@datagrok/sequence-translator 0.0.12 → 1.0.0

package/src/structures-works/sequence-codes-tools.ts

@@ -1,5 +1,5 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
+// import * as grok from 'datagrok-api/grok';
+// import * as ui from 'datagrok-api/ui';
 // import * as DG from 'datagrok-api/dg';
 import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS} from './map';
 import {asoGapmersNucleotidesToBioSpring, asoGapmersNucleotidesToGcrs,
@@ -13,24 +13,105 @@ import {asoGapmersNucleotidesToBioSpring, asoGapmersNucleotidesToGcrs,
 const noTranslationTableAvailable = 'No translation table available';
 export const undefinedInputSequence = 'Type of input sequence is undefined';
 
-export function isValidSequence(sequence: string): {
+export function getFormat(sequence: string): string | null {
+  const possibleSynthesizers = getListOfPossibleSynthesizersByFirstMatchedCode(sequence);
+
+  if (possibleSynthesizers.length == 0)
+    return null;
+
+  let outputIndex = 0;
+
+  const firstUniqueCharacters = ['r', 'd'];
+  const nucleotides = ['A', 'U', 'T', 'C', 'G'];
+
+  possibleSynthesizers.forEach((synthesizer) => {
+    const codes = getAllCodesOfSynthesizer(synthesizer);
+    while (outputIndex < sequence.length) {
+      const matchedCode = codes.find((c) => c == sequence.slice(outputIndex, outputIndex + c.length));
+
+      if (matchedCode == null)
+        break;
+
+      if ( // for mistake pattern 'rAA'
+        outputIndex > 1 &&
+        nucleotides.includes(sequence[outputIndex]) &&
+        firstUniqueCharacters.includes(sequence[outputIndex - 2])
+      ) break;
+
+      if ( // for mistake pattern 'ArA'
+        firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
+        nucleotides.includes(sequence[outputIndex])
+      ) {
+        outputIndex++;
+        break;
+      }
+
+      outputIndex += matchedCode.length;
+    }
+  });
+
+  const indexOfFirstNotValidChar = (outputIndex == sequence.length) ? -1 : outputIndex;
+  if (indexOfFirstNotValidChar != -1)
+    return possibleSynthesizers[0];
+
+  const possibleTechnologies = getListOfPossibleTechnologiesByFirstMatchedCode(sequence, possibleSynthesizers[0]);
+
+  if (possibleTechnologies.length == 0)
+    return null;
+
+  outputIndex = 0;
+
+  possibleTechnologies.forEach((technology: string) => {
+    const codes = Object.keys(map[possibleSynthesizers[0]][technology]);
+    while (outputIndex < sequence.length) {
+      const matchedCode = codes.find((c) => c == sequence.slice(outputIndex, outputIndex + c.length));
+
+      if (matchedCode == null)
+        break;
+
+      if ( // for mistake pattern 'rAA'
+        outputIndex > 1 &&
+        nucleotides.includes(sequence[outputIndex]) &&
+        firstUniqueCharacters.includes(sequence[outputIndex - 2])
+      ) break;
+
+      if ( // for mistake pattern 'ArA'
+        firstUniqueCharacters.includes(sequence[outputIndex + 1]) &&
+        nucleotides.includes(sequence[outputIndex])
+      ) {
+        outputIndex++;
+        break;
+      }
+
+      outputIndex += matchedCode.length;
+    }
+  });
+
+  return possibleSynthesizers[0];
+}
+
+export function isValidSequence(sequence: string, format: string | null): {
   indexOfFirstNotValidChar: number,
-  synthesizer: string | null,
-  technology: string | null
+  synthesizer: string[] | null,
+  technology: string[] | null
 } {
-  let possibleSynthesizers = getListOfPossibleSynthesizersByFirstMatchedCode(sequence);
-
-  if (possibleSynthesizers.length > 1) {
-    const synthesizer = ui.choiceInput('Choose synthesizer from list: ', possibleSynthesizers[0], possibleSynthesizers);
-    ui.dialog('Choose Synthesizer')
-      .add(ui.panel([synthesizer.root], {style: {fontWeight: 'bold'}}))
-      .onOK(() => possibleSynthesizers = [synthesizer.value])
-      .onCancel(() => {
-        possibleSynthesizers = [possibleSynthesizers[0]];
-        grok.shell.warning('Input sequence is expected to be in format ' + possibleSynthesizers[0]);
-      })
-      .show();
-  } else if (possibleSynthesizers.length == 0)
+  const possibleSynthesizers = format == null ?
+    getListOfPossibleSynthesizersByFirstMatchedCode(sequence) :
+    [format];
+
+  // if (possibleSynthesizers.length > 1) {
+  //   const synthesizer = ui.choiceInput('Choose synthesizer from list: ', possibleSynthesizers[0],
+  //  possibleSynthesizers);
+  //   ui.dialog('Choose Synthesizer')
+  //     .add(ui.panel([synthesizer.root], {style: {fontWeight: 'bold'}}))
+  //     .onOK(() => possibleSynthesizers = [synthesizer.value])
+  //     .onCancel(() => {
+  //       possibleSynthesizers = [possibleSynthesizers[0]];
+  //       grok.shell.warning('Input sequence is expected to be in format ' + possibleSynthesizers[0]);
+  //     })
+  //     .show();
+  // } else if (possibleSynthesizers.length == 0)
+  if (possibleSynthesizers.length == 0)
     return {indexOfFirstNotValidChar: 0, synthesizer: null, technology: null};
 
   let outputIndex = 0;
@@ -68,24 +149,26 @@ export function isValidSequence(sequence: string): {
   if (indexOfFirstNotValidChar != -1) {
     return {
       indexOfFirstNotValidChar: indexOfFirstNotValidChar,
-      synthesizer: possibleSynthesizers[0],
+      synthesizer: possibleSynthesizers,
       technology: null,
     };
   }
 
-  let possibleTechnologies = getListOfPossibleTechnologiesByFirstMatchedCode(sequence, possibleSynthesizers[0]);
-
-  if (possibleTechnologies.length > 1) {
-    const technology = ui.choiceInput('Choose technology from list: ', possibleTechnologies[0], possibleTechnologies);
-    ui.dialog('Choose Technology')
-      .add(ui.panel([technology.root], {style: {fontWeight: 'bold'}}))
-      .onOK(() => possibleTechnologies = [technology.value])
-      .onCancel(() => {
-        possibleTechnologies = [possibleTechnologies[0]];
-        grok.shell.warning('Input sequence is expected to be in format ' + possibleTechnologies[0]);
-      })
-      .show();
-  } else if (possibleTechnologies.length == 0)
+  const possibleTechnologies = getListOfPossibleTechnologiesByFirstMatchedCode(sequence, possibleSynthesizers[0]);
+
+  // if (possibleTechnologies.length > 1) {
+  //   const technology = ui.choiceInput('Choose technology from list: ', possibleTechnologies[0],
+  // possibleTechnologies);
+  //   ui.dialog('Choose Technology')
+  //     .add(ui.panel([technology.root], {style: {fontWeight: 'bold'}}))
+  //     .onOK(() => possibleTechnologies = [technology.value])
+  //     .onCancel(() => {
+  //       possibleTechnologies = [possibleTechnologies[0]];
+  //       grok.shell.warning('Input sequence is expected to be in format ' + possibleTechnologies[0]);
+  //     })
+  //     .show();
+  // } else if (possibleTechnologies.length == 0)
+  if (possibleTechnologies.length == 0)
     return {indexOfFirstNotValidChar: 0, synthesizer: null, technology: null};
 
   outputIndex = 0;
@@ -118,8 +201,8 @@ export function isValidSequence(sequence: string): {
 
   return {
     indexOfFirstNotValidChar: indexOfFirstNotValidChar,
-    synthesizer: possibleSynthesizers[0],
-    technology: possibleTechnologies[outputIndex],
+    synthesizer: possibleSynthesizers,
+    technology: [possibleTechnologies[outputIndex]],
   };
 }
 
@@ -159,7 +242,7 @@ function getListOfPossibleTechnologiesByFirstMatchedCode(sequence: string, synth
 }
 
 export function convertSequence(sequence: string, output: {
-  indexOfFirstNotValidChar: number, synthesizer: string | null, technology: string | null}) {
+  indexOfFirstNotValidChar: number, synthesizer: string[] | null, technology: string[] | null}) {
   if (output.indexOfFirstNotValidChar != -1) {
     return {
       // type: '',
@@ -167,15 +250,15 @@ export function convertSequence(sequence: string, output: {
       Error: undefinedInputSequence,
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.RAW_NUCLEOTIDES && output.technology == TECHNOLOGIES.DNA) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.RAW_NUCLEOTIDES)) {//&& output.technology!.includes(TECHNOLOGIES.DNA)) {
     return {
-      type: SYNTHESIZERS.RAW_NUCLEOTIDES + ' ' + TECHNOLOGIES.DNA,
+      type: SYNTHESIZERS.RAW_NUCLEOTIDES, // + ' ' + TECHNOLOGIES.DNA,
       Nucleotides: sequence,
       BioSpring: asoGapmersNucleotidesToBioSpring(sequence),
       GCRS: asoGapmersNucleotidesToGcrs(sequence),
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.BIOSPRING && output.technology == TECHNOLOGIES.ASO_GAPMERS) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.BIOSPRING) && output.technology!.includes(TECHNOLOGIES.ASO_GAPMERS)) {
     return {
       type: SYNTHESIZERS.BIOSPRING + ' ' + TECHNOLOGIES.ASO_GAPMERS,
       Nucleotides: asoGapmersBioSpringToNucleotides(sequence),
@@ -183,7 +266,7 @@ export function convertSequence(sequence: string, output: {
       GCRS: asoGapmersBioSpringToGcrs(sequence),
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.GCRS && output.technology == TECHNOLOGIES.ASO_GAPMERS) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS) && output.technology!.includes(TECHNOLOGIES.ASO_GAPMERS)) {
     return {
       type: SYNTHESIZERS.GCRS + ' ' + TECHNOLOGIES.ASO_GAPMERS,
       Nucleotides: asoGapmersGcrsToNucleotides(sequence),
@@ -192,7 +275,7 @@ export function convertSequence(sequence: string, output: {
       GCRS: sequence,
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.RAW_NUCLEOTIDES && output.technology == TECHNOLOGIES.RNA) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.RAW_NUCLEOTIDES) && output.technology!.includes(TECHNOLOGIES.RNA)) {
     return {
       type: SYNTHESIZERS.RAW_NUCLEOTIDES + ' ' + TECHNOLOGIES.RNA,
       Nucleotides: sequence,
@@ -201,7 +284,7 @@ export function convertSequence(sequence: string, output: {
       GCRS: siRnaNucleotidesToGcrs(sequence),
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.BIOSPRING && output.technology == TECHNOLOGIES.SI_RNA) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.BIOSPRING) && output.technology!.includes(TECHNOLOGIES.SI_RNA)) {
     return {
       type: SYNTHESIZERS.BIOSPRING + ' ' + TECHNOLOGIES.SI_RNA,
       Nucleotides: siRnaBioSpringToNucleotides(sequence),
@@ -210,7 +293,7 @@ export function convertSequence(sequence: string, output: {
       GCRS: siRnaBioSpringToGcrs(sequence),
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.AXOLABS && output.technology == TECHNOLOGIES.SI_RNA) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.AXOLABS)) {
     return {
       type: SYNTHESIZERS.AXOLABS + ' ' + TECHNOLOGIES.SI_RNA,
       Nucleotides: siRnaAxolabsToNucleotides(sequence),
@@ -219,7 +302,7 @@ export function convertSequence(sequence: string, output: {
       GCRS: siRnaAxolabsToGcrs(sequence),
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.GCRS && output.technology == TECHNOLOGIES.SI_RNA) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS) && output.technology!.includes(TECHNOLOGIES.SI_RNA)) {
     return {
       type: SYNTHESIZERS.GCRS + ' ' + TECHNOLOGIES.SI_RNA,
       Nucleotides: siRnaGcrsToNucleotides(sequence),
@@ -229,7 +312,7 @@ export function convertSequence(sequence: string, output: {
       GCRS: sequence,
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.GCRS) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.GCRS)) {
     return {
       type: SYNTHESIZERS.GCRS,
       Nucleotides: gcrsToNucleotides(sequence),
@@ -237,7 +320,7 @@ export function convertSequence(sequence: string, output: {
       Mermade12: gcrsToMermade12(sequence),
     };
   }
-  if (output.synthesizer == SYNTHESIZERS.MERMADE_12) {
+  if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12)) {
     return {
       type: SYNTHESIZERS.MERMADE_12,
       Nucleotides: noTranslationTableAvailable,

package/src/tests/smiles-tests.ts

@@ -1,5 +1,6 @@
 import {category, expect, test} from '@datagrok-libraries/utils/src/test';
 import {sequenceToSmiles} from '../structures-works/from-monomers';
+import {SYNTHESIZERS} from '../structures-works/map';
 
 category('sequence-translator', () => {
   test('AGGTCCTCTTGACTTAGGCC', async () => {
@@ -23,7 +24,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))C[C@@H]1OP(=O)(O)OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))C[C@@H]1O';
 
-    expect(sequenceToSmiles('AGGTCCTCTTGACTTAGGCC'), expected);
+    expect(sequenceToSmiles('AGGTCCTCTTGACTTAGGCC', false, SYNTHESIZERS.RAW_NUCLEOTIDES), expected);
   });
 
   test('invabasic/galnac1', async () => {
@@ -34,7 +35,7 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)sgg(invabasic)(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)sgg(invabasic)(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('invabasic/galnac2', async () => {
@@ -45,7 +46,7 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)sgsg(invabasic)(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)sgsg(invabasic)(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('invabasic/galnac3', async () => {
@@ -56,7 +57,7 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)sggs(invabasic)(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)sggs(invabasic)(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('invabasic/galnac4', async () => {
@@ -67,7 +68,7 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)sgg(invabasic)s(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)sgg(invabasic)s(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('usCfCfUfGfAf', async () => {
@@ -77,7 +78,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](F)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1O';
-    expect(sequenceToSmiles('usCfCfUfGfAf'), expected);
+    expect(sequenceToSmiles('usCfCfUfGfAf', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('usAfsusgsgsg', async () => {
@@ -87,7 +88,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('usAfsusgsgsg'), expected);
+    expect(sequenceToSmiles('usAfsusgsgsg', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('UfUfUfsCfsuacg', async () => {
@@ -99,7 +100,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('UfUfUfsCfsuacg'), expected);
+    expect(sequenceToSmiles('UfUfUfsCfsuacg', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('susususauasu', async () => {
@@ -110,7 +111,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('susususauasu'), expected);
+    expect(sequenceToSmiles('susususauasu', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('CfGfCfsGfsCf', async () => {
@@ -119,7 +120,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](F)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](F)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](F)[C@@H]1O';
-    expect(sequenceToSmiles('CfGfCfsGfsCf'), expected);
+    expect(sequenceToSmiles('CfGfCfsGfsCf', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('acacacsacsac', async () => {
@@ -133,7 +134,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('acacacsacsac'), expected);
+    expect(sequenceToSmiles('acacacsacsac', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('cccgggusug', async () => {
@@ -147,7 +148,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('cccgggusug'), expected);
+    expect(sequenceToSmiles('cccgggusug', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('UfAfCfGfGfCfAfUf', async () => {
@@ -160,7 +161,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](F)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1O';
-    expect(sequenceToSmiles('UfAfCfGfGfCfAfUf'), expected);
+    expect(sequenceToSmiles('UfAfCfGfGfCfAfUf', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)sucuCfuUf', async () => {
@@ -172,7 +173,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](F)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)sucuCfuUf'), expected);
+    expect(sequenceToSmiles('(invabasic)sucuCfuUf', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)sAfgcugUf', async () => {
@@ -184,7 +185,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)sAfgcugUf'), expected);
+    expect(sequenceToSmiles('(invabasic)sAfgcugUf', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)cuCfuUfsc', async () => {
@@ -196,7 +197,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)cuCfuUfsc'), expected);
+    expect(sequenceToSmiles('(invabasic)cuCfuUfsc', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)scususu(GalNAc-2-JNJ)', async () => {
@@ -209,7 +210,7 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)scususu(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)scususu(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu', async () => {
@@ -236,7 +237,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(S)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu'), expected);
+    expect(sequenceToSmiles('(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)asacgGfuGfCfAfacucuauuca', async () => {
@@ -261,7 +262,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)asacgGfuGfCfAfacucuauuca'), expected);
+    expect(sequenceToSmiles('(invabasic)asacgGfuGfCfAfacucuauuca', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)scsgguGfcAfAfCfucuauucuga', async () => {
@@ -286,7 +287,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)scsgguGfcAfAfCfucuauucuga'), expected);
+    expect(sequenceToSmiles('(invabasic)scsgguGfcAfAfCfucuauucuga', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)scsaacUfcUfAfUfucuggacuua', async () => {
@@ -311,7 +312,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)scsaacUfcUfAfUfucuggacuua'), expected);
+    expect(sequenceToSmiles('(invabasic)scsaacUfcUfAfUfucuggacuua', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)sasacuCfuAfUfUfcuggacuuua', async () => {
@@ -336,7 +337,7 @@ category('sequence-translator', () => {
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1OP(=O)(O)' +
     'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)sasacuCfuAfUfUfcuggacuuua'), expected);
+    expect(sequenceToSmiles('(invabasic)sasacuCfuAfUfUfcuggacuuua', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)usAfscug(invabasic)(GalNAc-2-JNJ)', async () => {
@@ -350,7 +351,7 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)usAfscug(invabasic)(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)usAfscug(invabasic)(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)sasuaaCfcUf(GalNAc-2-JNJ)', async () => {
@@ -365,7 +366,7 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)sasuaaCfcUf(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)sasuaaCfcUf(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)sasuaaCfcUfCfUfuguaguuaua(GalNAc-2-JNJ)', async () => {
@@ -392,7 +393,8 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)sasuaaCfcUfCfUfuguaguuaua(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)sasuaaCfcUfCfUfuguaguuaua(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS),
+      expected);
   });
 
   test('(invabasic)scsaucacguUfGfCfagccgucuua(invabasic)(GalNAc-2-JNJ)', async () => {
@@ -422,7 +424,8 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)scsaucacguUfGfCfagccgucuua(invabasic)(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)scsaucacguUfGfCfagccgucuua(invabasic)(GalNAc-2-JNJ)',
+      false, SYNTHESIZERS.AXOLABS), expected);
   });
 
   test('(invabasic)susguuUfgCfCfUfacaucuacua(GalNAc-2-JNJ)', async () => {
@@ -449,6 +452,7 @@ category('sequence-translator', () => {
     '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)';
-    expect(sequenceToSmiles('(invabasic)susguuUfgCfCfUfacaucuacua(GalNAc-2-JNJ)'), expected);
+    expect(sequenceToSmiles('(invabasic)susguuUfgCfCfUfacaucuacua(GalNAc-2-JNJ)', false, SYNTHESIZERS.AXOLABS),
+      expected);
   });
 });

package/{test-SequenceTranslator-c2bbc2b235db-afc0e1c5.html → test-SequenceTranslator-089b6516ed77-d62c21a9.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=c2bbc2b235db. Commit afc0e1c5.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=089b6516ed77. Commit d62c21a9.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=c2bbc2b235db. Commit afc0e1c5.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-05-13 15:45:08</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">26.07s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">2.12s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: Unable to find JS function "test"
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=089b6516ed77. Commit d62c21a9.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-06-09 13:34:01</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">12.701s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">0.313s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: Unable to find JS function "test"
     at ExecutionContext._evaluateInternal (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/puppeteer/src/common/ExecutionContext.ts:273:13)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)
     at ExecutionContext.evaluate (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/puppeteer/src/common/ExecutionContext.ts:140:12)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)