@datagrok/sequence-translator 1.1.0 → 1.1.5

package/files/codes-to-symbols.json

@@ -1,5 +1,6 @@
 {
   "Axolabs": {
+    "(GalNAc)": "(GalNAc)",
     "Af": "2'-fluoro-A",
     "Cf": "2'-fluoro-C",
     "Gf": "2'-fluoro-G",

package/files/formats-to-helm.json

@@ -1,6 +1,7 @@
 {
   "Axolabs": {
     "nucleoside": {
+      "(GalNAc)": "[GalNAc]",
       "Uf": "[fR](U)p",
       "Af": "[fR](A)p",
       "Cf": "[fR](C)p",
@@ -16,6 +17,7 @@
   },
   "BioSpring": {
     "nucleoside": {
+      "(GalNAc)": "[GalNAc]",
       "A": "r(A)p",
       "T": "r(T)p",
       "G": "r(G)p",
@@ -36,6 +38,7 @@
   },
   "Mermade12": {
     "nucleoside": {
+      "(GalNAc)": "[GalNAc]",
       "h": "[25r](U)[sp]",
       "e": "[25r](A)[sp]",
       "f": "[25r](C)[sp]",
@@ -54,6 +57,7 @@
       "G": "[25r](G)p"
     },
     "phosphateBackbone": {
+      "<empty>": "[sp]"
     }
   }
 }

package/files/monomer-lib.json

@@ -1,4 +1,32 @@
 [
+  {
+    "symbol": "(GalNAc)",
+    "name": "GalNAc",
+    "molfile": "\nDatagrok monomer library Nucleotides MODIFICATION|GalNAc2\n\n  0  0  0  0  0  0  0  0  0  0999 V3000\nM  V30 BEGIN CTAB\nM  V30 COUNTS 111 113 0 0 0\nM  V30 BEGIN ATOM\nM  V30 1 O -20.731300 -0.702700 0.000000 0\nM  V30 2 C -19.397600 0.067300 0.000000 0\nM  V30 3 C -18.063800 -0.702700 0.000000 0\nM  V30 4 C -16.730300 0.067300 0.000000 0\nM  V30 5 N -15.396500 -0.702700 0.000000 0\nM  V30 6 C -14.062800 0.067300 0.000000 0\nM  V30 7 C -12.729300 -0.702700 0.000000 0\nM  V30 8 C -11.395500 0.067300 0.000000 0\nM  V30 9 C -10.062000 -0.702700 0.000000 0\nM  V30 10 C -8.728300 0.067300 0.000000 0\nM  V30 11 N -7.394700 -0.702700 0.000000 0\nM  V30 12 O -18.063800 -2.242700 0.000000 0\nM  V30 13 O -14.062800 1.607300 0.000000 0\nM  V30 14 O -8.728300 1.607300 0.000000 0\nM  V30 15 C -5.854700 -0.702700 0.000000 0\nM  V30 16 C -5.854700 0.837300 0.000000 0\nM  V30 17 C -5.854700 -2.242700 0.000000 0\nM  V30 18 C -3.484800 -3.012700 0.000000 0\nM  V30 19 C -2.454400 -4.157000 0.000000 0\nM  V30 20 C -0.948000 -3.836800 0.000000 0\nM  V30 21 N 0.082400 -4.981300 0.000000 0\nM  V30 22 C 1.588800 -4.661200 0.000000 0\nM  V30 23 C 2.619200 -5.805600 0.000000 0\nM  V30 24 C 4.125600 -5.485500 0.000000 0\nM  V30 25 N 5.156000 -6.629700 0.000000 0\nM  V30 26 C 6.662400 -6.309600 0.000000 0\nM  V30 27 C 7.692800 -7.454100 0.000000 0\nM  V30 28 C 9.199200 -7.133900 0.000000 0\nM  V30 29 C 10.229600 -8.278400 0.000000 0\nM  V30 30 C 11.736000 -7.958300 0.000000 0\nM  V30 31 O 12.766400 -9.102700 0.000000 0\nM  V30 32 O -0.472200 -2.372300 0.000000 0\nM  V30 33 O 7.138200 -4.845000 0.000000 0\nM  V30 34 C 14.272800 -8.782400 0.000000 0\nM  V30 35 C 15.303200 -9.926700 0.000000 0\nM  V30 36 C 16.809800 -9.606500 0.000000 0\nM  V30 37 C 17.285600 -8.142100 0.000000 0\nM  V30 38 C 16.255200 -6.997500 0.000000 0\nM  V30 39 O 14.748600 -7.317800 0.000000 0\nM  V30 40 C 16.731200 -5.532900 0.000000 0\nM  V30 41 O 18.791800 -7.821800 0.000000 0\nM  V30 42 O 17.840400 -10.751000 0.000000 0\nM  V30 43 N 14.827400 -11.391400 0.000000 0\nM  V30 44 C 15.732500 -12.637200 0.000000 0\nM  V30 45 C 15.256700 -14.101800 0.000000 0\nM  V30 46 O 17.253700 -12.396300 0.000000 0\nM  V30 47 O 18.262800 -5.372000 0.000000 0\nM  V30 48 O -4.949400 -3.488500 0.000000 0\nM  V30 49 C -4.521000 0.067300 0.000000 0\nM  V30 50 C -1.941400 0.202600 0.000000 0\nM  V30 51 C -0.607700 -0.567400 0.000000 0\nM  V30 52 C 0.726000 0.202600 0.000000 0\nM  V30 53 N 2.059600 -0.567400 0.000000 0\nM  V30 54 C 3.393300 0.202600 0.000000 0\nM  V30 55 C 4.727100 -0.567400 0.000000 0\nM  V30 56 C 6.060600 0.202600 0.000000 0\nM  V30 57 N 7.394300 -0.567400 0.000000 0\nM  V30 58 C 8.728100 0.202600 0.000000 0\nM  V30 59 C 10.061800 -0.567400 0.000000 0\nM  V30 60 C 11.395300 0.202600 0.000000 0\nM  V30 61 C 14.062800 0.202600 0.000000 0\nM  V30 62 O 15.396400 -0.567400 0.000000 0\nM  V30 63 O 0.726000 1.742600 0.000000 0\nM  V30 64 O 8.728100 1.742600 0.000000 0\nM  V30 65 C 16.730100 0.202600 0.000000 0\nM  V30 66 C 18.063800 -0.567600 0.000000 0\nM  V30 67 C 19.397600 0.202600 0.000000 0\nM  V30 68 C 19.397400 1.742600 0.000000 0\nM  V30 69 C 18.063800 2.512600 0.000000 0\nM  V30 70 O 16.730100 1.742600 0.000000 0\nM  V30 71 C 18.064000 4.052600 0.000000 0\nM  V30 72 O 20.731100 2.512600 0.000000 0\nM  V30 73 O 20.731300 -0.567400 0.000000 0\nM  V30 74 N 18.063800 -2.107600 0.000000 0\nM  V30 75 C 19.309600 -3.012700 0.000000 0\nM  V30 76 C 19.309600 -4.552700 0.000000 0\nM  V30 77 O 20.681800 -2.313500 0.000000 0\nM  V30 78 O 19.470900 4.679100 0.000000 0\nM  V30 79 O -3.187200 -0.702700 0.000000 0\nM  V30 80 C 12.729100 -0.567400 0.000000 0\nM  V30 81 C -3.919000 3.227700 0.000000 0\nM  V30 82 C -2.412600 2.907600 0.000000 0\nM  V30 83 C -1.382200 4.051900 0.000000 0\nM  V30 84 N 0.124200 3.731700 0.000000 0\nM  V30 85 C 1.154600 4.876200 0.000000 0\nM  V30 86 C 2.661000 4.556100 0.000000 0\nM  V30 87 C 3.691400 5.700500 0.000000 0\nM  V30 88 N 5.197800 5.380400 0.000000 0\nM  V30 89 C 6.228200 6.524800 0.000000 0\nM  V30 90 C 7.734600 6.204500 0.000000 0\nM  V30 91 C 8.765000 7.349000 0.000000 0\nM  V30 92 C 10.271400 7.028800 0.000000 0\nM  V30 93 C 11.301800 8.173300 0.000000 0\nM  V30 94 O 12.808200 7.853200 0.000000 0\nM  V30 95 O -1.858000 5.516700 0.000000 0\nM  V30 96 O 5.752400 7.989400 0.000000 0\nM  V30 97 C 13.838600 8.997600 0.000000 0\nM  V30 98 C 15.345000 8.677300 0.000000 0\nM  V30 99 C 16.375600 9.821900 0.000000 0\nM  V30 100 C 15.899600 11.286300 0.000000 0\nM  V30 101 C 14.393400 11.606800 0.000000 0\nM  V30 102 O 13.362800 10.462200 0.000000 0\nM  V30 103 C 13.917600 13.071400 0.000000 0\nM  V30 104 O 16.930000 12.430800 0.000000 0\nM  V30 105 O 17.882000 9.501800 0.000000 0\nM  V30 106 N 15.820800 7.212700 0.000000 0\nM  V30 107 C 17.285600 6.736700 0.000000 0\nM  V30 108 C 17.761400 5.272100 0.000000 0\nM  V30 109 O 18.374400 7.825700 0.000000 0\nM  V30 110 O 15.062000 14.101800 0.000000 0\nM  V30 111 O -4.824100 1.981700 0.000000 0\nM  V30 END ATOM\nM  V30 BEGIN BOND\nM  V30 1 1 2 3\nM  V30 2 1 3 4\nM  V30 3 1 6 7\nM  V30 4 1 7 8\nM  V30 5 1 8 9\nM  V30 6 1 9 10\nM  V30 7 1 1 2\nM  V30 8 1 3 12\nM  V30 9 1 4 5\nM  V30 10 1 5 6\nM  V30 11 2 6 13\nM  V30 12 1 10 11\nM  V30 13 1 11 15\nM  V30 14 1 15 16\nM  V30 15 1 15 17\nM  V30 16 2 10 14\nM  V30 17 1 18 19\nM  V30 18 1 19 20\nM  V30 19 1 22 23\nM  V30 20 1 23 24\nM  V30 21 1 26 27\nM  V30 22 1 27 28\nM  V30 23 1 28 29\nM  V30 24 1 29 30\nM  V30 25 2 26 33\nM  V30 26 2 20 32\nM  V30 27 1 20 21\nM  V30 28 1 21 22\nM  V30 29 1 24 25\nM  V30 30 1 25 26\nM  V30 31 1 30 31\nM  V30 32 1 31 34\nM  V30 33 1 35 36\nM  V30 34 1 36 37\nM  V30 35 1 37 38\nM  V30 36 1 34 35\nM  V30 37 1 38 39\nM  V30 38 1 34 39\nM  V30 39 1 38 40\nM  V30 40 1 35 43\nM  V30 41 1 43 44\nM  V30 42 1 44 45\nM  V30 43 2 44 46\nM  V30 44 1 36 42\nM  V30 45 1 37 41\nM  V30 46 1 40 47\nM  V30 47 1 18 48\nM  V30 48 1 15 49\nM  V30 49 1 50 51\nM  V30 50 1 51 52\nM  V30 51 1 54 55\nM  V30 52 1 55 56\nM  V30 53 1 58 59\nM  V30 54 1 59 60\nM  V30 55 2 58 64\nM  V30 56 2 52 63\nM  V30 57 1 52 53\nM  V30 58 1 53 54\nM  V30 59 1 56 57\nM  V30 60 1 57 58\nM  V30 61 1 61 62\nM  V30 62 1 62 65\nM  V30 63 1 66 67\nM  V30 64 1 67 68\nM  V30 65 1 68 69\nM  V30 66 1 65 66\nM  V30 67 1 69 70\nM  V30 68 1 65 70\nM  V30 69 1 69 71\nM  V30 70 1 66 74\nM  V30 71 1 74 75\nM  V30 72 1 75 76\nM  V30 73 2 75 77\nM  V30 74 1 67 73\nM  V30 75 1 68 72\nM  V30 76 1 71 78\nM  V30 77 1 50 79\nM  V30 78 1 49 79\nM  V30 79 1 60 80\nM  V30 80 1 80 61\nM  V30 81 1 81 82\nM  V30 82 1 82 83\nM  V30 83 1 85 86\nM  V30 84 1 86 87\nM  V30 85 1 89 90\nM  V30 86 1 90 91\nM  V30 87 1 91 92\nM  V30 88 1 92 93\nM  V30 89 2 89 96\nM  V30 90 2 83 95\nM  V30 91 1 83 84\nM  V30 92 1 84 85\nM  V30 93 1 87 88\nM  V30 94 1 88 89\nM  V30 95 1 93 94\nM  V30 96 1 94 97\nM  V30 97 1 98 99\nM  V30 98 1 99 100\nM  V30 99 1 100 101\nM  V30 100 1 97 98\nM  V30 101 1 101 102\nM  V30 102 1 97 102\nM  V30 103 1 101 103\nM  V30 104 1 98 106\nM  V30 105 1 106 107\nM  V30 106 1 107 108\nM  V30 107 2 107 109\nM  V30 108 1 99 105\nM  V30 109 1 100 104\nM  V30 110 1 103 110\nM  V30 111 1 81 111\nM  V30 112 1 16 111\nM  V30 113 1 17 48\nM  V30 END BOND\nM  V30 END CTAB\nM  END\n",
+    "author": "SequenceTranslator",
+    "id": 0,
+    "rgroups": [
+      {
+        "capGroupSmiles": "O[*:1]",
+        "alternateId": "R1-OH",
+        "capGroupName": "OH",
+        "label": "R1"
+      },
+      {
+        "capGroupSmiles": "O[*:2]",
+        "alternateId": "R2-OH",
+        "capGroupName": "OH",
+        "label": "R2"
+      }
+    ],
+    "smiles": "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",
+    "polymerType": "RNA",
+    "monomerType": "Backbone",
+    "createDate": null,
+    "meta": {
+      "molecularWeight": 1273.3
+    }
+  },
   {
     "symbol": "2'-fluoro-A",
     "name": "2'-fluoro-A",
@@ -1090,5 +1118,25 @@
     "meta": {
       "molecularWeight": 306.17
     }
+  },
+  {
+    "monomerType": "Branch",
+    "smiles": "[H:1]n1cc(C)c(N)nc1=O",
+    "name": "5-Methylcytosine",
+    "author": "Pistoia Alliance HELM project",
+    "molfile": "HELM Core Monomer library\nHELMMonomers071816.sdf \n\n 10 10  0  0  0  0  0  0  0  0999 V2000\n   23.0624   -3.8327    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   23.0624   -5.3327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   21.7674   -6.0827    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   20.4624   -5.3327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   20.4624   -3.8327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   21.7674   -3.0827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   21.7674   -1.5827    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   21.7674   -7.5827    0.0000 R1  0  0  0  0  0  0  0  0  0  0  0  0\n   24.3614   -6.0827    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   19.1634   -3.0827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0        0\n  2  3  1  0        0\n  3  4  1  0        0\n  4  5  2  0        0\n  5  6  1  0        0\n  1  6  2  0        0\n  6  7  1  0        0\n  3  8  1  0        0\n  2  9  2  0        0\n  5 10  1  0        0\nA    8\nR1\nM  END\n",
+    "naturalAnalog": "C",
+    "rgroups": [
+      {
+        "capGroupSMILES": "[*:1][H]",
+        "alternateId": "R1-H",
+        "capGroupName": "H",
+        "label": "R1"
+      }
+    ],
+    "symbol": "m5C",
+    "createDate": null,
+    "polymerType": "RNA",
+    "id": 0
   }
 ]

package/package.json

@@ -1,33 +1,33 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.1.0",
+  "version": "1.1.5",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"
   },
-  "description": "SequenceTranslator is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform, used to translate [oligonucleotide](https://en.wikipedia.org/wiki/Oligonucleotide) sequences between [different representations](https://github.com/datagrok-ai/public/tree/master/packages/SequenceTranslator#sequence-representations).",
+  "description": "SequenceTranslator translates [oligonucleotide](https://en.wikipedia.org/wiki/Oligonucleotide) sequences between [different representations](https://github.com/datagrok-ai/public/tree/master/packages/SequenceTranslator#sequence-representations).",
   "repository": {
     "type": "git",
     "url": "https://github.com/datagrok-ai/public.git",
     "directory": "packages/SequenceTranslator"
   },
   "dependencies": {
+    "@datagrok-libraries/bio": "^5.32.1",
     "@datagrok-libraries/chem-meta": "^1.0.9",
-    "@datagrok-libraries/utils": "^1.17.2",
     "@datagrok-libraries/tutorials": "^1.3.2",
-    "cash-dom": "^8.1.0",
-    "datagrok-api": "^1.10.2",
+    "@datagrok-libraries/utils": "^1.17.2",
     "@types/react": "^18.0.15",
-    "@datagrok-libraries/bio": "^5.32.1",
-    "datagrok-tools": "^4.1.2",
-    "npm": "^8.11.0",
+    "cash-dom": "^8.1.0",
+    "datagrok-api": "^1.15.2",
     "openchemlib": "6.0.1",
     "save-svg-as-png": "^1.4.17",
     "ts-loader": "^9.3.1",
     "typescript": "^4.7.4"
   },
   "devDependencies": {
+    "@datagrok/bio": "^2.10.0",
+    "@datagrok/chem": "1.7.2",
     "@types/jquery": "^3.5.14",
     "@types/js-yaml": "^4.0.5",
     "@types/node-fetch": "^2.6.2",
@@ -35,16 +35,13 @@
     "@typescript-eslint/eslint-plugin": "latest",
     "@typescript-eslint/parser": "parser",
     "css-loader": "^6.7.3",
-    "datagrok-tools": "^4.7.10",
     "eslint": "^7.32.0",
     "eslint-config-google": "latest",
     "style-loader": "^3.3.1",
     "ts-loader": "^9.3.1",
     "typescript": "^4.7.4",
     "webpack": "^5.75.0",
-    "webpack-cli": "latest",
-    "@datagrok/chem": "1.5.7",
-    "@datagrok/bio": "^2.1.12"
+    "webpack-cli": "latest"
   },
   "scripts": {
     "link-api": "npm link datagrok-api",

package/src/model/axolabs/const.ts

@@ -20,8 +20,8 @@ export const SS = 'SS' as const;
 export const AS = 'AS' as const;
 export const STRANDS = [SS, AS];
 export const STRAND_NAME = {
-  [SS]: 'Sense Strand',
-  [AS]: 'Antisense Strand',
+  [SS]: 'Sense strand',
+  [AS]: 'Anti sense',
 }
 
 export const THREE_PRIME = 'THREE_PRIME' as const;

package/src/model/const.ts

@@ -3,7 +3,6 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-export const DELIMITER = ';'; // what is the need for this?
 export const NUCLEOTIDES = ['A', 'G', 'C', 'U', 'T'];
 
 export const TECHNOLOGIES = {

package/src/model/format-translation/conversion-utils.ts

@@ -27,13 +27,14 @@ export function getTranslatedSequences(sequence: string, indexOfFirstInvalidChar
       return [format, translation];
     }).filter(([format, translation]) => translation)
   )
-  const nucleotides = getNucleotidesSequence(result[DEFAULT_FORMATS.HELM], MonomerLibWrapper.getInstance());
+  const helm = (sourceFormat === DEFAULT_FORMATS.HELM) ? sequence : result[DEFAULT_FORMATS.HELM];
+  const nucleotides = getNucleotidesSequence(helm, MonomerLibWrapper.getInstance());
   if (nucleotides)
     result['Nucleotides'] = nucleotides;
   return result;
 }
 
-function getNucleotidesSequence(helmString: string, monomerLib: MonomerLibWrapper): string | null {
+export function getNucleotidesSequence(helmString: string, monomerLib: MonomerLibWrapper): string | null {
   const re = new RegExp('\\([^()]*\\)', 'g');
   const branches = helmString.match(re);
   if (!branches)

package/src/model/format-translation/format-converter.ts

@@ -48,7 +48,7 @@ function getHelmToCodeDict(infoObj: CodesInfo) {
   const result: {[key: string]: string | string[]} = {};
   Object.values(infoObj).forEach((obj: {[code: string]: string}) => {
     Object.entries(obj).forEach(([code, helm]) => {
-      const key = helm.replace(/\)p/g, ')');
+      const key = helm.replace(/\)p/g, ')').replace(/\]p/g, ']');
       if (result[key] === undefined) {
         result[key] = [code];
       } else {
@@ -76,6 +76,7 @@ function helmToFormat(helmSequence: string, targetFormat: string): string {
     return helmCodes.includes(match) ? dict[match] :
       (match === 'p' || match === '.') ? match : '?';
   }).replace(/\?+/g, UNKNOWN_SYMBOL).replace(/p\.|\./g, '');
+  result = result.replace(/<empty>/g, '');
   // remove double slash in LCMS codes
   result = result.replace(/\/\//g, '/');
   return result;
@@ -103,5 +104,6 @@ function formatToHelm(sequence: string, sourceFormat: string): string {
   if (helm[helm.length - 1] === PHOSPHATE_SYMBOL)
     helm = helm.slice(0, -1);
   helm = helm.replace(phosphateRegExp, (match, group) => group);
+  helm = helm.replace(/<empty>/g, '');
   return `${HELM_WRAPPER.LEFT + helm + HELM_WRAPPER.RIGHT}`;
 }

package/src/model/monomer-lib/lib-wrapper.ts

@@ -4,6 +4,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {_package} from '../../package';
+import {DEFAULT_FORMATS} from '../const';
 
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 
@@ -29,6 +30,14 @@ export class MonomerLibWrapper {
     formattedObject[REQ.NAME] = sourceObj[REQ.SYMBOL];
     formattedObject[REQ.SYMBOL] = sourceObj[REQ.SYMBOL];
     formattedObject[REQ.MOLFILE] = sourceObj[REQ.MOLFILE];
+    const formats = this.getAllFormats();
+    formats.forEach((format) => {
+      if (format === DEFAULT_FORMATS.HELM)
+        return;
+      const map = codesToSymbolsDictionary[format];
+      const codes = Object.keys(map).filter((code) => map[code] === sourceObj.symbol);
+      formattedObject[format] = codes.join(', ');
+    })
 
     return formattedObject;
   }
@@ -86,6 +95,10 @@ export class MonomerLibWrapper {
     return Object.keys(codesToSymbolsDictionary[format]);
   }
 
+  getAllFormats(): string[] {
+    return Object.keys(codesToSymbolsDictionary);
+  }
+
   getTableForViewer(): DG.DataFrame {
     const formattedObjects = this.allMonomers.map((monomer) => this.formatMonomerForViewer(monomer));
     const df = DG.DataFrame.fromObjects(formattedObjects)!;

package/src/model/sequence-to-structure-utils/sdf-tab.ts

@@ -8,6 +8,7 @@ import {download} from '../helpers';
 import {SequenceToMolfileConverter} from './sequence-to-molfile';
 import {linkStrandsV3000} from './mol-transformations';
 import {DEFAULT_FORMATS} from '../const';
+import {FormatDetector} from '../parsing-validation/format-detector';
 
 export type StrandData = {
   strand: string,
@@ -18,7 +19,9 @@ export type StrandData = {
 export function getMolfileForStrand(strand: string, invert: boolean): string {
   if (strand === '')
     return '';
-  const format = DEFAULT_FORMATS.AXOLABS;
+  const format = (new FormatDetector(strand)).getFormat();
+  if (!format)
+    return '';
   let molfile = '';
   try {
     molfile = (new SequenceToMolfileConverter(strand, invert, format)).convert();

package/src/package-test.ts

@@ -1,6 +1,8 @@
 import * as DG from 'datagrok-api/dg';
 import {runTests, tests, TestContext} from '@datagrok-libraries/utils/src/test';
-import './tests/smiles-tests';
+import './tests/formats-to-helm';
+import './tests/helm-to-nucleotides';
+import './tests/formats-support';
 
 export const _package = new DG.Package();
 export {tests};

package/src/package.ts

@@ -13,6 +13,7 @@ import {MonomerLibWrapper} from './model/monomer-lib/lib-wrapper';
 import {FormatDetector} from './model/parsing-validation/format-detector';
 import {SequenceValidator} from './model/parsing-validation/sequence-validator';
 import {demoDesignPatternUI, demoVisualizeDuplexUI, demoTranslateSequenceUI} from './demo/demo-st-ui';
+import {FormatConverter} from './model/format-translation/format-converter';
 
 class StPackage extends DG.Package {
   private _monomerLib?: IMonomerLib;
@@ -34,7 +35,7 @@ class StPackage extends DG.Package {
       this._monomerLib = await libHelper.readLibrary(LIB_PATH, DEFAULT_LIB_FILENAME);
     } catch (err: any) {
       const errMsg: string = err.hasOwnProperty('message') ? err.message : err.toString();
-      throw new Error('Sequence Translator: Loading monomer library error: ' + errMsg);
+      throw new Error('Loading monomer library: ' + errMsg);
     } finally {
       pi.close();
     }
@@ -93,7 +94,6 @@ export function getMolfileFromGcrsSequence(sequence: string, invert: boolean): s
 
 //name: linkStrands
 //input: object strands
-//input: bool invert
 //output: string result
 export function linkStrands(strands: { senseStrands: string[], antiStrands: string[] }): string {
   return linkStrandsV3000(strands, true);
@@ -122,3 +122,13 @@ export async function demoDesignPattern(): Promise<void> {
 export async function demoVisualizeDuplex(): Promise<void> {
   await demoVisualizeDuplexUI();
 }
+
+//name: translateOligonucleotideSequence
+//input: string sequence
+//input: string sourceFormat
+//input: string targetFormat
+//output: string result
+export async function translateOligonucleotideSequence(sequence: string, sourceFormat: string, targetFormat: string): Promise<string> {
+  await initSequenceTranslatorLibData();
+  return (new FormatConverter(sequence, sourceFormat)).convertTo(targetFormat);
+}

package/src/tests/const.ts

@@ -1,17 +1,24 @@
-export const axolabsToSmiles: {[key: string]: string} = {
-  'usCfCfUfGfAf': 'CO[C@@H]1[C@H](OP(=O)(S)OC[C@H]2O[C@@H](n3ccc(N)nc3=O)[C@H](F)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3ccc(N)nc3=O)[C@H](F)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3ccc(=O)[nH]c3=O)[C@H](F)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](F)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@H](F)[C@@H]2O)[C@@H](CO)O[C@H]1n1ccc(=O)[nH]c1=O',
+type Dict = {[key: string]: string};
 
-  'usAfsusgsgsg': 'CO[C@@H]1[C@H](OP(=O)(S)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc43)[C@H](F)[C@@H]2OP(=O)(S)OC[C@H]2O[C@@H](n3ccc(=O)[nH]c3=O)[C@H](OC)[C@@H]2OP(=O)(S)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](OC)[C@@H]2OP(=O)(S)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](OC)[C@@H]2OP(=O)(S)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](OC)[C@@H]2O)[C@@H](CO)O[C@H]1n1ccc(=O)[nH]c1=O',
-
-  'UfUfUfsCfsuacg': 'CO[C@@H]1[C@H](OP(=O)(O)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](OC)[C@@H]2O)[C@@H](COP(=O)(O)O[C@@H]2[C@@H](COP(=O)(O)O[C@@H]3[C@@H](COP(=O)(S)O[C@@H]4[C@@H](COP(=O)(S)O[C@@H]5[C@@H](COP(=O)(O)O[C@@H]6[C@@H](COP(=O)(O)O[C@@H]7[C@@H](CO)O[C@@H](n8ccc(=O)[nH]c8=O)[C@@H]7F)O[C@@H](n7ccc(=O)[nH]c7=O)[C@@H]6F)O[C@@H](n6ccc(=O)[nH]c6=O)[C@@H]5F)O[C@@H](n5ccc(N)nc5=O)[C@@H]4F)O[C@@H](n4ccc(=O)[nH]c4=O)[C@@H]3OC)O[C@@H](n3cnc4c(N)ncnc43)[C@@H]2OC)O[C@H]1n1ccc(N)nc1=O',
-
-  'susususauasu': 'CO[C@@H]1[C@H](O)[C@@H](COP(=O)(S)O[C@@H]2[C@@H](COP(=O)(O)O[C@@H]3[C@@H](COP(=O)(O)O[C@@H]4[C@@H](COP(=O)(S)O[C@@H]5[C@@H](COP(=O)(S)O[C@@H]6[C@@H](COP(=O)(S)O[C@@H]7[C@@H](COP(=O)(O)S)O[C@@H](n8ccc(=O)[nH]c8=O)[C@@H]7OC)O[C@@H](n7ccc(=O)[nH]c7=O)[C@@H]6OC)O[C@@H](n6ccc(=O)[nH]c6=O)[C@@H]5OC)O[C@@H](n5cnc6c(N)ncnc65)[C@@H]4OC)O[C@@H](n4ccc(=O)[nH]c4=O)[C@@H]3OC)O[C@@H](n3cnc4c(N)ncnc43)[C@@H]2OC)O[C@H]1n1ccc(=O)[nH]c1=O',
+export const formatsToHelm: {[key: string]: Dict} = {
+  'Axolabs': {
+    'UfAfsCfsGfuacg': 'RNA1{[fR](U)p.[fR](A)[sp].[fR](C)[sp].[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$'
+  },
+  'BioSpring': {
+    'AT*GC*123456789': 'RNA1{r(A)p.r(T)[sp].r(G)p.r(C)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)p.d([m5C])}$$$$'
+  },
+  'Mermade12': {
+    'hefglijkLIJKHEFG': 'RNA1{[25r](U)[sp].[25r](A)[sp].[25r](C)[sp].[25r](G)[sp].[fR](U)[sp].[fR](A)[sp].[fR](C)[sp].[fR](G)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$'
+  }
+}
 
-  'CfGfCfsGfsCf': 'Nc1ccn([C@@H]2O[C@H](COP(=O)(S)O[C@@H]3[C@@H](COP(=O)(S)O[C@@H]4[C@@H](COP(=O)(O)O[C@@H]5[C@@H](COP(=O)(O)O[C@@H]6[C@@H](CO)O[C@@H](n7ccc(N)nc7=O)[C@@H]6F)O[C@@H](n6cnc7c(=O)[nH]c(N)nc76)[C@@H]5F)O[C@@H](n5ccc(N)nc5=O)[C@@H]4F)O[C@@H](n4cnc5c(=O)[nH]c(N)nc54)[C@@H]3F)[C@@H](O)[C@H]2F)c(=O)n1',
+export const helmToNucleotides: Dict = {
+  'RNA1{[fR](U)p.[fR](A)[sp].[fR](C)[sp].[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$': 'UACGUACG',
 
-  'acacacsacsac': 'CO[C@@H]1[C@H](O)[C@@H](COP(=O)(O)O[C@@H]2[C@@H](COP(=O)(S)O[C@@H]3[C@@H](COP(=O)(O)O[C@@H]4[C@@H](COP(=O)(S)O[C@@H]5[C@@H](COP(=O)(O)O[C@@H]6[C@@H](COP(=O)(O)O[C@@H]7[C@@H](COP(=O)(O)O[C@@H]8[C@@H](COP(=O)(O)O[C@@H]9[C@@H](COP(=O)(O)O[C@@H]%10[C@@H](CO)O[C@@H](n%11cnc%12c(N)ncnc%12%11)[C@@H]%10OC)O[C@@H](n%10ccc(N)nc%10=O)[C@@H]9OC)O[C@@H](n9cnc%10c(N)ncnc%109)[C@@H]8OC)O[C@@H](n8ccc(N)nc8=O)[C@@H]7OC)O[C@@H](n7cnc8c(N)ncnc87)[C@@H]6OC)O[C@@H](n6ccc(N)nc6=O)[C@@H]5OC)O[C@@H](n5cnc6c(N)ncnc65)[C@@H]4OC)O[C@@H](n4ccc(N)nc4=O)[C@@H]3OC)O[C@@H](n3cnc4c(N)ncnc43)[C@@H]2OC)O[C@H]1n1ccc(N)nc1=O',
+  'RNA1{r(A)p.r(T)[sp].r(G)p.r(C)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)p.d([m5C])}$$$$': 'ATGCUACGUACGC',
 
-  'cccgggusug': 'CO[C@@H]1[C@H](OP(=O)(O)OC[C@H]2O[C@@H](n3ccc(N)nc3=O)[C@H](OC)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3ccc(N)nc3=O)[C@H](OC)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](OC)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](OC)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](OC)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3ccc(=O)[nH]c3=O)[C@H](OC)[C@@H]2OP(=O)(S)OC[C@H]2O[C@@H](n3ccc(=O)[nH]c3=O)[C@H](OC)[C@@H]2OP(=O)(O)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](OC)[C@@H]2O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O',
+  'RNA1{[25r](U)[sp].[25r](A)[sp].[25r](C)[sp].[25r](G)[sp].[fR](U)[sp].[fR](A)[sp].[fR](C)[sp].[fR](G)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$': 'UACGUACGUACGUACG'
+}
 
-  'UfAfCfGfGfCfAfUf': 'Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O[C@@H]3[C@@H](COP(=O)(O)O[C@@H]4[C@@H](CO)O[C@@H](n5ccc(=O)[nH]c5=O)[C@@H]4F)O[C@@H](n4cnc5c(N)ncnc54)[C@@H]3F)[C@@H](OP(=O)(O)OC[C@H]3O[C@@H](n4cnc5c(=O)[nH]c(N)nc54)[C@H](F)[C@@H]3OP(=O)(O)OC[C@H]3O[C@@H](n4cnc5c(=O)[nH]c(N)nc54)[C@H](F)[C@@H]3OP(=O)(O)OC[C@H]3O[C@@H](n4ccc(N)nc4=O)[C@H](F)[C@@H]3OP(=O)(O)OC[C@H]3O[C@@H](n4cnc5c(N)ncnc54)[C@H](F)[C@@H]3OP(=O)(O)OC[C@H]3O[C@@H](n4ccc(=O)[nH]c4=O)[C@H](F)[C@@H]3O)[C@H]2F)c(=O)n1'
+export const helmToMolfile: Dict = {
 }

package/src/tests/formats-support.ts

@@ -0,0 +1,40 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {DEFAULT_FORMATS} from '../model/const';
+import {FormatConverter} from '../model/format-translation/format-converter';
+import {getJsonData} from '../model/data-loading-utils/json-loader';
+import {formatsToHelm} from './const';
+import {SequenceValidator} from '../model/parsing-validation/sequence-validator';
+import {getTranslatedSequences} from '../model/format-translation/conversion-utils';
+import {_package} from '../package';
+
+function getTranslationObject(sequence: string, format: string): {[format: string]: string} {
+  const indexOfInvalidChar = (new SequenceValidator(sequence)).getInvalidCodeIndex(format);
+  return getTranslatedSequences(sequence, indexOfInvalidChar, format);
+}
+
+const inputs = {
+  [DEFAULT_FORMATS.AXOLABS]: 'Afcgacsu',
+  [DEFAULT_FORMATS.HELM]: 'RNA1{[fR](A)p.[25r](C)p.[25r](G)p.[25r](A)p.[25r](C)[sp].[25r](U)}$$$$'
+}
+
+category('Formats support', () => {
+  before(async () => {
+    await getJsonData();
+    await _package.initMonomerLib();
+  });
+
+  Object.entries(inputs).forEach(([format, sequence]) => {
+    test(`All formats for ${format}`, async () => {
+      const output = getTranslationObject(sequence, format);
+      const result = Object.keys(output).length;
+      // +1 due to nucleotides
+      const expected = Object.keys(formatsToHelm).length + 1;
+      expect(result, expected);
+    });
+  });
+});

package/src/tests/formats-to-helm.ts

@@ -0,0 +1,53 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {DEFAULT_FORMATS} from '../model/const';
+import {FormatConverter} from '../model/format-translation/format-converter';
+import {getJsonData} from '../model/data-loading-utils/json-loader';
+import {formatsToHelm} from './const';
+import {_package} from '../package';
+
+function getHelm(strand: string, format: string): string {
+  return (new FormatConverter(strand, format).convertTo(DEFAULT_FORMATS.HELM));
+}
+
+function getFromat(helm: string, format: string): string {
+  return (new FormatConverter(helm, DEFAULT_FORMATS.HELM).convertTo(format));
+}
+
+category('Formats to HELM', () => {
+  before(async () => {
+    await getJsonData();
+    await _package.initMonomerLib();
+  });
+
+  for (const format of Object.keys(formatsToHelm)) {
+    for (const [strand, helm] of Object.entries(formatsToHelm[format])) {
+      test(`${format} to HELM`, async () => {
+        const expected = helm;
+        const result = getHelm(strand, format);
+        expect(result, expected);
+      });
+    }
+  }
+});
+
+category('HELM to Formats', () => {
+  before(async () => {
+    await getJsonData();
+    await _package.initMonomerLib();
+  });
+
+  for (const format of Object.keys(formatsToHelm)) {
+    for (const [strand, helm] of Object.entries(formatsToHelm[format])) {
+      test(`${format} to HELM`, async () => {
+        const expected = strand;
+        const result = getFromat(helm, format);
+        expect(result, expected);
+      });
+    }
+  }
+});

package/src/tests/helm-to-nucleotides.ts

@@ -0,0 +1,28 @@
+/* Do not change these import lines to match external modules in webpack configuration */
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {DEFAULT_FORMATS} from '../model/const';
+import {FormatConverter} from '../model/format-translation/format-converter';
+import {getNucleotidesSequence} from '../model/format-translation/conversion-utils';
+import {getJsonData} from '../model/data-loading-utils/json-loader';
+import {helmToNucleotides} from './const';
+import {_package} from '../package';
+import {MonomerLibWrapper} from '../model/monomer-lib/lib-wrapper';
+
+category('HELM to Nucleotides', () => {
+  before(async () => {
+    await getJsonData();
+    await _package.initMonomerLib();
+  });
+
+  Object.entries(helmToNucleotides).forEach(([helm, nucleotide], idx) => {
+    test(`Sequence ${idx + 1} to nucleotides`, async () => {
+      const expected = nucleotide;
+      const result = getNucleotidesSequence(helm, MonomerLibWrapper.getInstance());
+      expect(result, expected);
+    });
+  })
+});

package/src/view/const/view.ts

@@ -5,6 +5,6 @@ import * as DG from 'datagrok-api/dg';
 
 export const MAIN_TAB = 'SEQUENCE';
 export const AXOLABS_TAB = 'PATTERN';
-export const SDF_TAB = 'DUPLEX';
+export const SDF_TAB = 'SDF';
 
 export const DEFAULT_AXOLABS_INPUT = 'Afcgacsu';