@datagrok/sequence-translator 1.0.17 → 1.1.4

package/src/tests/smiles-tests.ts

@@ -1,458 +0,0 @@
-import {category, expect, test} from '@datagrok-libraries/utils/src/test';
-import {sequenceToSmiles} from '../utils/structures-works/from-monomers';
-import {SYNTHESIZERS} from '../hardcode-to-be-eliminated/map';
-
-category('sequence-translator', () => {
-  // test('AGGTCCTCTTGACTTAGGCC', async () => {
-  //   const expected = 'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[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=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(O)' +
-  //   'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[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]1OP(=O)(O)' +
-  //   'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[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=C(C)C(=O)NC2(=O))C[C@@H]1OP(=O)(O)' +
-  //   'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[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[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=C(C)C(=O)NC2(=O))C[C@@H]1OP(=O)(O)' +
-  //   'OC[C@H]1O[C@@H](N2C=C(C)C(=O)NC2(=O))C[C@@H]1OP(=O)(O)' +
-  //   'OC[C@H]1O[C@@H](N2C3N=CN=C(N)C=3N=C2)C[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=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', false, SYNTHESIZERS.RAW_NUCLEOTIDES), expected);
-  // });
-
-  // test('invabasic/galnac1', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(O)' +
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(O)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('invabasic/galnac2', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=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]1OP(=O)(O)' +
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(O)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('invabasic/galnac3', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(S)' +
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(O)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('invabasic/galnac4', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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=C(N)NC(=O)C=3N=C2)[C@H](OC)[C@@H]1OP(=O)(O)' +
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  test('usCfCfUfGfAf', async () => {
-    const expected = '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(N)=NC2(=O))[C@H](F)[C@@H]1OP(=O)(O)' +
-    '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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  test('usAfsusgsgsg', async () => {
-    const expected = '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](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  test('UfUfUfsCfsuacg', async () => {
-    const expected = '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](N2C=CC(=O)NC2(=O))[C@H](F)[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](F)[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=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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  test('susususauasu', async () => {
-    const expected = 'OP(=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]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](N2C3N=CN=C(N)C=3N=C2)[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]1OP(=O)(S)' +
-    'OC[C@H]1O[C@@H](N2C=CC(=O)NC2(=O))[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('susususauasu', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  test('CfGfCfsGfsCf', async () => {
-    const expected = '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=C(N)NC(=O)C=3N=C2)[C@H](F)[C@@H]1OP(=O)(O)' +
-    '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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  test('acacacsacsac', async () => {
-    const expected = '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=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=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)(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]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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  test('cccgggusug', async () => {
-    const expected =
-    '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](N2C=CC(N)=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=C(N)NC(=O)C=3N=C2)[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=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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  test('UfAfCfGfGfCfAfUf', async () => {
-    const expected =
-    '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=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1OP(=O)(O)' +
-    '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=C(N)NC(=O)C=3N=C2)[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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  // test('(invabasic)sucuCfuUf', async () => {
-  //   const expected =
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=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](N2C=CC(N)=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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('(invabasic)sAfgcugUf', async () => {
-  //   const expected =
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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](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@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=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', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  test('(invabasic)cuCfuUfsc', async () => {
-    const expected =
-    'O[C@@H]1C[C@@H]O[C@H]1COP(=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](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](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]1OP(=O)(S)' +
-    'OC[C@H]1O[C@@H](N2C=CC(N)=NC2(=O))[C@H](OC)[C@@H]1O';
-    expect(sequenceToSmiles('(invabasic)cuCfuUfsc', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  // test('(invabasic)scususu(GalNAc-2-JNJ)', async () => {
-  //   const expected =
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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](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]1OP(=O)(O)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  test('(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu', async () => {
-    const expected =
-    'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(O)' +
-    '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](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[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](N2C=CC(N)=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](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]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](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@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=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]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(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](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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  test('(invabasic)asacgGfuGfCfAfacucuauuca', async () => {
-    const expected =
-    'O[C@@H]1C[C@@H]O[C@H]1COP(=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](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]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](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](F)[C@@H]1OP(=O)(O)' +
-    '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](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](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](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)(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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  });
-
-  // test('(invabasic)scsgguGfcAfAfCfucuauucuga', async () => {
-  //   const expected =
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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=C(N)NC(=O)C=3N=C2)[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](OC)[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](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](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(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(N)=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]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](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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('(invabasic)scsaacUfcUfAfUfucuggacuua', async () => {
-  //   const expected =
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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](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](N2C=CC(=O)NC2(=O))[C@H](F)[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](N2C=CC(=O)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]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(N)=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=C(N)NC(=O)C=3N=C2)[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]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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('(invabasic)sasacuCfuAfUfUfcuggacuuua', async () => {
-  //   const expected =
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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](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](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](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](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]1OP(=O)(O)' +
-  //   '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](N2C=CC(N)=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=C(N)NC(=O)C=3N=C2)[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]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](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](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', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('(invabasic)usAfscug(invabasic)(GalNAc-2-JNJ)', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(O)' +
-  //   '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](N2C3N=CN=C(N)C=3N=C2)[C@H](F)[C@@H]1OP(=O)(S)' +
-  //   '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](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)' +
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(O)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('(invabasic)sasuaaCfcUf(GalNAc-2-JNJ)', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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]1OP(=O)(O)' +
-  //   '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](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](F)[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](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1OP(=O)(O)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('(invabasic)sasuaaCfcUfCfUfuguaguuaua(GalNAc-2-JNJ)', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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]1OP(=O)(O)' +
-  //   '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](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](F)[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](N2C=CC(=O)NC2(=O))[C@H](F)[C@@H]1OP(=O)(O)' +
-  //   '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](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](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](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)(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](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]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]1OP(=O)(O)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS),
-  //     expected);
-  // });
-
-  // test('(invabasic)scsaucacguUfGfCfagccgucuua(invabasic)(GalNAc-2-JNJ)', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(S)' +
-  //   '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(=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]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]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]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](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](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(N)=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=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](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](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]1OP(=O)(O)' +
-  //   'O[C@@H]1C[C@@H]O[C@H]1COP(=O)(O)' +
-  //   '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)',
-  //     false, SYNTHESIZERS.AXOLABS), expected);
-  // });
-
-  // test('(invabasic)susguuUfgCfCfUfacaucuacua(GalNAc-2-JNJ)', async () => {
-  //   const expected = 'O[C@@H]1C[C@@H]O[C@H]1COP(=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](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](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](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](OC)[C@@H]1OP(=O)(O)' +
-  //   '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(N)=NC2(=O))[C@H](F)[C@@H]1OP(=O)(O)' +
-  //   '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=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=CN=C(N)C=3N=C2)[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](N2C=CC(N)=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]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](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)(O)' +
-  //   '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)', false, SYNTHESIZERS.AXOLABS),
-  //     expected);
-  // });
-});

package/src/utils/helpers.ts

@@ -1,28 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-
-export function sortByStringLengthInDescendingOrder(array: string[]): string[] {
-  return array.sort(function(a, b) { return b.length - a.length; });
-}
-
-export function stringify(items: string[]): string {
-  return '["' + items.join('", "') + '"]';
-}
-
-export function download(name: string, href: string): void {
-  const element = document.createElement('a');
-  element.setAttribute('href', 'data:text/plain;charset=utf-8,' + href);
-  element.setAttribute('download', name);
-  element.click();
-}
-
-export function removeEmptyRows(t: DG.DataFrame, colToCheck: DG.Column): DG.DataFrame {
-  for (let i = t.rowCount - 1; i > -1; i--) {
-    if (colToCheck.getString(i) === '')
-      t.rows.removeAt(i, 1, false);
-  }
-  return t;
-}
-
-export function differenceOfTwoArrays(a: string[], b: string[]): string[] {
-  return a.filter((x) => !b.includes(x));
-}

package/src/utils/parse.ts

@@ -1,27 +0,0 @@
-export const CELL_STRUCTURE = {
-  DUPLEX: {
-    BEFORE_SS: 'SS ',
-    BEFORE_AS: '\r\nAS ',
-  },
-  TRIPLEX_OR_DIMER: {
-    BEFORE_SS: 'SS ',
-    BEFORE_AS1: '\r\nAS1 ',
-    BEFORE_AS2: '\r\nAS2 ',
-  },
-};
-
-export function parseStrandsFromDuplexCell(s: string): { SS: string, AS: string } {
-  const arr = s
-    .slice(CELL_STRUCTURE.DUPLEX.BEFORE_SS.length)
-    .split(CELL_STRUCTURE.DUPLEX.BEFORE_AS);
-  return {SS: arr[0], AS: arr[1]};
-}
-
-export function parseStrandsFromTriplexOrDimerCell(s: string): { SS: string, AS1: string, AS2: string } {
-  const arr1 = s
-    .slice(CELL_STRUCTURE.TRIPLEX_OR_DIMER.BEFORE_SS.length)
-    .split(CELL_STRUCTURE.TRIPLEX_OR_DIMER.BEFORE_AS1);
-  const arr2 = arr1[1]
-    .split(CELL_STRUCTURE.TRIPLEX_OR_DIMER.BEFORE_AS2);
-  return {SS: arr1[0], AS1: arr2[0], AS2: arr2[1]};
-}

package/src/utils/sdf-add-columns.ts

@@ -1,118 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-import {COL_NAMES, GENERATED_COL_NAMES, SEQUENCE_TYPES} from '../autostart/constants';
-import * as grok from 'datagrok-api/grok';
-import {removeEmptyRows} from '../utils/helpers';
-import {parseStrandsFromDuplexCell, parseStrandsFromTriplexOrDimerCell} from './parse';
-import {isValidSequence} from '../sdf-tab/sequence-codes-tools';
-import {batchMolWeight, molecularWeight, saltMass, saltMolWeigth} from '../autostart/calculations';
-import {weightsObj} from '../hardcode-to-be-eliminated/map';
-
-export class SdfColumnsExistsError extends Error {
-  constructor(message: string) {
-    super();
-  }
-}
-
-export function sdfAddColumns(
-  df: DG.DataFrame, saltNamesList: string[], saltsMolWeightList: number[], onError: (rowI: number, err: any) => void
-): DG.DataFrame {
-  const sequenceCol = df.getCol(COL_NAMES.SEQUENCE);
-  const saltCol = df.getCol(COL_NAMES.SALT);
-  const equivalentsCol = df.getCol(COL_NAMES.EQUIVALENTS);
-  const typeCol = df.getCol(COL_NAMES.TYPE);
-  const chemistryNameCol = df.getCol(COL_NAMES.CHEMISTRY_NAME);
-
-  if (GENERATED_COL_NAMES.some((colName) => df.columns.contains(colName)))
-    throw new SdfColumnsExistsError('Columns already exist');
-
-  df = removeEmptyRows(df, sequenceCol);
-
-  df.columns.addNewString(COL_NAMES.COMPOUND_NAME).init((i: number) => {
-    let res: string = '';
-    try {
-      res = ([SEQUENCE_TYPES.DUPLEX, SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) ?
-        chemistryNameCol.get(i) :
-        sequenceCol.get(i);
-    } catch (err) {
-      onError(i, err);
-    }
-    return res;
-  });
-
-  df.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => {
-    let res: string = '';
-    try {
-      if ([SEQUENCE_TYPES.SENSE_STRAND, SEQUENCE_TYPES.ANTISENSE_STRAND].includes(typeCol.get(i))) {
-        res = sequenceCol.get(i);
-      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
-        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
-        res = `${chemistryNameCol.get(i)}; duplex of SS: ${obj.SS} and AS: ${obj.AS}`;
-      } else if ([SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) {
-        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
-        res = `${chemistryNameCol.get(i)}; duplex of SS: ${obj.SS} and AS1: ${obj.AS1} and AS2: ${obj.AS2}`;
-      }
-    } catch (err) {
-      onError(i, err);
-    }
-    return res;
-  });
-
-  df.columns.addNewFloat(COL_NAMES.COMPOUND_MOL_WEIGHT).init((i: number) => {
-    let res: number = Number.NaN;
-    try {
-      if ([SEQUENCE_TYPES.SENSE_STRAND, SEQUENCE_TYPES.ANTISENSE_STRAND].includes(typeCol.get(i))) {
-        res = (isValidSequence(sequenceCol.get(i), null).indexOfFirstNotValidChar == -1) ?
-          molecularWeight(sequenceCol.get(i), weightsObj) :
-          DG.FLOAT_NULL;
-      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
-        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
-        res = (Object.values(obj).every((seq) => isValidSequence(seq, null).indexOfFirstNotValidChar == -1)) ?
-          molecularWeight(obj.SS, weightsObj) + molecularWeight(obj.AS, weightsObj) :
-          DG.FLOAT_NULL;
-      } else if ([SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) {
-        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
-        res = (Object.values(obj).every((seq) => isValidSequence(seq, null).indexOfFirstNotValidChar == -1)) ?
-          molecularWeight(obj.SS, weightsObj) + molecularWeight(obj.AS1, weightsObj) +
-          molecularWeight(obj.AS2, weightsObj) :
-          DG.FLOAT_NULL;
-      }
-    } catch (err) {
-      onError(i, err);
-    }
-    return res;
-  });
-
-  df.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) => {
-    let res: number = Number.NaN;
-    try {
-      res = saltMass(saltNamesList, saltsMolWeightList, equivalentsCol, i, saltCol);
-    } catch (err) {
-      onError(i, err);
-    }
-    return res;
-  });
-
-  df.columns.addNewFloat(COL_NAMES.SALT_MOL_WEIGHT).init((i: number) => {
-    let res: number = Number.NaN;
-    try {
-      res = saltMolWeigth(saltNamesList, saltCol, saltsMolWeightList, i);
-    } catch (err) {
-      onError(i, err);
-    }
-    return res;
-  });
-
-  const compoundMolWeightCol = df.getCol(COL_NAMES.COMPOUND_MOL_WEIGHT);
-  const saltMassCol = df.getCol(COL_NAMES.SALT_MASS);
-  df.columns.addNewFloat(COL_NAMES.BATCH_MOL_WEIGHT).init((i: number) => {
-    let res: number = Number.NaN;
-    try {
-      res = batchMolWeight(compoundMolWeightCol, saltMassCol, i);
-    } catch (err) {
-      onError(i, err);
-    }
-    return res;
-  });
-
-  return df;
-}