@datagrok/sequence-translator 1.0.16 → 1.1.0

package/src/helpers.ts

@@ -1,28 +0,0 @@
-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

@@ -1,262 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import * as rxjs from 'rxjs';
-import {convertSequence, undefinedInputSequence, isValidSequence} from '../structures-works/sequence-codes-tools';
-import {map} from '../structures-works/map';
-import {MODIFICATIONS} from '../structures-works/const';
-import {sequenceToSmiles, sequenceToMolV3000} from '../structures-works/from-monomers';
-import $ from 'cash-dom';
-import {download} from '../helpers';
-import {extractAtomDataV3000} from '../structures-works/mol-transformations';
-import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
-
-const defaultInput = 'fAmCmGmAmCpsmU'; // todo: capitalize constants
-const sequenceWasCopied = 'Copied'; // todo: wrap hardcoded literals into constants
-const tooltipSequence = 'Copy sequence';
-
-export async function mainView(onSequenceChanged: (seq: string) => void): Promise<HTMLDivElement> {
-  const onInput: rxjs.Subject<string> = new rxjs.Subject<string>();
-
-  async function updateTableAndMolecule(sequence: string, inputFormat: string): Promise<void> {
-    moleculeSvgDiv.innerHTML = '';
-    outputTableDiv.innerHTML = '';
-    const pi = DG.TaskBarProgressIndicator.create('Rendering table and molecule...');
-
-    try {
-      sequence = sequence.replace(/\s/g, '');
-      const output = isValidSequence(sequence, null);
-      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;
-
-        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, ''),
-        });
-      }
-
-      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 formCanvasWidth = 500;
-        const formCanvasHeight = 170;
-        const formCanvas = ui.canvas(
-          formCanvasWidth * window.devicePixelRatio, formCanvasHeight * window.devicePixelRatio);
-        formCanvas.style.width = `${formCanvasWidth}px`;
-        formCanvas.style.height = `${formCanvasHeight}px`;
-
-        formCanvas.addEventListener('click', async () => {
-          try {
-            const mol = sequenceToMolV3000(
-              inputSequenceField.value.replace(/\s/g, ''), false, true,
-              output.synthesizer![0],
-            );
-            console.log(mol);
-
-            const addDiv = ui.div([], {style: {overflowX: 'scroll'}});
-
-            // addDiv size required, but now available before dialog show()
-            const coordinates = extractAtomDataV3000(mol);
-            const cw: number = $(window).width() * 0.80; // addDiv.clientWidth
-            const ch: number = $(window).height() * 0.70; // addDiv.clientHeight
-            const molWidth: number = Math.max(...coordinates.x) - Math.min(...coordinates.x);
-            const molHeight: number = Math.max(...coordinates.y) - Math.min(...coordinates.y);
-
-            const wR: number = cw / molWidth;
-            const hR: number = ch / molHeight;
-            const r: number = hR; // Math.max(wR, hR);
-            const dlgCanvasWidth = r * molWidth;
-            const dlgCanvasHeight = r * molHeight;
-
-            const dlgCanvas = ui.canvas(dlgCanvasWidth * window.devicePixelRatio, dlgCanvasHeight * window.devicePixelRatio);
-            dlgCanvas.style.width = `${dlgCanvasWidth}px`;
-            dlgCanvas.style.height = `${dlgCanvasHeight}px`;
-
-            // // @ts-ignore
-            // OCL.StructureView.drawMolecule(dlgCanvas, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
-            // await grok.chem.canvasMol(0, 0, dlgCanvas.width, dlgCanvas.height, dlgCanvas, mol, null,
-            //   {setNewCoords: false, normalizeDepiction: false, straightenDepiction: false});
-            await grok.functions.call('Chem:canvasMol', {
-              x: 0, y: 0, w: dlgCanvas.width, h: dlgCanvas.height, canvas: dlgCanvas,
-              molString: mol, scaffoldMolString: '',
-              options: {normalizeDepiction: false, straightenDepiction: false}
-            });
-
-            addDiv.appendChild(dlgCanvas);
-            ui.dialog('Molecule: ' + inputSequenceField.value)
-              .add(addDiv)
-              .showModal(true);
-          } catch (err) {
-            const errStr = errorToConsole(err);
-            console.error(errStr);
-          }
-        });
-        $(formCanvas).on('mouseover', () => $(formCanvas).css('cursor', 'zoom-in'));
-        $(formCanvas).on('mouseout', () => $(formCanvas).css('cursor', 'default'));
-        const mol = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, true,
-          output.synthesizer![0]);
-        // // @ts-ignore
-        // OCL.StructureView.drawMolecule(formCanvas, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
-        await grok.functions.call('Chem:canvasMol', {
-          x: 0, y: 0, w: formCanvas.width, h: formCanvas.height, canvas: formCanvas,
-          molString: mol, scaffoldMolString: '',
-          options: {normalizeDepiction: false, straightenDepiction: false}
-        });
-        moleculeSvgDiv.append(formCanvas);
-      } else
-        moleculeSvgDiv.innerHTML = '';
-    } finally {
-      pi.close();
-    }
-  }
-
-  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) => {
-    // Send event to DG.debounce()
-    onInput.next(sequence);
-  });
-
-  DG.debounce<string>(onInput, 300).subscribe((sequence) => {
-    updateTableAndMolecule(sequence, inputFormatChoiceInput.value!);
-    onSequenceChanged(sequence);
-  });
-
-  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, allowEdit: false},
-  );
-
-  const overhangModificationsGrid = DG.Viewer.grid(
-    DG.DataFrame.fromColumns([
-      DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
-    ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
-  );
-  updateTableAndMolecule(defaultInput, inputFormatChoiceInput.value!);
-
-  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 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.');
-
-  $(codesTablesDiv).hide();
-  const switchInput = ui.switchInput('Codes', false, (v: boolean) => (v) ?
-    $(codesTablesDiv).show() :
-    $(codesTablesDiv).hide(),
-  );
-
-  const downloadMolFileIcon = ui.iconFA('download', async () => {
-    const clearSequence = inputSequenceField.value.replace(/\s/g, '');
-    const result = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), 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 = [
-    downloadMolFileIcon,
-    copySmilesIcon,
-    switchInput.root,
-  ];
-
-  const v = grok.shell.v;
-  const tabControl = grok.shell.sidebar;
-  tabControl.onTabChanged.subscribe((_) => {
-    v.setRibbonPanels([(tabControl.currentPane.name == 'MAIN') ? topPanel : []]);
-  });
-  v.setRibbonPanels([topPanel]);
-
-  return ui.box(
-    ui.splitH([
-      ui.splitV([
-        ui.panel([
-          appMainDescription,
-          ui.div([
-            ui.h1('Input sequence'),
-            ui.div([], 'input-base'),
-            inputSequenceField.root,
-          ], 'inputSequence'),
-          ui.div([inputFormatChoiceInput], {style: {padding: '5px 0'}}),
-          ui.block([
-            ui.h1('Output'),
-            outputTableDiv,
-          ]),
-          moleculeSvgDiv,
-        ], 'sequence'),
-      ]),
-      codesTablesDiv,
-    ], {style: {height: '100%', width: '100%'}}),
-  );
-}

package/src/structures-works/const.ts

@@ -1,5 +0,0 @@
-import * as map from './map';
-
-export const MODIFICATIONS = map.MODIFICATIONS;
-
-export const standardPhosphateLinkSmiles = 'OP(=O)(O)O';

package/src/structures-works/converters.ts

@@ -1,323 +0,0 @@
-import {lcmsToGcrs, MODIFICATIONS} from './map';
-import * as DG from 'datagrok-api/dg';
-import {DELIMITER} from './map';
-import {sortByStringLengthInDescendingOrder} from '../helpers';
-//name: gcrsToLcms
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: LCMS}
-export function gcrsToLcms(sequence: string): string {
-  try {
-    const df = DG.DataFrame.fromCsv(lcmsToGcrs);
-    const arr1: string[] = df.getCol('GCRS').toList();
-    const arr2: string[] = df.getCol('LCMS').toList();
-    const obj: { [i: string]: string } = {};
-    arr1.forEach((element, index) => obj[element] = arr2[index]);
-    obj[DELIMITER] = DELIMITER;
-    const codes = arr1
-      .concat(DELIMITER)
-      .concat(Object.keys(MODIFICATIONS));
-    const sortedCodes = sortByStringLengthInDescendingOrder(codes);
-    let i = 0;
-    let r1 = '';
-    while (i < sequence.length) {
-      const matchedCode = sortedCodes.find((c) => c == sequence.slice(i, i + c.length))!;
-      r1 += obj[sequence.slice(i, i + matchedCode.length)];
-      i += matchedCode.length;
-    }
-    while (r1.indexOf('//') != -1)
-      r1 = r1.replace('//', '/');
-    return r1;
-  } catch {
-    return '<error>';
-  }
-}
-
-//name: asoGapmersNucleotidesToBioSpring
-//input: string nucleotides {semType: DNA nucleotides}
-//output: string result {semType: BioSpring / Gapmers}
-export function asoGapmersNucleotidesToBioSpring(nucleotides: string): string {
-  let count: number = -1;
-  const objForEdges: { [index: string]: string } = {
-    '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': '5*', 'A': '6*', 'C': '7*', 'G': '8*'};
-  const objForCenter: { [index: string]: string } = {
-    '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': 'T*', 'A': 'A*', 'C': '9*', 'G': 'G*'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|T|C|G)/g, function(x: string) {
-    count++;
-    return (count > 4 && count < 15) ? objForCenter[x] : objForEdges[x];
-  }).slice(0, (nucleotides.endsWith('(invabasic)') || nucleotides.endsWith('(GalNAc-2-JNJ)')) ?
-    nucleotides.length : 2 * count + 1);
-}
-
-//name: asoGapmersNucleotidesToGcrs
-//input: string nucleotides {semType: DNA nucleotides}
-//output: string result {semType: GCRS / Gapmers}
-export function asoGapmersNucleotidesToGcrs(nucleotides: string): string {
-  let count: number = -1;
-  const objForEdges: { [index: string]: string } = {
-    '(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'T': 'moeUnps',
-    'A': 'moeAnps', 'C': 'moe5mCnps', 'G': 'moeGnps'};
-  const objForCenter: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'C': '5mCps', 'A': 'Aps', 'T': 'Tps', 'G': 'Gps'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|T|C|G)/g, function(x: string) {
-    count++;
-    if (count < 5) return (count == 4) ? objForEdges[x].slice(0, -3) + 'ps' : objForEdges[x];
-    if (count < 15) return (count == 14) ? objForCenter[x].slice(0, -2) + 'nps' : objForCenter[x];
-    return objForEdges[x];
-  }).slice(0, (nucleotides.endsWith('(invabasic)') || nucleotides.endsWith('(GalNAc-2-JNJ)')) ?
-    nucleotides.length : -3);
-}
-
-//name: asoGapmersBioSpringToNucleotides
-//input: string nucleotides {semType: BioSpring / Gapmers}
-//output: string result {semType: DNA nucleotides}
-export function asoGapmersBioSpringToNucleotides(nucleotides: string): string {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '*': '', '5': 'T', '6': 'A', '7': 'C', '8': 'G', '9': 'C'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|\*|5|6|7|8|9)/g, function(x: string) {return obj[x];});
-}
-
-//name: asoGapmersBioSpringToGcrs
-//input: string nucleotides {semType: BioSpring / Gapmers}
-//output: string result {semType: GCRS / Gapmers}
-export function asoGapmersBioSpringToGcrs(nucleotides: string): string {
-  let count: number = -1;
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '5*': 'moeUnps', '6*': 'moeAnps', '7*': 'moe5mCnps', '8*': 'moeGnps', '9*': '5mCps', 'A*': 'Aps', 'T*': 'Tps',
-    'G*': 'Gps', 'C*': 'Cps', '5': 'moeU', '6': 'moeA', '7': 'moe5mC', '8': 'moeG',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|5\*|6\*|7\*|8\*|9\*|A\*|T\*|G\*|C\*|5|6|7|8)/g,
-    function(x: string) {
-      count++;
-      return (count == 4) ? obj[x].slice(0, -3) + 'ps' : (count == 14) ? obj[x].slice(0, -2) + 'nps' : obj[x];
-    });
-}
-
-
-//name: asoGapmersGcrsToBioSpring
-//input: string nucleotides {semType: GCRS / Gapmers}
-//output: string result {semType: BioSpring / Gapmers}
-export function asoGapmersGcrsToBioSpring(nucleotides: string): string {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'fU': '1', 'fA': '2', 'fC': '3', 'fG': '4', 'mU': '5', 'mA': '6', 'mC': '7', 'mG': '8',
-    'moeT': '5', 'moeA': '6', 'moe5mC': '7', 'moeG': '8', 'moeU': '5', '5mC': '9', 'nps': '*', 'ps': '*', 'U': 'T',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|fU|fA|fC|fG|mU|mA|mC|mG|moeT|moeA|moe5mC|moeG|moeU|5mC|nps|ps|U)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: asoGapmersGcrsToNucleotides
-//input: string nucleotides {semType: GCRS / Gapmers}
-//output: string result {semType: DNA nucleotides}
-export function asoGapmersGcrsToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'moe': '', '5m': '', 'n': '', 'ps': '', 'U': 'T'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|moe|5m|n|ps|U)/g, function(x: string) {return obj[x];});
-}
-
-//name: siRnaBioSpringToNucleotides
-//input: string nucleotides {semType: BioSpring / siRNA}
-//output: string result {semType: RNA nucleotides}
-export function siRnaBioSpringToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '1': 'U', '2': 'A', '3': 'C', '4': 'G', '5': 'U', '6': 'A', '7': 'C', '8': 'G', '*': ''};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|1|2|3|4|5|6|7|8|\*)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaBioSpringToAxolabs
-//input: string nucleotides {semType: BioSpring / siRNA}
-//output: string result {semType: Axolabs / siRNA}
-export function siRnaBioSpringToAxolabs(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '1': 'Uf', '2': 'Af', '3': 'Cf', '4': 'Gf', '5': 'u', '6': 'a', '7': 'c', '8': 'g', '*': 's'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|1|2|3|4|5|6|7|8|\*)/g,
-    function(x: string) {return obj[x];});
-}
-
-
-//name: siRnaBioSpringToGcrs
-//input: string nucleotides {semType: BioSpring / siRNA}
-//output: string result {semType: GCRS}
-export function siRnaBioSpringToGcrs(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    '1': 'fU', '2': 'fA', '3': 'fC', '4': 'fG', '5': 'mU', '6': 'mA', '7': 'mC', '8': 'mG', '*': 'ps'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|1|2|3|4|5|6|7|8|\*)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaAxolabsToGcrs
-//input: string nucleotides {semType: Axolabs / siRNA}
-//output: string result {semType: GCRS}
-export function siRnaAxolabsToGcrs(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'Uf': 'fU', 'Af': 'fA', 'Cf': 'fC', 'Gf': 'fG', 'u': 'mU', 'a': 'mA', 'c': 'mC', 'g': 'mG', 's': 'ps',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|Uf|Af|Cf|Gf|u|a|c|g|s)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaAxolabsToBioSpring
-//input: string nucleotides {semType: Axolabs / siRNA}
-//output: string result {semType: BioSpring / siRNA}
-export function siRnaAxolabsToBioSpring(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'Uf': '1', 'Af': '2', 'Cf': '3', 'Gf': '4', 'u': '5', 'a': '6', 'c': '7', 'g': '8', 's': '*',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|Uf|Af|Cf|Gf|u|a|c|g|s)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaAxolabsToNucleotides
-//input: string nucleotides {semType: Axolabs / siRNA}
-//output: string result {semType: RNA nucleotides}
-export function siRnaAxolabsToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'Uf': 'U', 'Af': 'A', 'Cf': 'C', 'Gf': 'G', 'u': 'U', 'a': 'A', 'c': 'C', 'g': 'G', 's': '',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|Uf|Af|Cf|Gf|u|a|c|g|s)/g,
-    function(x: string) {return obj[x];});
-}
-
-
-//name: siRnaGcrsToNucleotides
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: RNA nucleotides}
-export function siRnaGcrsToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'fU': 'U', 'fA': 'A', 'fC': 'C', 'fG': 'G', 'mU': 'U', 'mA': 'A', 'mC': 'C', 'mG': 'G', 'ps': '',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|fU|fA|fC|fG|mU|mA|mC|mG|ps)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaGcrsToBioSpring
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: BioSpring / siRNA}
-export function siRnaGcrsToBioSpring(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'fU': '1', 'fA': '2', 'fC': '3', 'fG': '4', 'mU': '5', 'mA': '6', 'mC': '7', 'mG': '8', 'ps': '*',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|fU|fA|fC|fG|mU|mA|mC|mG|ps)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaGcrsToAxolabs
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: Axolabs / siRNA}
-export function siRnaGcrsToAxolabs(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'fU': 'Uf', 'fA': 'Af', 'fC': 'Cf', 'fG': 'Gf', 'mU': 'u', 'mA': 'a', 'mC': 'c', 'mG': 'g', 'ps': 's',
-  };
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|fU|fA|fC|fG|mU|mA|mC|mG|ps)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: siRnaNucleotideToBioSpringSenseStrand
-//input: string nucleotides {semType: RNA nucleotides}
-//output: string result {semType: BioSpring / siRNA}
-export function siRnaNucleotideToBioSpringSenseStrand(nucleotides: string) {
-  let count: number = -1;
-  const objForLeftEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': '6*', 'U': '5*', 'G': '8*', 'C': '7*'};
-  const objForRightEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': '*6', 'U': '*5', 'G': '*8', 'C': '*7'};
-  const objForOddIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': '6', 'U': '5', 'G': '8', 'C': '7'};
-  const objForEvenIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': '2', 'U': '1', 'G': '4', 'C': '3'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C)/g, function(x: string) {
-    count++;
-    if (count < 2) return objForLeftEdge[x];
-    if (count > nucleotides.length - 3) return objForRightEdge[x];
-    return (count % 2 == 0) ? objForEvenIndices[x] : objForOddIndices[x];
-  });
-}
-
-//name: siRnaNucleotidesToGcrs
-//input: string nucleotides {semType: RNA nucleotides}
-//output: string result {semType: GCRS}
-export function siRnaNucleotidesToGcrs(nucleotides: string) {
-  let count: number = -1;
-  const objForLeftEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': 'mAps', 'U': 'mUps', 'G': 'mGps', 'C': 'mCps'};
-  const objForRightEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': 'psmA', 'U': 'psmU', 'G': 'psmG', 'C': 'psmC'};
-  const objForEvenIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'fA', 'U': 'fU', 'G': 'fG', 'C': 'fC'};
-  const objForOddIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'mA', 'U': 'mU', 'G': 'mG', 'C': 'mC'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C)/g, function(x: string) {
-    count++;
-    if (count < 2) return objForLeftEdge[x];
-    if (count > nucleotides.length - 3) return objForRightEdge[x];
-    return (count % 2 == 0) ? objForEvenIndices[x] : objForOddIndices[x];
-  });
-}
-
-//name: siRnaNucleotideToAxolabsSenseStrand
-//input: string nucleotides {semType: RNA nucleotides}
-//output: string result {semType: Axolabs}
-export function siRnaNucleotideToAxolabsSenseStrand(nucleotides: string) {
-  let count: number = -1;
-  const objForLeftEdge: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': 'as', 'U': 'us', 'G': 'gs', 'C': 'cs'};
-  const objForSomeIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'Af', 'U': 'Uf', 'G': 'Gf', 'C': 'Cf'};
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'A': 'a', 'U': 'u', 'G': 'g', 'C': 'c'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C)/g, function(x: string) {
-    count++;
-    if (count < 2) return objForLeftEdge[x];
-    if (count == 6 || (count > 7 && count < 11)) return objForSomeIndices[x];
-    if (count == nucleotides.length - 1) return 'a';
-    return obj[x];
-  });
-}
-
-//name: siRnaNucleotideToAxolabsAntisenseStrand
-//input: string nucleotides {semType: RNA nucleotides}
-//output: string result {semType: Axolabs}
-export function siRnaNucleotideToAxolabsAntisenseStrand(nucleotides: string) {
-  let count: number = -1;
-  const objForSmallLinkages: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'as', 'U': 'us', 'G': 'gs', 'C': 'cs'};
-  const objForBigLinkages: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'Afs', 'U': 'Ufs', 'G': 'Gfs', 'C': 'Cfs'};
-  const objForSomeIndices: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'Af', 'U': 'Uf', 'G': 'Gf', 'C': 'Cf'};
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)',
-    '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)', 'A': 'a', 'U': 'u', 'G': 'g', 'C': 'c'};
-  return nucleotides.replace(/(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C)/g, function(x: string) {
-    count++;
-    if (count > 19 && count < 22) return objForSmallLinkages[x];
-    if (count == 0) return 'us';
-    if (count == 1) return objForBigLinkages[x];
-    return (count == 5 || count == 7 || count == 8 || count == 13 || count == 15) ? objForSomeIndices[x] : obj[x];
-  });
-}
-
-//name: gcrsToNucleotides
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: RNA nucleotides}
-export function gcrsToNucleotides(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'mAps': 'A', 'mUps': 'U', 'mGps': 'G', 'mCps': 'C', 'fAps': 'A', 'fUps': 'U', 'fGps': 'G', 'fCps': 'C',
-    'fU': 'U', 'fA': 'A', 'fC': 'C', 'fG': 'G', 'mU': 'U', 'mA': 'A', 'mC': 'C', 'mG': 'G',
-  };
-  return nucleotides.replace(
-    /(\(invabasic\)|\(GalNAc-2-JNJ\)|mAps|mUps|mGps|mCps|fAps|fUps|fGps|fCps|fU|fA|fC|fG|mU|mA|mC|mG)/g,
-    function(x: string) {return obj[x];});
-}
-
-//name: gcrsToMermade12
-//input: string nucleotides {semType: GCRS}
-//output: string result {semType: Mermade 12 / siRNA}
-export function gcrsToMermade12(nucleotides: string) {
-  const obj: {[index: string]: string} = {'(invabasic)': '(invabasic)', '(GalNAc-2-JNJ)': '(GalNAc-2-JNJ)',
-    'mAps': 'e', 'mUps': 'h', 'mGps': 'g', 'mCps': 'f', 'fAps': 'i', 'fUps': 'l', 'fGps': 'k', 'fCps': 'j', 'fU': 'L',
-    'fA': 'I', 'fC': 'J', 'fG': 'K', 'mU': 'H', 'mA': 'E', 'mC': 'F', 'mG': 'G',
-  };
-  return nucleotides.replace(
-    /(\(invabasic\)|\(GalNAc-2-JNJ\)|mAps|mUps|mGps|mCps|fAps|fUps|fGps|fCps|fU|fA|fC|fG|mU|mA|mC|mG)/g,
-    function(x: string) {return obj[x];});
-}