@datagrok/sequence-translator 1.4.1 → 1.4.3

package/src/polytool/types.ts

@@ -9,12 +9,15 @@ export enum PolyToolEnumeratorTypes {
 
 export type PolyToolEnumeratorType = typeof PolyToolEnumeratorTypes[keyof typeof PolyToolEnumeratorTypes];
 
-export type PolyToolPlaceholders = { [position: number]: string[] };
+export type PolyToolPlaceholders = { position: number, monomers: string[] } [];
+
+export type PolyToolPlaceholdersBreadth = { start: number, end: number, monomers: string[] }[];
 
 export type PolyToolEnumeratorParams = {
   type: PolyToolEnumeratorType;
   /** position key is zero-based */
-  placeholders: PolyToolPlaceholders;
+  placeholders?: PolyToolPlaceholders;
+  placeholdersBreadth?: PolyToolPlaceholdersBreadth;
   keepOriginal?: boolean;
   trivialName?: boolean;
 }

package/src/tests/polytool-convert-tests.ts

@@ -6,7 +6,7 @@ import {before, after, category, expect, test, expectArray, testEvent, delay} fr
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
@@ -23,9 +23,8 @@ category('PolyTool: Convert', () => {
   before(async () => {
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
-    // Clear settings to test default
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true);
+
+    await monomerLibHelper.loadMonomerLibForTests();
   });
 
   after(async () => {
@@ -43,11 +42,11 @@ category('PolyTool: Convert', () => {
         'R-F-D(2)-T-G-H-F-Y-P-NH2(2)',
       ],
       tgt: [
-        'PEPTIDE1{[R].[F].[C].[T].[G].[H].[F].[Y].[P].[C].[meI]}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$',
-        'PEPTIDE1{[C].[T].[G].[H].[F].[Y].[P].[C].[meI]}$PEPTIDE1,PEPTIDE1,1:R3-8:R3$$$',
-        'PEPTIDE1{[R].[F].[C].[T].[G].[H].[F].[Y].[P].[C]}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$',
-        'PEPTIDE1{[C].[T].[G].[H].[F].[H].[P].[C]}$PEPTIDE1,PEPTIDE1,1:R3-8:R3$$$',
-        'PEPTIDE1{[R].[F].[D].[T].[G].[H].[F].[Y].[P].[NH2]}$PEPTIDE1,PEPTIDE1,10:R2-3:R3$$$',
+        'PEPTIDE1{R.F.C.T.G.H.F.Y.P.C.[meI]}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$',
+        'PEPTIDE1{C.T.G.H.F.Y.P.C.[meI]}$PEPTIDE1,PEPTIDE1,1:R3-8:R3$$$',
+        'PEPTIDE1{R.F.C.T.G.H.F.Y.P.C}$PEPTIDE1,PEPTIDE1,3:R3-10:R3$$$',
+        'PEPTIDE1{C.T.G.H.F.H.P.C}$PEPTIDE1,PEPTIDE1,1:R3-8:R3$$$',
+        'PEPTIDE1{R.F.D.T.G.H.F.Y.P.[NH2]}$PEPTIDE1,PEPTIDE1,10:R2-3:R3$$$',
       ]
     }
   };

package/src/tests/polytool-enumerate-breadth-tests.ts

@@ -0,0 +1,116 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, after, category, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {
+  getUserLibSettings, setUserLibSettings
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+
+import {PolyToolEnumeratorParams, PolyToolEnumeratorTypes} from '../polytool/types';
+import {doPolyToolEnumerateHelm} from '../polytool/pt-enumeration-helm';
+
+import {_package} from '../package-test';
+
+category('PolyTool: Enumerate', () => {
+  let helmHelper: IHelmHelper;
+  let monomerLibHelper: IMonomerLibHelper;
+  let userLibSettings: UserLibSettings; //backup
+
+  before(async () => {
+    helmHelper = await getHelmHelper(); // initialize JSDraw2 and org
+
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+
+    await monomerLibHelper.loadMonomerLibForTests();
+  });
+
+  after(async () => {
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadMonomerLib(true);
+  });
+
+  const tests: {
+    [testName: string]: { src: string, params: PolyToolEnumeratorParams, tgt: { seq: string, name: string }[] }
+  } = {
+    'breadth1': {
+      src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
+      params: {
+        type: PolyToolEnumeratorTypes.Single,
+        placeholdersBreadth: [
+          {start: 2, end: 4, monomers: ['K']},
+        ],
+      },
+      tgt: [
+        {seq: 'PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-W3K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-G4K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5K'},
+      ],
+    },
+    'breadth1-with-original': {
+      src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
+      params: {
+        type: PolyToolEnumeratorTypes.Single,
+        placeholdersBreadth: [
+          {start: 2, end: 4, monomers: ['K']},
+        ],
+        keepOriginal: true,
+      },
+      tgt: [
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: ''},
+        {seq: 'PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-W3K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-G4K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5K'},
+      ],
+    },
+    'breadth2': {
+      src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
+      params: {
+        type: PolyToolEnumeratorTypes.Single,
+        placeholdersBreadth: [
+          {start: 2, end: 4, monomers: ['K', 'Y']},
+        ],
+      },
+      tgt: [
+        {seq: 'PEPTIDE1{[Ac(1)].F.K.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-W3K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-G4K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-W3Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-G4Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5Y'},
+      ],
+    },
+    'breadth-double': {
+      src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
+      params: {
+        type: PolyToolEnumeratorTypes.Single,
+        placeholdersBreadth: [
+          {start: 2, end: 4, monomers: ['K']},
+          {start: 2, end: 4, monomers: ['Y']},
+        ],
+      },
+      tgt: [
+        {seq: "PEPTIDE1{[Ac(1)].F.Y.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-W3K-K3Y"},
+        {seq: "PEPTIDE1{[Ac(1)].F.K.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-W3K-G4Y"},
+        {seq: "PEPTIDE1{[Ac(1)].F.K.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-W3K-P5Y"},
+        {seq: "PEPTIDE1{[Ac(1)].F.Y.K.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-G4K-W3Y"},
+        {seq: "PEPTIDE1{[Ac(1)].F.W.Y.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-G4K-K4Y"},
+        {seq: "PEPTIDE1{[Ac(1)].F.W.K.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-G4K-P5Y"},
+        {seq: "PEPTIDE1{[Ac(1)].F.Y.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-P5K-W3Y"},
+        {seq: "PEPTIDE1{[Ac(1)].F.W.Y.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-P5K-G4Y"},
+        {seq: "PEPTIDE1{[Ac(1)].F.W.G.Y.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0", name: "-P5K-K5Y"}
+      ]
+    }
+  };
+
+  for (const [testName, testData] of Object.entries(tests)) {
+    test(`${testName}`, async () => {
+      const res = doPolyToolEnumerateHelm(testData.src, '', testData.params);
+      expectArray(res, testData.tgt.map((r) => [r.seq, r.name]));
+    });
+  }
+});

package/src/tests/polytool-enumerate-tests.ts

@@ -7,7 +7,7 @@ import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {PolyToolEnumeratorParams, PolyToolEnumeratorTypes} from '../polytool/types';
@@ -26,8 +26,7 @@ category('PolyTool: Enumerate', () => {
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
     // Clear settings to test default
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true);
+    await monomerLibHelper.loadMonomerLibForTests();
   });
 
   after(async () => {
@@ -36,42 +35,42 @@ category('PolyTool: Enumerate', () => {
   });
 
   const tests: {
-    [testName: string]: { src: string, params: PolyToolEnumeratorParams, tgt: [string, string][] }
+    [testName: string]: { src: string, params: PolyToolEnumeratorParams, tgt: { seq: string, name: string }[] }
   } = {
     'single1': {
       src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
       params: {
         type: PolyToolEnumeratorTypes.Single,
-        placeholders: {
-          [4]: ['K', 'P', 'F4COO'],
-          [6]: ['Y', 'T'],
-        },
+        placeholders: [
+          {position: 4, monomers: ['K', 'P', 'F4COO']},
+          {position: 6, monomers: ['Y', 'T']},
+        ],
       },
       tgt: [
-        ['PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5K'],
-        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5P'],
-        ['PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5[F4COO]'],
-        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-[Tic]7Y'],
-        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', '-[Tic]7T'],
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5P'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5[F4COO]'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', name: '-[Tic]7Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', name: '-[Tic]7T'},
       ]
     },
     'single-with-original': {
       src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
       params: {
         type: PolyToolEnumeratorTypes.Single,
-        placeholders: {
-          [4]: ['K', 'P', 'F4COO'],
-          [6]: ['Y', 'T'],
-        },
+        placeholders: [
+          {position: 4, monomers: ['K', 'P', 'F4COO']},
+          {position: 6, monomers: ['Y', 'T']},
+        ],
         keepOriginal: true,
       },
       tgt: [
-        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', ''],
-        ['PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5K'],
-        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5P'],
-        ['PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5[F4COO]'],
-        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-[Tic]7Y'],
-        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', '-[Tic]7T'],
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: ''},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5K'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5P'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', name: '-P5[F4COO]'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', name: '-[Tic]7Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', name: '-[Tic]7T'},
       ]
     },
     'matrix1': {
@@ -79,25 +78,25 @@ category('PolyTool: Enumerate', () => {
       params:
         {
           type: PolyToolEnumeratorTypes.Matrix,
-          placeholders: {
-            [1]: ['D', 'L'],
-            [4]: ['K', 'P', 'F4COO'],
-            [6]: ['Y', 'T'],
-          }
+          placeholders: [
+            {position: 1, monomers: ['D', 'L']},
+            {position: 4, monomers: ['K', 'P', 'F4COO']},
+            {position: 6, monomers: ['Y', 'T']},
+          ]
         },
       tgt: [
-        ['PEPTIDE1{[Ac(1)].D.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-F2D-P5K-[Tic]7Y'],
-        ['PEPTIDE1{[Ac(1)].D.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0', '-F2D-P5K-[Tic]7T'],
-        ['PEPTIDE1{[Ac(1)].D.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-F2D-P5P-[Tic]7Y'],
-        ['PEPTIDE1{[Ac(1)].D.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', '-F2D-P5P-[Tic]7T'],
-        ['PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-F2D-P5[F4COO]-[Tic]7Y'],
-        ['PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0', '-F2D-P5[F4COO]-[Tic]7T'],
-        ['PEPTIDE1{[Ac(1)].L.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-F2L-P5K-[Tic]7Y'],
-        ['PEPTIDE1{[Ac(1)].L.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0', '-F2L-P5K-[Tic]7T'],
-        ['PEPTIDE1{[Ac(1)].L.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-F2L-P5P-[Tic]7Y'],
-        ['PEPTIDE1{[Ac(1)].L.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', '-F2L-P5P-[Tic]7T'],
-        ['PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-F2L-P5[F4COO]-[Tic]7Y'],
-        ['PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0', '-F2L-P5[F4COO]-[Tic]7T'],
+        {seq: 'PEPTIDE1{[Ac(1)].D.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2D-P5K-[Tic]7Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].D.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2D-P5K-[Tic]7T'},
+        {seq: 'PEPTIDE1{[Ac(1)].D.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2D-P5P-[Tic]7Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].D.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2D-P5P-[Tic]7T'},
+        {seq: 'PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2D-P5[F4COO]-[Tic]7Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2D-P5[F4COO]-[Tic]7T'},
+        {seq: 'PEPTIDE1{[Ac(1)].L.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2L-P5K-[Tic]7Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].L.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2L-P5K-[Tic]7T'},
+        {seq: 'PEPTIDE1{[Ac(1)].L.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2L-P5P-[Tic]7Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].L.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2L-P5P-[Tic]7T'},
+        {seq: 'PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2L-P5[F4COO]-[Tic]7Y'},
+        {seq: 'PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0', name: '-F2L-P5[F4COO]-[Tic]7T'},
       ],
     }
   };
@@ -105,7 +104,7 @@ category('PolyTool: Enumerate', () => {
   for (const [testName, testData] of Object.entries(tests)) {
     test(`${testName}`, async () => {
       const res = doPolyToolEnumerateHelm(testData.src, '', testData.params);
-      expectArray(res, testData.tgt);
+      expectArray(res, testData.tgt.map((r) => [r.seq, r.name]));
     });
   }
 });

package/src/tests/polytool-unrule-tests.ts

@@ -0,0 +1,10 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+
+import {doPolyToolUnrule} from '../polytool/pt-unrule';
+import {getRules} from '../polytool/pt-rules';
+
+import {_package} from '../package-test';

package/src/tests/toAtomicLevel-tests.ts

@@ -0,0 +1,72 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {before, after, category, expect, test, expectArray, testEvent, delay} from '@datagrok-libraries/utils/src/test';
+import {Monomer, MonomerLibData} from '@datagrok-libraries/bio/src/types/index';
+
+import {PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
+import {getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
+import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
+
+import {_package} from '../package-test';
+
+category('toAtomicLevel', () => {
+  let userLibSettings: UserLibSettings;
+  let monomerLibHelper: IMonomerLibHelper;
+  let rdKitModule: RDModule;
+
+  before(async () => {
+
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+    rdKitModule = await getRdKitModule();
+
+    await monomerLibHelper.loadMonomerLibForTests();
+  });
+
+  after(async () => {
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
+  });
+
+  test('override', async () => {
+    const systemMonomerLib = monomerLibHelper.getMonomerLib();
+    const rLibStr = await _package.files.readAsText('tests/polytool-reaction-lib.json');
+    const rLib: Monomer[] = JSON.parse(rLibStr);
+    const ggazM = rLib.find((m) => m.symbol === 'GGaz')!;
+    expect(ggazM != null, true, `Monomer 'GGaz' not found.`);
+
+    const overrideMonomerLibData: MonomerLibData = {[PolymerTypes.PEPTIDE]: {'GGaz': ggazM}};
+    const overriddenMonomerLib = systemMonomerLib.override(overrideMonomerLibData);
+
+    const seqHelper = await getSeqHelper();
+
+    const helmCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'helm',
+      ['PEPTIDE1{F.P.Y.[GGaz].H.A.A.G.G.A.C}|PEPTIDE2{A.A.A}$PEPTIDE1,PEPTIDE2,4:R4-1:R1|PEPTIDE1,PEPTIDE1,11:R2-4:R3$$$V2.0']);
+    helmCol.semType = DG.SEMTYPE.MACROMOLECULE;
+    helmCol.meta.units = NOTATION.HELM;
+    const talRes = await seqHelper.helmToAtomicLevel(helmCol, false, false, overriddenMonomerLib);
+
+    expect(talRes.molCol != null, true, 'Result molCol is null');
+    const molfile = talRes.molCol!.get(0)!;
+    expect(!!molfile, true, 'Molfile is empty');
+
+    const mol = rdKitModule.get_mol(molfile);
+    try {
+      const molInchi = mol.get_inchi();
+      const molInchiKey = rdKitModule.get_inchikey_for_inchi(molInchi);
+
+      expect(mol.get_num_bonds(), 103);
+      expect(mol.get_num_atoms(), 98);
+      expect(molInchiKey, 'XPQUTLNSNIMERR-WKBTUBAPSA-N');
+    } finally {
+      mol.delete();
+    }
+  });
+});