@datagrok/sequence-translator 1.0.9 → 1.0.10

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.0.9",
+  "version": "1.0.10",
   "author": {
     "name": "Vadym Kovadlo",
     "email": "vkovadlo@datagrok.ai"
@@ -13,7 +13,7 @@
     "directory": "packages/SequenceTranslator"
   },
   "dependencies": {
-    "@datagrok-libraries/utils": "^1.9.2",
+    "@datagrok-libraries/utils": "^1.11.1",
     "@types/react": "^18.0.15",
     "datagrok-api": "^1.6.0",
     "datagrok-tools": "^4.1.2",

package/src/autostart/registration.ts

@@ -1,11 +1,12 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import {siRnaAxolabsToGcrs, gcrsToNucleotides, asoGapmersBioSpringToGcrs, gcrsToMermade12,
-} from '../structures-works/converters';
+import {siRnaBioSpringToGcrs, siRnaAxolabsToGcrs, gcrsToNucleotides, asoGapmersBioSpringToGcrs, gcrsToMermade12,
+  siRnaNucleotidesToGcrs} from '../structures-works/converters';
 import {map, COL_NAMES, MODIFICATIONS} from '../structures-works/map';
 import {isValidSequence} from '../structures-works/sequence-codes-tools';
 import {sequenceToMolV3000} from '../structures-works/from-monomers';
+import {linkV3000} from '../structures-works/mol-transformations';
 
 import {SALTS_CSV} from '../salts';
 import {USERS_CSV} from '../users';
@@ -54,6 +55,10 @@ function molecularWeight(sequence: string, weightsObj: {[index: string]: number}
   return weight - 61.97;
 }
 
+function parseStrandsFromDuplexCell(s: string): string[] {
+  return s.slice(3).split('\r\nAS ');
+}
+
 async function saveTableAsSdFile(table: DG.DataFrame) {
   if (!table.columns.contains('Compound Name')) {
     grok.shell.warning(
@@ -67,9 +72,23 @@ async function saveTableAsSdFile(table: DG.DataFrame) {
   let result = '';
   for (let i = 0; i < table.rowCount; 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`;
+    if (typeColumn.get(i) == 'Duplex') {
+      const array = parseStrandsFromDuplexCell(structureColumn.get(i));
+      const as = sequenceToMolV3000(array[1], true, true, format) +
+      '\n' + `> <Sequence>\nAnti Sense\n\n`;
+      const ss = sequenceToMolV3000(array[0], false, true, format) +
+      '\n' + `> <Sequence>\nSense Strand\n\n`;
+      result += linkV3000([ss, as], true, true) + '\n\n';
+    } else if (typeColumn.get(i) == 'SS') {
+      const molSS = sequenceToMolV3000(structureColumn.get(i), false, true, format) +
+      '\n' + `> <Sequence>\nSense Strand\n\n`;
+      result += molSS;
+    } else if (typeColumn.get(i) == 'AS') {
+      const molAS = sequenceToMolV3000(structureColumn.get(i), true, true, format) +
+        '\n' + `> <Sequence>\nAnti Sense\n\n`;
+      result += molAS;
+    }
+
     for (const col of table.columns) {
       if (col.name != COL_NAMES.SEQUENCE)
         result += `> <${col.name}>\n${col.get(i)}\n\n`;
@@ -90,6 +109,13 @@ export function autostartOligoSdFileSubscription() {
       grok.events.onContextMenu.subscribe((args) => {
         const seqCol = args.args.context.table.currentCol; // /^[fsACGUacgu]{6,}$/
         if (DG.Detector.sampleCategories(seqCol,
+          (s) => /(\(invabasic\)|\(GalNAc-2-JNJ\)|A|U|G|C){6,}$/.test(s))) {
+          args.args.menu.item('Convert raw nucleotides to GCRS', () => {
+            args.args.context.table.columns.addNewString(seqCol.name + ' to GCRS').init((i: number) => {
+              return siRnaNucleotidesToGcrs(seqCol.get(i));
+            });
+          });
+        } else 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) => {
@@ -121,7 +147,7 @@ export function autostartOligoSdFileSubscription() {
           (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));
+              return siRnaBioSpringToGcrs(seqCol.get(i));
             });
           });
         }
@@ -141,6 +167,7 @@ export function oligoSdFile(table: DG.DataFrame) {
   const saltCol = table.getCol(COL_NAMES.SALT);
   const equivalentsCol = table.getCol(COL_NAMES.EQUIVALENTS);
   const typeColumn = table.getCol(COL_NAMES.TYPE);
+  const chemistryNameCol = table.getCol(COL_NAMES.CHEMISTRY_NAME);
 
   const molWeightCol = saltsDf.getCol('MOLWEIGHT');
   const saltNamesList = saltsDf.getCol('DISPLAY').toList();
@@ -154,12 +181,17 @@ export function oligoSdFile(table: DG.DataFrame) {
         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) => {
+      return (typeColumn.get(i) == 'Duplex') ? chemistryNameCol.get(i) : sequenceCol.get(i);
+    });
 
-    t.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => (i > 2 && typeColumn.get(i) == 'Duplex') ?
-      sequenceCol.get(i) + '; duplex of SS: ' + sequenceCol.get(i - 2) + ' and AS: ' + sequenceCol.get(i - 1) :
-      sequenceCol.get(i),
-    );
+    t.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => {
+      if (typeColumn.get(i) == 'Duplex') {
+        const arr = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        return chemistryNameCol.get(i) + '; duplex of SS: ' + arr[0] + ' and AS: ' + arr[1];
+      }
+      return sequenceCol.get(i);
+    });
 
     const weightsObj: {[code: string]: number} = {};
     for (const synthesizer of Object.keys(map)) {
@@ -172,6 +204,15 @@ export function oligoSdFile(table: DG.DataFrame) {
       weightsObj[key] = value.molecularWeight;
 
     t.columns.addNewFloat(COL_NAMES.CPD_MW).init((i: number) => {
+      if (typeColumn.get(i) == 'Duplex') {
+        const arr = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        return (
+          isValidSequence(arr[0], null).indexOfFirstNotValidChar == -1 &&
+          isValidSequence(arr[1], null).indexOfFirstNotValidChar == -1
+        ) ?
+          molecularWeight(arr[0], weightsObj) + molecularWeight(arr[1], weightsObj) :
+          DG.FLOAT_NULL;
+      }
       return (isValidSequence(sequenceCol.get(i), null).indexOfFirstNotValidChar == -1) ?
         molecularWeight(sequenceCol.get(i), weightsObj) :
         DG.FLOAT_NULL;

package/src/axolabs/constants.ts

@@ -1,5 +1,5 @@
 const rnaColor = 'rgb(255,230,153)';
-const invAbasicColor = 'rgb(255,230,153)';
+const invAbasicColor = 'rgb(203,119,211)';
 export const axolabsMap:
   {[index: string]: {fullName: string, symbols: [string, string, string, string], color: string}} =
 {

package/src/axolabs/define-pattern.ts

@@ -703,6 +703,7 @@ export function defineAxolabsPattern() {
       grok.shell.v = grok.shell.getTableView(tables.value!.name);
       grok.shell.info(((createAsStrand.value) ? 'Columns were' : 'Column was') +
       ' added to table \'' + tables.value!.name + '\'');
+      updateOutputExamples();
     }
   });
 

package/src/main/main-view.ts

@@ -19,8 +19,7 @@ export function mainView() {
     try {
       sequence = sequence.replace(/\s/g, '');
       const output = isValidSequence(sequence, null);
-      output.synthesizer = [inputFormat];
-      // inputFormatChoiceInput.value = output.synthesizer![0];
+      inputFormatChoiceInput.value = output.synthesizer![0];
       const outputSequenceObj = convertSequence(sequence, output);
       const tableRows = [];
 

package/src/package-test.ts

@@ -1,13 +1,16 @@
 import * as DG from 'datagrok-api/dg';
-import {runTests, tests} from '@datagrok-libraries/utils/src/test';
+import {runTests, tests, TestContext} from '@datagrok-libraries/utils/src/test';
 import './tests/smiles-tests';
 
 export const _package = new DG.Package();
 export {tests};
 
 //name: test
+//input: string category {optional: true}
+//input: string test {optional: true}
+//input: object testContext {optional: true}
 //output: dataframe result
-export async function test(): Promise<DG.DataFrame> {
-  const data = await runTests();
+export async function test(category: string, test: string, testContext: TestContext): Promise<DG.DataFrame> {
+  const data = await runTests({category, test, testContext});
   return DG.DataFrame.fromObjects(data)!;
 }

package/src/structures-works/converters.ts

@@ -96,9 +96,10 @@ export function asoGapmersBioSpringToGcrs(nucleotides: string): string {
 //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(/(\(invabasic\)|\(GalNAc-2-JNJ\)|moeT|moeA|moe5mC|moeG|moeU|5mC|nps|ps|U)/g,
+  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];});
 }
 

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

@@ -78,6 +78,480 @@ M  V30 END COLLECTION
 M  V30 END CTAB
 M  END`;
 
+const GALNAC = `
+Datagrok monomer library Nucleotides                            
+
+0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 111 113 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 O -20.7313 -0.7027 0 0
+M  V30 2 C -19.3976 0.0673 0 0
+M  V30 3 C -18.0638 -0.7027 0 0
+M  V30 4 C -16.7303 0.0673 0 0
+M  V30 5 N -15.3965 -0.7027 0 0
+M  V30 6 C -14.0628 0.0673 0 0
+M  V30 7 C -12.7293 -0.7027 0 0
+M  V30 8 C -11.3955 0.0673 0 0
+M  V30 9 C -10.062 -0.7027 0 0
+M  V30 10 C -8.7283 0.0673 0 0
+M  V30 11 N -7.3947 -0.7027 0 0
+M  V30 12 O -18.0638 -2.2427 0 0
+M  V30 13 O -14.0628 1.6073 0 0
+M  V30 14 O -8.7283 1.6073 0 0
+M  V30 15 C -5.8547 -0.7027 0 0
+M  V30 16 C -5.8547 0.8373 0 0
+M  V30 17 C -5.8547 -2.2427 0 0
+M  V30 18 C -3.4848 -3.0127 0 0
+M  V30 19 C -2.4544 -4.157 0 0
+M  V30 20 C -0.948 -3.8368 0 0
+M  V30 21 N 0.0824 -4.9813 0 0
+M  V30 22 C 1.5888 -4.6612 0 0
+M  V30 23 C 2.6192 -5.8056 0 0
+M  V30 24 C 4.1256 -5.4855 0 0
+M  V30 25 N 5.156 -6.6297 0 0
+M  V30 26 C 6.6624 -6.3096 0 0
+M  V30 27 C 7.6928 -7.4541 0 0
+M  V30 28 C 9.1992 -7.1339 0 0
+M  V30 29 C 10.2296 -8.2784 0 0
+M  V30 30 C 11.736 -7.9583 0 0
+M  V30 31 O 12.7664 -9.1027 0 0
+M  V30 32 O -0.4722 -2.3723 0 0
+M  V30 33 O 7.1382 -4.845 0 0
+M  V30 34 C 14.2728 -8.7824 0 0
+M  V30 35 C 15.3032 -9.9267 0 0
+M  V30 36 C 16.8098 -9.6065 0 0
+M  V30 37 C 17.2856 -8.1421 0 0
+M  V30 38 C 16.2552 -6.9975 0 0
+M  V30 39 O 14.7486 -7.3178 0 0
+M  V30 40 C 16.7312 -5.5329 0 0
+M  V30 41 O 18.7918 -7.8218 0 0
+M  V30 42 O 17.8404 -10.751 0 0
+M  V30 43 N 14.8274 -11.3914 0 0
+M  V30 44 C 15.7325 -12.6372 0 0
+M  V30 45 C 15.2567 -14.1018 0 0
+M  V30 46 O 17.2537 -12.3963 0 0
+M  V30 47 O 18.2628 -5.372 0 0
+M  V30 48 O -4.9494 -3.4885 0 0
+M  V30 49 C -4.521 0.0673 0 0
+M  V30 50 C -1.9414 0.2026 0 0
+M  V30 51 C -0.6077 -0.5674 0 0
+M  V30 52 C 0.726 0.2026 0 0
+M  V30 53 N 2.0596 -0.5674 0 0
+M  V30 54 C 3.3933 0.2026 0 0
+M  V30 55 C 4.7271 -0.5674 0 0
+M  V30 56 C 6.0606 0.2026 0 0
+M  V30 57 N 7.3943 -0.5674 0 0
+M  V30 58 C 8.7281 0.2026 0 0
+M  V30 59 C 10.0618 -0.5674 0 0
+M  V30 60 C 11.3953 0.2026 0 0
+M  V30 61 C 14.0628 0.2026 0 0
+M  V30 62 O 15.3964 -0.5674 0 0
+M  V30 63 O 0.726 1.7426 0 0
+M  V30 64 O 8.7281 1.7426 0 0
+M  V30 65 C 16.7301 0.2026 0 0
+M  V30 66 C 18.0638 -0.5676 0 0
+M  V30 67 C 19.3976 0.2026 0 0
+M  V30 68 C 19.3974 1.7426 0 0
+M  V30 69 C 18.0638 2.5126 0 0
+M  V30 70 O 16.7301 1.7426 0 0
+M  V30 71 C 18.064 4.0526 0 0
+M  V30 72 O 20.7311 2.5126 0 0
+M  V30 73 O 20.7313 -0.5674 0 0
+M  V30 74 N 18.0638 -2.1076 0 0
+M  V30 75 C 19.3096 -3.0127 0 0
+M  V30 76 C 19.3096 -4.5527 0 0
+M  V30 77 O 20.6818 -2.3135 0 0
+M  V30 78 O 19.4709 4.6791 0 0
+M  V30 79 O -3.1872 -0.7027 0 0
+M  V30 80 C 12.7291 -0.5674 0 0
+M  V30 81 C -3.919 3.2277 0 0
+M  V30 82 C -2.4126 2.9076 0 0
+M  V30 83 C -1.3822 4.0519 0 0
+M  V30 84 N 0.1242 3.7317 0 0
+M  V30 85 C 1.1546 4.8762 0 0
+M  V30 86 C 2.661 4.5561 0 0
+M  V30 87 C 3.6914 5.7005 0 0
+M  V30 88 N 5.1978 5.3804 0 0
+M  V30 89 C 6.2282 6.5248 0 0
+M  V30 90 C 7.7346 6.2045 0 0
+M  V30 91 C 8.765 7.349 0 0
+M  V30 92 C 10.2714 7.0288 0 0
+M  V30 93 C 11.3018 8.1733 0 0
+M  V30 94 O 12.8082 7.8532 0 0
+M  V30 95 O -1.858 5.5167 0 0
+M  V30 96 O 5.7524 7.9894 0 0
+M  V30 97 C 13.8386 8.9976 0 0
+M  V30 98 C 15.345 8.6773 0 0
+M  V30 99 C 16.3756 9.8219 0 0
+M  V30 100 C 15.8996 11.2863 0 0
+M  V30 101 C 14.3934 11.6068 0 0
+M  V30 102 O 13.3628 10.4622 0 0
+M  V30 103 C 13.9176 13.0714 0 0
+M  V30 104 O 16.93 12.4308 0 0
+M  V30 105 O 17.882 9.5018 0 0
+M  V30 106 N 15.8208 7.2127 0 0
+M  V30 107 C 17.2856 6.7367 0 0
+M  V30 108 C 17.7614 5.2721 0 0
+M  V30 109 O 18.3744 7.8257 0 0
+M  V30 110 O 15.062 14.1018 0 0
+M  V30 111 O -4.8241 1.9817 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 2 3
+M  V30 2 1 3 4
+M  V30 3 1 6 7
+M  V30 4 1 7 8
+M  V30 5 1 8 9
+M  V30 6 1 9 10
+M  V30 7 1 1 2
+M  V30 8 1 3 12
+M  V30 9 1 4 5
+M  V30 10 1 5 6
+M  V30 11 2 6 13
+M  V30 12 1 10 11
+M  V30 13 1 11 15
+M  V30 14 1 15 16
+M  V30 15 1 15 17
+M  V30 16 2 10 14
+M  V30 17 1 18 19
+M  V30 18 1 19 20
+M  V30 19 1 22 23
+M  V30 20 1 23 24
+M  V30 21 1 26 27
+M  V30 22 1 27 28
+M  V30 23 1 28 29
+M  V30 24 1 29 30
+M  V30 25 2 26 33
+M  V30 26 2 20 32
+M  V30 27 1 20 21
+M  V30 28 1 21 22
+M  V30 29 1 24 25
+M  V30 30 1 25 26
+M  V30 31 1 30 31
+M  V30 32 1 31 34
+M  V30 33 1 35 36
+M  V30 34 1 36 37
+M  V30 35 1 37 38
+M  V30 36 1 34 35
+M  V30 37 1 38 39
+M  V30 38 1 34 39
+M  V30 39 1 38 40
+M  V30 40 1 35 43
+M  V30 41 1 43 44
+M  V30 42 1 44 45
+M  V30 43 2 44 46
+M  V30 44 1 36 42
+M  V30 45 1 37 41
+M  V30 46 1 40 47
+M  V30 47 1 18 48
+M  V30 48 1 15 49
+M  V30 49 1 50 51
+M  V30 50 1 51 52
+M  V30 51 1 54 55
+M  V30 52 1 55 56
+M  V30 53 1 58 59
+M  V30 54 1 59 60
+M  V30 55 2 58 64
+M  V30 56 2 52 63
+M  V30 57 1 52 53
+M  V30 58 1 53 54
+M  V30 59 1 56 57
+M  V30 60 1 57 58
+M  V30 61 1 61 62
+M  V30 62 1 62 65
+M  V30 63 1 66 67
+M  V30 64 1 67 68
+M  V30 65 1 68 69
+M  V30 66 1 65 66
+M  V30 67 1 69 70
+M  V30 68 1 65 70
+M  V30 69 1 69 71
+M  V30 70 1 66 74
+M  V30 71 1 74 75
+M  V30 72 1 75 76
+M  V30 73 2 75 77
+M  V30 74 1 67 73
+M  V30 75 1 68 72
+M  V30 76 1 71 78
+M  V30 77 1 50 79
+M  V30 78 1 49 79
+M  V30 79 1 60 80
+M  V30 80 1 80 61
+M  V30 81 1 81 82
+M  V30 82 1 82 83
+M  V30 83 1 85 86
+M  V30 84 1 86 87
+M  V30 85 1 89 90
+M  V30 86 1 90 91
+M  V30 87 1 91 92
+M  V30 88 1 92 93
+M  V30 89 2 89 96
+M  V30 90 2 83 95
+M  V30 91 1 83 84
+M  V30 92 1 84 85
+M  V30 93 1 87 88
+M  V30 94 1 88 89
+M  V30 95 1 93 94
+M  V30 96 1 94 97
+M  V30 97 1 98 99
+M  V30 98 1 99 100
+M  V30 99 1 100 101
+M  V30 100 1 97 98
+M  V30 101 1 101 102
+M  V30 102 1 97 102
+M  V30 103 1 101 103
+M  V30 104 1 98 106
+M  V30 105 1 106 107
+M  V30 106 1 107 108
+M  V30 107 2 107 109
+M  V30 108 1 99 105
+M  V30 109 1 100 104
+M  V30 110 1 103 110
+M  V30 111 1 81 111
+M  V30 112 1 16 111
+M  V30 113 1 17 48
+M  V30 END BOND
+M  V30 END CTAB
+M  END`;
+
+const GALNACPRIME = `
+Datagrok monomer library Nucleotides          
+
+0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 111 113 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 O 20.7313 0.7027 0 0
+M  V30 2 C 19.3976 -0.0673 0 0
+M  V30 3 C 18.0638 0.7027 0 0
+M  V30 4 C 16.7303 -0.0673 0 0
+M  V30 5 N 15.3965 0.7027 0 0
+M  V30 6 C 14.0628 -0.0673 0 0
+M  V30 7 C 12.7293 0.7027 0 0
+M  V30 8 C 11.3955 -0.0673 0 0
+M  V30 9 C 10.062 0.7027 0 0
+M  V30 10 C 8.7283 -0.0673 0 0
+M  V30 11 N 7.3947 0.7027 0 0
+M  V30 12 O 18.0638 2.2427 0 0
+M  V30 13 O 14.0628 -1.6073 0 0
+M  V30 14 O 8.7283 -1.6073 0 0
+M  V30 15 C 5.8547 0.7027 0 0
+M  V30 16 C 5.8547 -0.8373 0 0
+M  V30 17 C 5.8547 2.2427 0 0
+M  V30 18 C 3.4848 3.0127 0 0
+M  V30 19 C 2.4544 4.157 0 0
+M  V30 20 C 0.948 3.8368 0 0
+M  V30 21 N -0.0824 4.9813 0 0
+M  V30 22 C -1.5888 4.6612 0 0
+M  V30 23 C -2.6192 5.8056 0 0
+M  V30 24 C -4.1256 5.4855 0 0
+M  V30 25 N -5.156 6.6297 0 0
+M  V30 26 C -6.6624 6.3096 0 0
+M  V30 27 C -7.6928 7.4541 0 0
+M  V30 28 C -9.1992 7.1339 0 0
+M  V30 29 C -10.2296 8.2784 0 0
+M  V30 30 C -11.736 7.9583 0 0
+M  V30 31 O -12.7664 9.1027 0 0
+M  V30 32 O 0.4722 2.3723 0 0
+M  V30 33 O -7.1382 4.845 0 0
+M  V30 34 C -14.2728 8.7824 0 0
+M  V30 35 C -15.3032 9.9267 0 0
+M  V30 36 C -16.8098 9.6065 0 0
+M  V30 37 C -17.2856 8.1421 0 0
+M  V30 38 C -16.2552 6.9975 0 0
+M  V30 39 O -14.7486 7.3178 0 0
+M  V30 40 C -16.7312 5.5329 0 0
+M  V30 41 O -18.7918 7.8218 0 0
+M  V30 42 O -17.8404 10.751 0 0
+M  V30 43 N -14.8274 11.3914 0 0
+M  V30 44 C -15.7325 12.6372 0 0
+M  V30 45 C -15.2567 14.1018 0 0
+M  V30 46 O -17.2537 12.3963 0 0
+M  V30 47 O -18.2628 5.372 0 0
+M  V30 48 O 4.9494 3.4885 0 0
+M  V30 49 C 4.521 -0.0673 0 0
+M  V30 50 C 1.9414 -0.2026 0 0
+M  V30 51 C 0.6077 0.5674 0 0
+M  V30 52 C -0.726 -0.2026 0 0
+M  V30 53 N -2.0596 0.5674 0 0
+M  V30 54 C -3.3933 -0.2026 0 0
+M  V30 55 C -4.7271 0.5674 0 0
+M  V30 56 C -6.0606 -0.2026 0 0
+M  V30 57 N -7.3943 0.5674 0 0
+M  V30 58 C -8.7281 -0.2026 0 0
+M  V30 59 C -10.0618 0.5674 0 0
+M  V30 60 C -11.3953 -0.2026 0 0
+M  V30 61 C -14.0628 -0.2026 0 0
+M  V30 62 O -15.3964 0.5674 0 0
+M  V30 63 O -0.726 -1.7426 0 0
+M  V30 64 O -8.7281 -1.7426 0 0
+M  V30 65 C -16.7301 -0.2026 0 0
+M  V30 66 C -18.0638 0.5676 0 0
+M  V30 67 C -19.3976 -0.2026 0 0
+M  V30 68 C -19.3974 -1.7426 0 0
+M  V30 69 C -18.0638 -2.5126 0 0
+M  V30 70 O -16.7301 -1.7426 0 0
+M  V30 71 C -18.064 -4.0526 0 0
+M  V30 72 O -20.7311 -2.5126 0 0
+M  V30 73 O -20.7313 0.5674 0 0
+M  V30 74 N -18.0638 2.1076 0 0
+M  V30 75 C -19.3096 3.0127 0 0
+M  V30 76 C -19.3096 4.5527 0 0
+M  V30 77 O -20.6818 2.3135 0 0
+M  V30 78 O -19.4709 -4.6791 0 0
+M  V30 79 O 3.1872 0.7027 0 0
+M  V30 80 C -12.7291 0.5674 0 0
+M  V30 81 C 3.919 -3.2277 0 0
+M  V30 82 C 2.4126 -2.9076 0 0
+M  V30 83 C 1.3822 -4.0519 0 0
+M  V30 84 N -0.1242 -3.7317 0 0
+M  V30 85 C -1.1546 -4.8762 0 0
+M  V30 86 C -2.661 -4.5561 0 0
+M  V30 87 C -3.6914 -5.7005 0 0
+M  V30 88 N -5.1978 -5.3804 0 0
+M  V30 89 C -6.2282 -6.5248 0 0
+M  V30 90 C -7.7346 -6.2045 0 0
+M  V30 91 C -8.765 -7.349 0 0
+M  V30 92 C -10.2714 -7.0288 0 0
+M  V30 93 C -11.3018 -8.1733 0 0
+M  V30 94 O -12.8082 -7.8532 0 0
+M  V30 95 O 1.858 -5.5167 0 0
+M  V30 96 O -5.7524 -7.9894 0 0
+M  V30 97 C -13.8386 -8.9976 0 0
+M  V30 98 C -15.345 -8.6773 0 0
+M  V30 99 C -16.3756 -9.8219 0 0
+M  V30 100 C -15.8996 -11.2863 0 0
+M  V30 101 C -14.3934 -11.6068 0 0
+M  V30 102 O -13.3628 -10.4622 0 0
+M  V30 103 C -13.9176 -13.0714 0 0
+M  V30 104 O -16.93 -12.4308 0 0
+M  V30 105 O -17.882 -9.5018 0 0
+M  V30 106 N -15.8208 -7.2127 0 0
+M  V30 107 C -17.2856 -6.7367 0 0
+M  V30 108 C -17.7614 -5.2721 0 0
+M  V30 109 O -18.3744 -7.8257 0 0
+M  V30 110 O -15.062 -14.1018 0 0
+M  V30 111 O 4.8241 -1.9817 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 2 3
+M  V30 2 1 3 4
+M  V30 3 1 6 7
+M  V30 4 1 7 8
+M  V30 5 1 8 9
+M  V30 6 1 9 10
+M  V30 7 1 1 2
+M  V30 8 1 3 12
+M  V30 9 1 4 5
+M  V30 10 1 5 6
+M  V30 11 2 6 13
+M  V30 12 1 10 11
+M  V30 13 1 11 15
+M  V30 14 1 15 16
+M  V30 15 1 15 17
+M  V30 16 2 10 14
+M  V30 17 1 18 19
+M  V30 18 1 19 20
+M  V30 19 1 22 23
+M  V30 20 1 23 24
+M  V30 21 1 26 27
+M  V30 22 1 27 28
+M  V30 23 1 28 29
+M  V30 24 1 29 30
+M  V30 25 2 26 33
+M  V30 26 2 20 32
+M  V30 27 1 20 21
+M  V30 28 1 21 22
+M  V30 29 1 24 25
+M  V30 30 1 25 26
+M  V30 31 1 30 31
+M  V30 32 1 31 34
+M  V30 33 1 35 36
+M  V30 34 1 36 37
+M  V30 35 1 37 38
+M  V30 36 1 34 35
+M  V30 37 1 38 39
+M  V30 38 1 34 39
+M  V30 39 1 38 40
+M  V30 40 1 35 43
+M  V30 41 1 43 44
+M  V30 42 1 44 45
+M  V30 43 2 44 46
+M  V30 44 1 36 42
+M  V30 45 1 37 41
+M  V30 46 1 40 47
+M  V30 47 1 18 48
+M  V30 48 1 15 49
+M  V30 49 1 50 51
+M  V30 50 1 51 52
+M  V30 51 1 54 55
+M  V30 52 1 55 56
+M  V30 53 1 58 59
+M  V30 54 1 59 60
+M  V30 55 2 58 64
+M  V30 56 2 52 63
+M  V30 57 1 52 53
+M  V30 58 1 53 54
+M  V30 59 1 56 57
+M  V30 60 1 57 58
+M  V30 61 1 61 62
+M  V30 62 1 62 65
+M  V30 63 1 66 67
+M  V30 64 1 67 68
+M  V30 65 1 68 69
+M  V30 66 1 65 66
+M  V30 67 1 69 70
+M  V30 68 1 65 70
+M  V30 69 1 69 71
+M  V30 70 1 66 74
+M  V30 71 1 74 75
+M  V30 72 1 75 76
+M  V30 73 2 75 77
+M  V30 74 1 67 73
+M  V30 75 1 68 72
+M  V30 76 1 71 78
+M  V30 77 1 50 79
+M  V30 78 1 49 79
+M  V30 79 1 60 80
+M  V30 80 1 80 61
+M  V30 81 1 81 82
+M  V30 82 1 82 83
+M  V30 83 1 85 86
+M  V30 84 1 86 87
+M  V30 85 1 89 90
+M  V30 86 1 90 91
+M  V30 87 1 91 92
+M  V30 88 1 92 93
+M  V30 89 2 89 96
+M  V30 90 2 83 95
+M  V30 91 1 83 84
+M  V30 92 1 84 85
+M  V30 93 1 87 88
+M  V30 94 1 88 89
+M  V30 95 1 93 94
+M  V30 96 1 94 97
+M  V30 97 1 98 99
+M  V30 98 1 99 100
+M  V30 99 1 100 101
+M  V30 100 1 97 98
+M  V30 101 1 101 102
+M  V30 102 1 97 102
+M  V30 103 1 101 103
+M  V30 104 1 98 106
+M  V30 105 1 106 107
+M  V30 106 1 107 108
+M  V30 107 2 107 109
+M  V30 108 1 99 105
+M  V30 109 1 100 104
+M  V30 110 1 103 110
+M  V30 111 1 81 111
+M  V30 112 1 16 111
+M  V30 113 1 17 48
+M  V30 END BOND
+M  V30 END CTAB
+M  END`;
+
 export function getNucleotidesMol(smilesCodes: string[]) {
   const molBlocks: string[] = [];
 
@@ -85,6 +559,8 @@ export function getNucleotidesMol(smilesCodes: string[]) {
     smilesCodes[i] == 'OP(=O)(O)O' ? molBlocks.push(PHOSHATE) :
       smilesCodes[i] == 'OP(=O)(S)O' ? molBlocks.push(THIOPHOSHATE) :
         smilesCodes[i] == 'O[C@@H]1C[C@@H]O[C@H]1CO' ? molBlocks.push(rotateNucleotidesV3000(INVABASIC)) :
+          smilesCodes[i] == '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)' ? molBlocks.push(GALNAC) :
+            smilesCodes[i] == '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' ? molBlocks.push(GALNACPRIME) :
           molBlocks.push(rotateNucleotidesV3000(smilesCodes[i]));
   }