1 = r1.replace('//', '/');
+  return r1;
 }
 
 //name: asoGapmersNucleotidesToBioSpring

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

@@ -22,7 +22,8 @@ export function sequenceToMolV3000(sequence: string, inverted: boolean = false,
     if (dropdowns.includes(codesList[i])) {
       smilesCodes.push((i >= codesList.length / 2) ?
         MODIFICATIONS[codesList[i]].right : MODIFICATIONS[codesList[i]].left);
-      smilesCodes.push(stadardPhosphateLinkSmiles);
+      if (!(i < codesList.length - 1 && links.includes(codesList[i + 1])))
+        smilesCodes.push(stadardPhosphateLinkSmiles);
     } else {
       if (links.includes(codesList[i]) ||
         includesStandardLinkAlready.includes(codesList[i]) ||
@@ -36,7 +37,7 @@ 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 {

package/src/structures-works/map.ts

@@ -30,6 +30,7 @@ export const COL_NAMES = {
   EQUIVALENTS: 'Equivalents',
   PURITY: 'Purity',
   CPD_MW: 'Cpd MW',
+  SALT_MOL_WEIGHT: 'Salt MW',
   SALT_MASS: 'Salt mass',
   BATCH_MW: 'Batch MW',
   SOURCE: 'Source',
@@ -340,6 +341,12 @@ 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

@@ -78,7 +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++) {
@@ -88,10 +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';
@@ -213,14 +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 ';
@@ -231,7 +231,7 @@ export function linkV3000(molBlocks: string[], twoChains: boolean = false, oclRe
           collection[entries*i + j] + ' ';
       }
     }
-  }
+  //}
 
   //generate file
   twoChains? natom : natom++;
@@ -242,13 +242,15 @@ 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';
-  macroMolBlock += 'M  V30 END CTAB\n';
-  macroMolBlock += 'M  END\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 = macroMolBlock.replaceAll('CFG=1', '').replaceAll('CFG=2', '').replaceAll('CFG=3', '').replaceAll('CFG=4', '');
+  macroMolBlock += 'M  V30 END CTAB\n';
+  macroMolBlock += 'M  END';
 
   return macroMolBlock;
 }

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

@@ -3,20 +3,20 @@ 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$$$$\n';
+    result = linkV3000([molSS, molAS], true, useChirality) + '\n$$$$\n';
   else {
     result =
     molSS + '\n' +
-    `>  <Sequence>\nSense Strand\n\n$$$$\n` +
+    `> <Sequence>\nSense Strand\n$$$$\n` +
     molAS + '\n' +
-    `>  <Sequence>\nAnti Sense\n\n$$$$\n`;
+    `> <Sequence>\nAnti Sense\n$$$$\n`;
   }
 
   const element = document.createElement('a');
@@ -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'),