@datagrok/sequence-translator 1.0.14 → 1.0.15

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.0.14",
+  "version": "1.0.15",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"
@@ -13,7 +13,7 @@
     "directory": "packages/SequenceTranslator"
   },
   "dependencies": {
-    "@datagrok-libraries/utils": "^1.15.5",
+    "@datagrok-libraries/utils": "^1.17.2",
     "@types/react": "^18.0.15",
     "@datagrok-libraries/bio": "^5.11.1",
     "datagrok-api": "^1.7.2",
@@ -24,25 +24,6 @@
     "ts-loader": "^9.3.1",
     "typescript": "^4.7.4"
   },
-  "scripts": {
-    "link-api": "npm link datagrok-api",
-    "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio",
-    "debug-sequencetranslator": "grok publish",
-    "release-sequencetranslator": "grok publish localhost --release",
-    "build-sequencetranslator": "webpack",
-    "build": "webpack",
-    "debug-sequencetranslator-public": "grok publish public",
-    "release-sequencetranslator-public": "grok publish public --release",
-    "debug-sequencetranslator-local": "grok publish local",
-    "release-sequencetranslator-local": "grok publish local --release",
-    "test": "jest",
-    "test-dev": "set HOST=dev && jest",
-    "test-local": "set HOST=localhost && jest"
-  },
-  "sources": [
-    "css/style.css",
-    "vendors/openchemlib-full.js"
-  ],
   "devDependencies": {
     "@types/jest": "^27.0.0",
     "@types/jquery": "^3.5.14",
@@ -62,5 +43,27 @@
     "@types/node-fetch": "^2.6.2",
     "node-fetch": "^2.6.7"
   },
+  "grokDependencies": {
+    "@datagrok/chem": "1.3.32"
+  },
+  "scripts": {
+    "link-api": "npm link datagrok-api",
+    "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/bio",
+    "debug-sequencetranslator": "grok publish",
+    "release-sequencetranslator": "grok publish localhost --release",
+    "build-sequencetranslator": "webpack",
+    "build": "webpack",
+    "debug-sequencetranslator-public": "grok publish public",
+    "release-sequencetranslator-public": "grok publish public --release",
+    "debug-sequencetranslator-local": "grok publish local",
+    "release-sequencetranslator-local": "grok publish local --release",
+    "test": "jest",
+    "test-dev": "set HOST=dev && jest",
+    "test-local": "set HOST=localhost && jest"
+  },
+  "sources": [
+    "css/style.css",
+    "vendors/openchemlib-full.js"
+  ],
   "category": "Bioinformatics"
 }

package/scripts/build-monomer-lib.py

@@ -1,10 +1,8 @@
 from io import TextIOWrapper
 
-from rdkit.Chem import AllChem
 from rdkit import Chem
 
 import orjson
-import json
 
 import click
 
@@ -12,16 +10,55 @@ from click_default_group import DefaultGroup
 from rdkit.Chem.rdchem import Mol
 
 
-def smiles2molfile(smiles: str) -> str:
-    mol: Mol = Chem.MolFromSmiles(smiles)
+def molAddCollection(mol: Mol, name: str, title: str = None) -> str:
+    """
+    Get and postprocess (atom's CFG, title, e.t.c.) molblock
+    :param mol:    Mol molecule structure / object
+    :param name:   Monomer name to add to molblock title
+    :param title:  title to replace in Chem.MolToMolBlock() string output
+    :return:       molblock string
+    """
     res: str = Chem.MolToMolBlock(mol, forceV3000=True)  # MolToMolFile
-    return res
 
+    mb_line_list: list[str] = res.split('\n')
+    if title:
+        mb_line_list[1] = title
+
+    if name and name not in mb_line_list[1]:
+        mb_line_list[1] += '|' + name
+
+    end_bond_idx: int = mb_line_list.index('M  V30 END BOND')
+    chirality = [atom.GetChiralTag() for atom in mol.GetAtoms()]
+    begin_atom_idx = mb_line_list.index('M  V30 BEGIN ATOM')
+    end_atom_idx = mb_line_list.index('M  V30 END ATOM')
+    for atom_idx in range(1, end_atom_idx - begin_atom_idx):
+        line_idx = begin_atom_idx + atom_idx
+        atom_ch = chirality[atom_idx - 1]
+        if atom_ch != Chem.rdchem.CHI_UNSPECIFIED:
+            mb_line_list[line_idx] += " CFG={0}".format(int(atom_ch))
+
+    steabs: list[int] = [i + 1 for (i, ch) in enumerate(chirality) if ch != Chem.rdchem.CHI_UNSPECIFIED]
+    if len(steabs) > 0:
+        steabs_str: str = "M  V30 MDLV30/STEABS ATOMS=({count} {list})" \
+            .format(count=len(steabs), list=' '.join([str(idx) for idx in steabs]))
+
+        mb_line_list = mb_line_list[:(end_bond_idx + 1)] + \
+                       ["M  V30 BEGIN COLLECTION", steabs_str, "M  V30 END COLLECTION"] + \
+                       mb_line_list[(end_bond_idx + 1):]
 
-def molV2000toMolV3000(molV2K: str) -> str:
-    mol: str = Chem.MolFromMolBlock(molV2K)
-    res: str = Chem.MolToMolBlock(mol, forceV3000=True)
-    return res.replace('Pol', 'O  ')
+    return '\n'.join(mb_line_list)
+
+
+def molfile2molfile(src_mol: str, name: str) -> str:
+    mol: Mol = Chem.MolFromMolBlock(src_mol)
+    src_mf_lines = src_mol.split('\n')
+    title = src_mf_lines[1]
+    return molAddCollection(mol, name, title=title)
+
+
+def smiles2molfile(smiles: str, name: str) -> str:
+    mol: Mol = Chem.MolFromSmiles(smiles)
+    return molAddCollection(mol, name)
 
 
 CodesType = dict[str, dict[str, list[str]]]
@@ -29,13 +66,13 @@ CodesType = dict[str, dict[str, list[str]]]
 
 class Monomer:
     def __init__(self,
-                 symbol: str, name: str, smiles: str,
+                 symbol: str, name: str, molfile: str, smiles: str,
                  codes: CodesType):
         self.monomerType = 'Backbone'
         self.smiles = smiles
         self.name = name
         self.author = 'SequenceTranslator'
-        self.molfile = smiles2molfile(smiles)
+        self.molfile = molfile2molfile(molfile, name) if molfile else smiles2molfile(smiles, name)
         self.naturalAnalog = ''
         self.rgroups = [
             {
@@ -58,8 +95,9 @@ class Monomer:
 
     @staticmethod
     def from_json(src_json: {}):
-        obj = Monomer(src_json['symbol'], src_json['name'], src_json['smiles'], src_json['codes'])
-        obj.molfile = src_json['molfile']
+        obj = Monomer(src_json['symbol'], src_json['name'],
+                      src_json['molfile'], src_json['smiles'],
+                      src_json['codes'])
         return obj
 
     def to_json(self):
@@ -89,7 +127,7 @@ def codes2monomers(codes_json: {}) -> dict[str, Monomer]:
                     symbol = monomer_json['name']
                     name = monomer_json['name']
                     smiles = monomer_json['SMILES']
-                    monomers_res[monomer_name] = Monomer(symbol, name, smiles, {})
+                    monomers_res[monomer_name] = Monomer(symbol, name, None, smiles, {})
                 codes = monomers_res[monomer_name].codes
                 if codes_src not in codes:
                     codes[codes_src] = {}

package/src/axolabs/constants.ts

@@ -44,22 +44,22 @@ export const AXOLABS_MAP:
     color: 'rgb(255,192,0)',
   },
   'A': {
-    fullName: 'Adenine',
+    fullName: 'Adenosine',
     symbols: ['a', 'a', 'a', 'a'],
     color: RNA_COLOR,
   },
   'C': {
-    fullName: 'Cytosine',
+    fullName: 'Cytidine',
     symbols: ['c', 'c', 'c', 'c'],
     color: RNA_COLOR,
   },
   'G': {
-    fullName: 'Guanine',
+    fullName: 'Guanosine',
     symbols: ['g', 'g', 'g', 'g'],
     color: RNA_COLOR,
   },
   'U': {
-    fullName: 'Uracil',
+    fullName: 'Uridine',
     symbols: ['u', 'u', 'u', 'u'],
     color: RNA_COLOR,
   },

package/src/main/main-view.ts

@@ -1,36 +1,30 @@
 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(): Promise<HTMLDivElement> {
-  const monomersLibAddress = 'System:AppData/SequenceTranslator/helmLib.json';
+  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...');
     let errorsExist = false;
 
-    // external helm-like monomers library
-    const fileExists = await grok.dapi.files.exists(monomersLibAddress);
-    if (!fileExists) {
-      // todo: improve behaviour in this case
-      grok.shell.warning('Please, provide the file with monomers library as System:AppData/SequenceTranslator/helmLib.json');
-      pi.close();
-      return;
-    }
-
-    const monomersLib = await grok.dapi.files.readAsText(monomersLibAddress);
-
     try {
       sequence = sequence.replace(/\s/g, '');
       const output = isValidSequence(sequence, null);
@@ -46,16 +40,16 @@ export async function mainView(): Promise<HTMLDivElement> {
         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, ''),
+            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, ''),
         });
       }
 
@@ -67,27 +61,71 @@ export async function mainView(): Promise<HTMLDivElement> {
       );
 
       if (outputSequenceObj.type != undefinedInputSequence && outputSequenceObj.Error != undefinedInputSequence) {
-        const canvas = ui.canvas(300, 170);
-        canvas.addEventListener('click', () => {
-          const canv = ui.canvas($(window).width(), $(window).height());
-          const mol = sequenceToMolV3000(
-            inputSequenceField.value.replace(/\s/g, ''), false, true,
-            output.synthesizer![0],
-          );
-          console.log(mol);
-          // @ts-ignore
-          OCL.StructureView.drawMolecule(canv, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
-          ui.dialog('Molecule: ' + inputSequenceField.value)
-            .add(canv)
-            .showModal(true);
+        const formCanvasWidth = 500;
+        const formCanvasHeight = 170;
+        const formCanvas = ui.canvas(
+          formCanvasWidth * window.devicePixelRatio, formCanvasHeight * window.devicePixelRatio);
+        formCanvas.style.width = `${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: {setNewCoords: false, 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);
+          }
         });
-        $(canvas).on('mouseover', () => $(canvas).css('cursor', 'zoom-in'));
-        $(canvas).on('mouseout', () => $(canvas).css('cursor', 'default'));
+        $(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(canvas, OCL.Molecule.fromMolfile(mol), {suppressChiralText: true});
-        moleculeSvgDiv.append(canvas);
+        // // @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: {setNewCoords: false, normalizeDepiction: false, straightenDepiction: false}
+        });
+        moleculeSvgDiv.append(formCanvas);
       } else
         moleculeSvgDiv.innerHTML = '';
     } finally {
@@ -102,6 +140,11 @@ export async function mainView(): Promise<HTMLDivElement> {
   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!);
   });
 
@@ -139,9 +182,9 @@ export async function mainView(): Promise<HTMLDivElement> {
   );
 
   const overhangModificationsGrid = DG.Viewer.grid(
-      DG.DataFrame.fromColumns([
-        DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
-      ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
+    DG.DataFrame.fromColumns([
+      DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
+    ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
   );
   updateTableAndMolecule(defaultInput, inputFormatChoiceInput.value!);
 
@@ -171,7 +214,6 @@ export async function mainView(): Promise<HTMLDivElement> {
 
   const downloadMolFileIcon = ui.iconFA('download', async () => {
     const clearSequence = inputSequenceField.value.replace(/\s/g, '');
-    const monomersLib = await grok.dapi.files.readAsText(monomersLibAddress);
     const result = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, false,
       inputFormatChoiceInput.value!);
     download(clearSequence + '.mol', encodeURIComponent(result));
@@ -203,9 +245,8 @@ export async function mainView(): Promise<HTMLDivElement> {
           appMainDescription,
           ui.div([
             ui.h1('Input sequence'),
-            ui.div([
-              inputSequenceField.root,
-            ], 'input-base'),
+            ui.div([], 'input-base'),
+            inputSequenceField.root,
           ], 'inputSequence'),
           ui.div([inputFormatChoiceInput], {style: {padding: '5px 0'}}),
           ui.block([

package/src/package.ts

@@ -16,11 +16,11 @@ export let monomerWorks: MonomerWorks | null = null;
 
 export function getMonomerWorks() {
   return monomerWorks;
-};
+}
 
 export function getMonomerLib() {
   return monomerLib;
-};
+}
 
 //name: Sequence Translator
 //tags: app

package/src/structures-works/const.ts

@@ -1,18 +1,5 @@
-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',
-    right: 'OCC(O)CNC(=O)CCCC(=O)NC(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)',
-  },
-};
+import * as map from './map';
+
+export const MODIFICATIONS = map.MODIFICATIONS;
 
 export const standardPhosphateLinkSmiles = 'OP(=O)(O)O';

package/src/structures-works/converters.ts

@@ -1,33 +1,35 @@
-import {lcmsToGcrs} from './map';
+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 {
-  const df = DG.DataFrame.fromCsv(lcmsToGcrs);
-  const arr1 = df.getCol('GCRS').toList();
-  const arr2 = df.getCol('LCMS').toList();
-  const obj: {[i: string]: string} = {};
-  arr1.forEach((element, index) => obj[element] = arr2[index]);
-  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;
+  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>';
   }
-  while (r1.indexOf('//') != -1)
-    r1 = r1.replace('//', '/');
-  return r1;
 }
 
 //name: asoGapmersNucleotidesToBioSpring
@@ -35,9 +37,9 @@ export function gcrsToLcms(sequence: string): string {
 //output: string result {semType: BioSpring / Gapmers}
 export function asoGapmersNucleotidesToBioSpring(nucleotides: string): string {
   let count: number = -1;
-  const objForEdges: {[index: string]: string} = {
+  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} = {
+  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++;
@@ -51,7 +53,7 @@ export function asoGapmersNucleotidesToBioSpring(nucleotides: string): string {
 //output: string result {semType: GCRS / Gapmers}
 export function asoGapmersNucleotidesToGcrs(nucleotides: string): string {
   let count: number = -1;
-  const objForEdges: {[index: string]: string} = {
+  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)',