@datagrok/sequence-translator 0.0.8 → 0.0.9

package/jest.config.js

@@ -0,0 +1,33 @@
+module.exports = {
+  "roots": [
+    "<rootDir>/src"
+  ],
+  "testMatch": [
+    "**/__jest__/**/*.test.+(ts|tsx)"
+  ],
+  moduleFileExtensions: [
+    'ts',
+    'js',
+  ],
+  "transform": {
+    "^.+\\.(ts|tsx)$": "ts-jest"
+  },
+  transformIgnorePatterns: ['^.+\\.js$'],
+  globals: {
+    'ts-jest': {
+      'tsconfig': {
+          "target": "es6",
+          "module": "es2020",
+      }
+    }
+  },
+  reporters: [
+    "default",
+    [
+      "./node_modules/jest-html-reporter",
+      {
+        "includeConsoleLog": true
+      }
+    ]
+  ]
+}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
-  "friendlyName": "SequenceTranslator",
-  "version": "0.0.8",
+  "friendlyName": "Sequence Translator",
+  "version": "0.0.9",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/utils": "^0.1.0",
@@ -23,7 +23,10 @@
     "debug-sequencetranslator-public": "grok publish public --rebuild",
     "release-sequencetranslator-public": "grok publish public --rebuild --release",
     "debug-sequencetranslator-local": "grok publish local --rebuild",
-    "release-sequencetranslator-local": "grok publish local --rebuild --release"
+    "release-sequencetranslator-local": "grok publish local --rebuild --release",
+    "test": "set HOST=dev && jest",
+    "test-dev": "set HOST=dev && jest",
+    "test-local": "set HOST=localhost && jest"
   },
   "devDependencies": {
     "@typescript-eslint/eslint-plugin": "^4.29.1",
@@ -32,6 +35,11 @@
     "eslint": "^7.32.0",
     "eslint-config-google": "^0.14.0",
     "webpack": "^5.31.0",
-    "webpack-cli": "^4.6.0"
+    "webpack-cli": "^4.6.0",
+    "@types/jest": "latest",
+    "jest": "latest",
+    "jest-html-reporter": "latest",
+    "puppeteer": "^13.1.2",
+    "ts-jest": "^27.1.2"
   }
 }

package/setup.cmd

@@ -8,4 +8,4 @@ call npm link datagrok-api
 cd ../../packages/SequenceTranslator
 call npm install
 call npm link datagrok-api @datagrok-libraries/utils
-webpack
+webpack

package/src/ICDs.ts

@@ -0,0 +1,3 @@
+export const ICDS = `DISPLAY
+NO DATA
+`;

package/src/IDPs.ts

@@ -0,0 +1,3 @@
+export const IDPS = `DISPLAY
+NO DATA
+`;

package/src/__jest__/remote.test.ts

@@ -0,0 +1,49 @@
+/**
+ * @jest-environment jsdom
+ */
+
+import * as utils from './test-node';
+import puppeteer from 'puppeteer';
+
+const P_START_TIMEOUT: number = 100000;
+let browser: puppeteer.Browser;
+let page: puppeteer.Page;
+
+beforeAll(async () => {
+  let out = await utils.getBrowserPage(puppeteer);
+  browser = out.browser;
+  page = out.page;
+}, P_START_TIMEOUT);
+
+afterAll(async () => {
+  await browser.close();
+});
+
+it('TEST', async () => {
+  const target_package:string = process.env.TARGET_PACKAGE ?? 'SequenceTranslator';
+  console.log(`Testing ${target_package} package`);
+
+  //console.log(require('root-require')('package.json').version);
+  let r = await page.evaluate((target_package):Promise<object> => {
+    return new Promise<object>((resolve, reject) => {
+      (<any>window).grok.functions.eval(target_package + ':test()').then((df: any) => {
+        let cStatus = df.columns.byName('success');
+        let cMessage = df.columns.byName('result');
+        let cCat = df.columns.byName('category');
+        let cName = df.columns.byName('name');
+        let failed = false;
+        let report = '';
+        for (let i = 0; i < df.rowCount; i++)
+          if (!cStatus.get(i)) {
+            report += `${cCat.get(i)}.${cName.get(i)}: ${cMessage.get(i)}\n`;
+            failed = true;
+          }
+        resolve({report, failed});
+      }).catch((e: any) => reject(e));
+    });
+  }, target_package);
+  // @ts-ignore
+  console.log(r.report);
+  // @ts-ignore
+  expect(r.failed).toBe(false);
+}, 100000);

package/src/__jest__/test-node.ts

@@ -0,0 +1,96 @@
+import * as path from "path";
+import * as os from "os";
+import * as fs from "fs";
+// @ts-ignore
+import * as yaml from 'js-yaml';
+const fetch = require('node-fetch');
+
+export async function getToken(url: string, key: string) {
+  let response = await fetch(`${url}/users/login/dev/${key}`, {method: 'POST'});
+  let json = await response.json();
+  if (json.isSuccess == true)
+    return json.token;
+  else
+    throw 'Unable to login to server. Check your dev key';
+}
+
+export async function getWebUrl(url: string, token: string) {
+  let response = await fetch(`${url}/admin/plugins/admin/settings`, {headers: {Authorization: token}});
+  let json = await response.json();
+  return json.settings.webRoot;
+}
+
+const grokDir = path.join(os.homedir(), '.grok');
+const confPath = path.join(grokDir, 'config.yaml');
+
+function mapURL(conf: Config): Indexable {
+  let urls: Indexable = {};
+  for (let server in conf.servers) {
+    urls[conf['servers'][server]['url']] = conf['servers'][server];
+  }
+  return urls;
+}
+
+export function getDevKey(hostKey: string): {url: string, key: string} {
+  let config = yaml.load(fs.readFileSync(confPath, 'utf8')) as any;
+  let host = hostKey == '' ? config.default : hostKey;
+  host = host.trim();
+  let urls = mapURL(config);
+  let key = '';
+  let url = '';
+  try {
+    let url = new URL(host).href;
+    if (url.endsWith('/')) url = url.slice(0, -1);
+    if (url in urls) key = config['servers'][urls[url]]['key'];
+  } catch (error) {
+    if (config['servers'][host] == null)
+      throw `Unknown server alias. Please add it to ${confPath}`;
+    url = config['servers'][host]['url'];
+    key = config['servers'][host]['key'];
+  }
+  return {url, key};
+}
+
+export async function getBrowserPage(puppeteer: any): Promise<{browser: any, page: any}> {
+  let url:string = process.env.HOST ?? '';
+  let cfg = getDevKey(url);
+  url = cfg.url;
+
+  let key = cfg.key;
+  let token = await getToken(url, key);
+  url = await getWebUrl(url, token);
+  console.log(`Using web root: ${url}`);
+
+  let browser = await puppeteer.launch({
+    args: ['--disable-dev-shm-usage', '--disable-features=site-per-process'],
+    ignoreHTTPSErrors: true,
+  });
+
+  let page = await browser.newPage();
+  await page.goto(`${url}/oauth/`);
+  await page.setCookie({name: 'auth', value: token});
+  await page.evaluate((token: any) => {
+    window.localStorage.setItem('auth', token);
+  }, token);
+  await page.goto(url);
+  try {
+    await page.waitForSelector('.grok-preloader');
+    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 100000});
+  } catch (error) {
+    throw error;
+  }
+  return {browser, page};
+}
+
+
+interface Config {
+  servers: {
+    [alias: string]: {
+      url: string,
+      key: string
+    }
+  },
+  default: string,
+}
+
+interface Indexable { [key: string]: any }

package/src/package-test.ts

@@ -1,8 +1,9 @@
 import * as DG from 'datagrok-api/dg';
-import {runTests} from '@datagrok-libraries/utils/src/test';
+import {runTests, tests} from '@datagrok-libraries/utils/src/test';
 import './tests/smiles-tests';
 
 export const _package = new DG.Package();
+export {tests}
 
 //name: test
 //output: dataframe result

package/src/package.ts

@@ -6,9 +6,14 @@ import * as OCL from 'openchemlib/full.js';
 import $ from 'cash-dom';
 import {defineAxolabsPattern} from './defineAxolabsPattern';
 import {saveSenseAntiSense} from './structures-works/save-sense-antisense';
-import {sequenceToSmiles} from './structures-works/from-monomers';
+import {sequenceToSmiles, sequenceToMolV3000} from './structures-works/from-monomers';
 import {convertSequence, undefinedInputSequence} from './structures-works/sequence-codes-tools';
+import {map, COL_NAMES, MODIFICATIONS} from './structures-works/map';
 import {SALTS_CSV} from './salts';
+import {USERS_CSV} from './users';
+import {ICDS} from './ICDs';
+import {SOURCES} from './sources';
+import {IDPS} from './IDPs';
 
 export const _package = new DG.Package();
 
@@ -72,12 +77,8 @@ export function sequenceTranslator(): void {
         });
         switchInput.enabled = true;
       } else {
-        asoGapmersGrid.onCellPrepare(function(gc) {
-          gc.style.backColor = 0xFFFFFFFF;
-        });
-        omeAndFluoroGrid.onCellPrepare(function(gc) {
-          gc.style.backColor = 0xFFFFFFFF;
-        });
+        asoGapmersGrid.onCellPrepare(function(gc) {gc.style.backColor = 0xFFFFFFFF;});
+        omeAndFluoroGrid.onCellPrepare(function(gc) {gc.style.backColor = 0xFFFFFFFF;});
       }
 
       outputTableDiv.append(
@@ -92,18 +93,18 @@ export function sequenceTranslator(): void {
         const canvas = ui.canvas(300, 170);
         canvas.addEventListener('click', () => {
           const canv = ui.canvas($(window).width(), $(window).height());
-          const smiles = sequenceToSmiles(inputSequenceField.value.replace(/\s/g, ''));
+          const mol = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, true);
           // @ts-ignore
-          OCL.StructureView.drawMolecule(canv, OCL.Molecule.fromSmiles(smiles), {suppressChiralText: true});
+          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 smiles = sequenceToSmiles(inputSequenceField.value.replace(/\s/g, ''));
+        const mol = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, true);
         // @ts-ignore
-        OCL.StructureView.drawMolecule(canvas, OCL.Molecule.fromSmiles(smiles), {suppressChiralText: true});
+        OCL.StructureView.drawMolecule(canvas, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
         moleculeSvgDiv.append(canvas);
       } else
         moleculeSvgDiv.innerHTML = '';
@@ -216,8 +217,7 @@ export function sequenceTranslator(): void {
 
   const topPanel = [
     ui.iconFA('download', () => {
-      const smiles = sequenceToSmiles(inputSequenceField.value.replace(/\s/g, ''));
-      const result = `${OCL.Molecule.fromSmiles(smiles).toMolfile()}\n`;
+      const result = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''));
       const element = document.createElement('a');
       element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
       element.setAttribute('download', inputSequenceField.value.replace(/\s/g, '') + '.mol');
@@ -250,21 +250,23 @@ export function sequenceTranslator(): void {
 async function saveTableAsSdFile(table: DG.DataFrame) {
   if (!table.columns.contains('Compound Name')) {
     grok.shell.warning(
-      'File saved without columns \'Compound Name\', \'Compound Components\', \'Cpd MW\', \'Salt mass\', \'Batch MW\'');
+      'File saved without columns \'' +
+      [COL_NAMES.COMPOUND_NAME, COL_NAMES.COMPOUND_COMMENTS, COL_NAMES.CPD_MW,
+        COL_NAMES.SALT_MASS, COL_NAMES.BATCH_MW].join('\', \''),
+    );
   }
-  const structureColumn = table.columns.byName('Sequence');
+  const structureColumn = table.col(COL_NAMES.SEQUENCE)!;
+  const typeColumn = table.col(COL_NAMES.TYPE)!;
   let result = '';
   for (let i = 0; i < table.rowCount; i++) {
-    try {
-      const smiles = sequenceToSmiles(structureColumn.get(i));
-      const mol = OCL.Molecule.fromSmiles(smiles);
-      result += `\n${mol.toMolfile()}\n`;
-      for (const col of table.columns)
+    result += (typeColumn.get(i) == 'SS') ?
+      sequenceToMolV3000(structureColumn.get(i), false, true) + '\n' + `>  <Sequence>\nSense Strand\n\n` :
+      sequenceToMolV3000(structureColumn.get(i), true, true) + '\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 += '$$$$';
-    } catch (error) {
-      console.error(error);
     }
+    result += '$$$$\n\n';
   }
   const element = document.createElement('a');
   element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
@@ -272,83 +274,112 @@ async function saveTableAsSdFile(table: DG.DataFrame) {
   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() {
   grok.events.onViewAdded.subscribe((v: any) => {
-    if (v.type == 'TableView' && v.dataFrame.columns.contains('Type'))
+    if (v.type == 'TableView' && v.dataFrame.columns.contains(COL_NAMES.TYPE))
       oligoSdFile(v.dataFrame);
   });
 }
 
 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('Compound Name'))
+    if (t.columns.contains(COL_NAMES.COMPOUND_NAME))
       return grok.shell.error('Columns already exist!');
 
-    table.col('Source')?.init('Johnson and Johnson Pharma');
-    table.col('ICD')?.init('No Contract');
+    const sequence = t.col(COL_NAMES.SEQUENCE)!;
+    const equivalents = t.col(COL_NAMES.EQUIVALENTS)!;
 
-    const sequence = t.col('Sequence')!;
-    const salt = t.col('Salt')!;
-    const equivalents = t.col('Equivalents')!;
-
-    t.columns.addNewString('Compound Name').init((i: number) => sequence.get(i));
-    t.columns.addNewString('Compound Comments').init((i: number) => (i > 0 && i % 2 == 0) ?
+    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 chargeCol = saltsDf.col('CHARGE')!.toList();
-    const saltNames = saltsDf.col('DISPLAY')!.toList();
-    const molWeight = saltsDf.col('MOLWEIGHT')!.toList();
-    t.columns.addNewFloat('Cpd MW').init((i: number) => ((i + 1) % 3 == 0) ? DG.FLOAT_NULL : molWeight[i]);
-    t.columns.addNewFloat('Salt mass').init((i: number) => {
-      const v = chargeCol[saltNames.indexOf(salt.get(i))];
-      const n = (v == null) ? 0 : chargeCol[saltNames.indexOf(salt.get(i))];
-      return n * equivalents.get(i);
+    t.columns.addNewFloat(COL_NAMES.CPD_MW)
+      .init((i: number) => molecularWeight(sequence.get(i), weightsObj));
+    const mwCol = t.col(COL_NAMES.CPD_MW)!;
+    t.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) => {
+      const mw = mwCol.get(i);
+      return mw * equivalents.get(i);
     });
-    t.columns.addNewCalculated('Batch MW', '${Cpd MW} + ${Salt mass}', DG.COLUMN_TYPE.FLOAT, false);
+    t.columns.addNewCalculated(COL_NAMES.BATCH_MW,
+      '${' + COL_NAMES.CPD_MW + '} + ${' + COL_NAMES.SALT_MASS + '}', DG.COLUMN_TYPE.FLOAT, false,
+    );
 
     addColumnsPressed = true;
     return newDf = t;
   }
 
-  const columnsOrder = ['Chemistry', 'Number', 'Type', 'Chemistry Name', 'Internal compound ID',
-    'IDP', 'Sequence', 'Compound Name', 'Compound Comments', 'Salt', 'Equivalents', 'Purity', 'Cpd MW', 'Salt mass',
-    'Batch MW', 'Source', 'ICD', 'Owner'];
   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', async () => {
-          await addColumns(table, saltsDf);
-          grok.shell.tableView(table.name).grid.columns.setOrder(columnsOrder);
-        }, 'Add columns: Compound Name, Compound Components, Cpd MW, Salt mass, Batch MW', ''),
+        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);
-      const typeCol = view.grid.col('Type')!;
-      const saltCol = view.grid.col('Salt')!;
-      saltCol.cellType = 'html';
-      typeCol.cellType = 'html';
-      view.grid.onCellPrepare(function(gc: DG.GridCell) {
-        if (gc.isTableCell) {
-          if (gc.gridColumn.name == 'Type')
-            gc.style.element = ui.choiceInput('', gc.cell.value, ['AS', 'SS', 'Duplex']).root;
-          else if (gc.gridColumn.name == 'Salt') {
-            gc.style.element = ui.choiceInput('', gc.cell.value, saltsDf.columns.byIndex(1).toList(), () => {
-              view.dataFrame.col('Salt')!.set(gc.gridRow, '');
-            }).root;
-          }
-        }
-      });
 
-      table.onDataChanged.subscribe((_) => {
-        if (table.currentCol.name == 'IDP' && typeof table.currentCell.value != 'number')
-          grok.shell.error('Value should be numeric');
+      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(1).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);
+          });
+        }
       });
     }),
   ]);

package/src/sources.ts

@@ -0,0 +1,3 @@
+export const SOURCES = `DISPLAY
+NO DATA
+`;

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

@@ -1,5 +1,42 @@
 import {map, stadardPhosphateLinkSmiles, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS} from './map';
 import {isValidSequence} from './sequence-codes-tools';
+import {getNucleotidesMol} from './mol-transformations';
+
+export function sequenceToMolV3000(sequence: string, inverted: boolean = false, oclRender: boolean = false): string {
+  const obj = getObjectWithCodesAndSmiles(sequence);
+  let codes = sortByStringLengthInDescendingOrder(Object.keys(obj));
+  let i = 0;
+  const smilesCodes:string[] = [];
+  const codesList = [];
+  const links = ['s', 'ps', '*'];
+  const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
+  const dropdowns = Object.keys(MODIFICATIONS);
+  codes = codes.concat(dropdowns);
+  while (i < sequence.length) {
+    const code = codes.find((s: string) => s == sequence.slice(i, i + s.length))!;
+    i += code.length;
+    inverted ? codesList.unshift(code) : codesList.push(code);
+  }
+  for (let i = 0; i < codesList.length; i++) {
+    if (dropdowns.includes(codesList[i])) {
+      smilesCodes.push((i >= codesList.length / 2) ?
+        MODIFICATIONS[codesList[i]].right : MODIFICATIONS[codesList[i]].left);
+      smilesCodes.push(stadardPhosphateLinkSmiles);
+    } else {
+      if (links.includes(codesList[i]) ||
+        includesStandardLinkAlready.includes(codesList[i]) ||
+        (i < codesList.length - 1 && links.includes(codesList[i + 1]))
+      )
+        smilesCodes.push(obj[codesList[i]]);
+      else {
+        smilesCodes.push(obj[codesList[i]]);
+        smilesCodes.push(stadardPhosphateLinkSmiles);
+      }
+    }
+  }
+
+  return getNucleotidesMol(smilesCodes, oclRender);
+}
 
 export function sequenceToSmiles(sequence: string, inverted: boolean = false): string {
   const obj = getObjectWithCodesAndSmiles(sequence);
@@ -18,15 +55,9 @@ export function sequenceToSmiles(sequence: string, inverted: boolean = false): s
   }
   for (let i = 0; i < codesList.length; i++) {
     if (dropdowns.includes(codesList[i])) {
-      if (i == codesList.length -1 || (i < codesList.length - 1 && links.includes(codesList[i + 1]))) {
-        smiles += (i >= codesList.length / 2) ?
-          MODIFICATIONS[codesList[i]].right:
-          MODIFICATIONS[codesList[i]].left;
-      } else if (i < codesList.length - 1) {
-        smiles += (i >= codesList.length / 2) ?
-          MODIFICATIONS[codesList[i]].right + stadardPhosphateLinkSmiles:
-          MODIFICATIONS[codesList[i]].left + stadardPhosphateLinkSmiles;
-      }
+      smiles += (i >= codesList.length / 2) ?
+        MODIFICATIONS[codesList[i]].right + stadardPhosphateLinkSmiles:
+        MODIFICATIONS[codesList[i]].left + stadardPhosphateLinkSmiles;
     } else {
       if (links.includes(codesList[i]) ||
         includesStandardLinkAlready.includes(codesList[i]) ||

package/src/structures-works/map.ts

@@ -11,14 +11,36 @@ 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_MASS: 'Salt mass',
+  BATCH_MW: 'Batch MW',
+  SOURCE: 'Source',
+  ICD: 'ICD',
+  OWNER: 'Owner',
+};
 // interface CODES {
 // }
-export const MODIFICATIONS: {[index: string]: {left: string, right: string}} = {
+export const MODIFICATIONS: {[index: string]: {molecularWeight: number, left: string, right: string}} = {
   '(invabasic)': {
+    molecularWeight: 118.13,
     left: 'O[C@@H]1C[C@@H]O[C@H]1CO',
     right: 'O[C@@H]1C[C@@H]O[C@H]1CO',
   },
   '(GalNAc-2-JNJ)': {
+    molecularWeight: 1273.3,
     left: 'C(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)' +
     '(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)' +
     '(COCCC(=O)NCCCNC(=O)CCCCOC2OC(CO)C(O)C(O)C2NC(=O)C)NC(=O)CCCC(=O)NCC(O)CO',
@@ -49,7 +71,7 @@ export const map: {[synthesizer: string]:
             'name': 'Guanine',
             'weight': 329.21,
             'normalized': 'dG',
-            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O',
+            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'C': {
             'name': 'Cytosine',
@@ -75,7 +97,7 @@ export const map: {[synthesizer: string]:
             'name': 'Guanine',
             'weight': 329.21,
             'normalized': 'dG',
-            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O',
+            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'C': {
             'name': 'Cytosine',
@@ -139,7 +161,7 @@ export const map: {[synthesizer: string]:
             'name': 'Guanine',
             'weight': 329.21,
             'normalized': 'dG',
-            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O',
+            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'T': {
             'name': 'Tyrosine',
@@ -341,13 +363,13 @@ export const map: {[synthesizer: string]:
             'name': 'Guanine',
             'weight': 329.21,
             'normalized': 'dG',
-            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O',
+            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'dG': {
             'name': 'Guanine',
             'weight': 329.21,
             'normalized': 'dG',
-            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C)[C@@H]1O',
+            'SMILES': 'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)C[C@@H]1O',
           },
           'T': {
             'name': 'Tyrosine',