@datagrok/bio 2.15.5 → 2.15.6

package/files/monomer-libraries/polytool-lib.json

@@ -44,5 +44,57 @@
     "id": 0,
     "polymerType": "PEPTIDE",
     "symbol": "COOH"
+  },
+  {
+    "monomerType": "Backbone",
+    "smiles": "[H:1]NC(C#C)C([OH:2])=O",
+    "name": "Acetylenil Glycine",
+    "author": "Datagrok",
+    "molfile": "\n  MJ201900                      \n\n  8  7  0  0  0  0  0  0  0  0999 V2000\n    3.7485   -4.0401    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.4629   -4.4526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.1773   -4.0401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.8917   -4.4526    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    5.1773   -3.2152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    4.4630   -5.2776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7485   -5.6901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.0340   -4.4526    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  2  3  1  0  0  0  0\n  3  5  2  0  0  0  0\n  2  6  1  0  0  0  0\n  1  2  1  0  0  0  0\n  1  8  1  0  0  0  0\n  3  4  1  0  0  0  0\n  6  7  3  0  0  0  0\nM  RGP  2   4   2   8   1\nM  END",
+    "naturalAnalog": "G",
+    "rgroups": [
+      {
+        "capGroupSMILES": "[*:1][H]",
+        "alternateId": "R1-H",
+        "capGroupName": "H",
+        "label": "R1"
+      },
+      {
+        "capGroupSMILES": "O[*:2]",
+        "alternateId": "R2-OH",
+        "capGroupName": "OH",
+        "label": "R2"
+      }
+    ],
+    "createDate": null,
+    "id": 0,
+    "polymerType": "PEPTIDE",
+    "symbol": "aG"
+  },
+  {
+    "monomerType": "Backbone",
+    "smiles": "[H:1]NC(CN=[N+]=[N-])C([OH:2])=O",
+    "name": "Azido Glycine",
+    "author": "Datagrok",
+    "molfile": "\n  MJ201900                      \n\n 10  9  0  0  0  0  0  0  0  0999 V2000\n   -0.7143    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7144    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4288    0.0000    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    0.7144    1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0001   -0.8249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4288    0.0000    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7142   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.4511   -1.6510    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n   -2.2101   -2.0717    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0\n  2  3  1  0  0  0  0\n  3  5  2  0  0  0  0\n  2  6  1  0  0  0  0\n  1  2  1  0  0  0  0\n  1  7  1  0  0  0  0\n  3  4  1  0  0  0  0\n  6  8  1  0  0  0  0\n  8  9  2  0  0  0  0\n  9 10  2  0  0  0  0\nM  RGP  2   4   2   7   1\nM  END",
+    "naturalAnalog": "G",
+    "rgroups": [
+      {
+        "capGroupSMILES": "[*:1][H]",
+        "alternateId": "R1-H",
+        "capGroupName": "H",
+        "label": "R1"
+      },
+      {
+        "capGroupSMILES": "O[*:2]",
+        "alternateId": "R2-OH",
+        "capGroupName": "OH",
+        "label": "R2"
+      }
+    ],
+    "createDate": null,
+    "id": "0",
+    "polymerType": "PEPTIDE",
+    "symbol": "azG"
   }
 ]

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.15.5",
+  "version": "2.15.6",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -37,7 +37,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.44.1",
+    "@datagrok-libraries/bio": "^5.44.2",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.0",
     "@datagrok-libraries/ml": "^6.7.1",
@@ -62,7 +62,7 @@
     "@datagrok-libraries/js-draw-lite": "^0.0.8",
     "@datagrok/chem": "^1.12.1",
     "@datagrok/dendrogram": "^1.2.33",
-    "@datagrok/helm": "^2.5.0",
+    "@datagrok/helm": "^2.5.2",
     "@types/node": "^17.0.24",
     "@types/wu": "latest",
     "@typescript-eslint/eslint-plugin": "latest",

package/src/package-test.ts

@@ -2,12 +2,13 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {runTests, TestContext, tests, initAutoTests as initTests } from '@datagrok-libraries/utils/src/test';
+import {runTests, TestContext, tests, initAutoTests as initTests} from '@datagrok-libraries/utils/src/test';
 
 import './tests/_first-tests';
 import './tests/Palettes-test';
 import './tests/detectors-tests';
 import './tests/detectors-weak-and-likely-tests';
+import './tests/detectors-custom-notation-tests';
 import './tests/detectors-benchmark-tests';
 import './tests/msa-tests';
 import './tests/splitters-test';

package/src/tests/activity-cliffs-tests.ts

@@ -10,7 +10,7 @@ import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule
 import {BitArrayMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
@@ -32,8 +32,7 @@ category('activityCliffs', async () => {
     userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests();
   });
 
   after(async () => {

package/src/tests/detectors-custom-notation-tests.ts

@@ -0,0 +1,37 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {category, test} from '@datagrok-libraries/utils/src/test';
+import {ALIGNMENT, ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+
+import {_testNeg, _testPos, DetectorTestData, DfReaderFunc, PosCol} from './utils/detectors-utils';
+
+category('detectors: custom', () => {
+  const tests: DetectorTestData = {
+    'cyclized1': {
+      csv: `n,seq
+1,R-F-C(1)-T-G-H-F-Y-G-H-F-Y-G-H-F-Y-P-C(1)-meI
+2,C(1)-T-G-H-F-Y-P-C(1)-meI
+3,R-F-C(1)-T-G-H-F-Y-P-C(1)
+4,C(1)-T-G-H-F-H-P-C(1)
+5,R-F-D(2)-T-G-H-F-Y-P-NH2(2)
+6,R-F-aG(3)-T-G-H-F-Y-P-azG(3)-meI`,
+      pos: {'seq': new PosCol(NOTATION.CUSTOM, ALIGNMENT.SEQ, ALPHABET.UN, 13, true, '-')}
+    },
+  };
+
+  for (const [testName, testData] of Object.entries(tests)) {
+    test(`${testName}`, async () => {
+      const reader: DfReaderFunc = async (): Promise<DG.DataFrame> => {
+        return DG.DataFrame.fromCsv(testData.csv);
+      };
+      for (const negColName of testData.neg ?? [])
+        await _testNeg(reader, negColName);
+      for (const [posColName, posCol] of Object.entries(testData.pos ?? {})) {
+        await _testPos(reader, posColName, posCol.units, posCol.aligned,
+          posCol.alphabet, posCol.alphabetSize, posCol.alphabetIsMultichar, posCol.separator);
+      }
+    });
+  }
+});

package/src/tests/detectors-tests.ts

@@ -4,10 +4,12 @@ import * as DG from 'datagrok-api/dg';
 
 import {category, test, expect} from '@datagrok-libraries/utils/src/test';
 
-import {importFasta} from '../package';
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
+import {_testNeg, _testPos, DetectorTestData, DfReaderFunc, PosCol} from './utils/detectors-utils';
+import {importFasta} from '../package';
+
 /*
 // snippet to list df columns of semType='Macromolecule' (false positive)
 const df = grok.shell.tableByName('SPGI');
@@ -19,20 +21,6 @@ for (let i = 0; i < df.columns.length; i++) {
 }
  */
 
-type DfReaderFunc = () => Promise<DG.DataFrame>;
-
-
-class PosCol {
-  constructor(
-    public readonly units: string,
-    public readonly aligned: string | null,
-    public readonly alphabet: string | null,
-    public readonly alphabetSize: number,
-    public readonly alphabetIsMultichar?: boolean,
-    public readonly separator?: string,
-  ) { };
-}
-
 category('detectors', () => {
   const enum csvTests {
     fastaDna1 = 'csvFastaDna1',
@@ -57,7 +45,7 @@ category('detectors', () => {
     helmSameLength = 'helmSameLength',
   }
 
-  const csvData2: { [testName: string]: { csv: string, neg?: string[], pos?: { [colName: string]: PosCol } } } = {
+  const csvData2: DetectorTestData = {
     'negEmpty': {
       csv: `id,col1
 1,
@@ -166,6 +154,12 @@ PEPTIDE1{Ab(1).Y.V.K.H.P.F.W.R.W.Y.A.A.A.C(1).G.NH2}$$$$
 PEPTIDE1{Ad(1).S.W.Y.C.K.H.P.M.W.A.A.A.A.C(1)-G-NH2}$$$$`,
       pos: {'seq': new PosCol(NOTATION.HELM, null, null, 19, undefined, undefined)}
     },
+    'fastaNonDigitAlphabet': {
+      csv: `flagC
+"NMe-pyridazineH"
+"Pyrrolo[2,3-c]pyridazineH"`,
+      neg: ['flagC']
+    }
   };
 
   const readCsv2: (key: keyof typeof csvData2) => DfReaderFunc = (key: keyof typeof csvData2) => {
@@ -517,20 +511,6 @@ export async function _testNegList(list: string[]): Promise<void> {
   }
 }
 
-export async function _testNeg(readDf: DfReaderFunc, colName: string) {
-  const df: DG.DataFrame = await readDf();
-  const col: DG.Column = df.getCol(colName)!;
-  const semType: string = await grok.functions
-    .call('Bio:detectMacromolecule', {col: col}) as unknown as string;
-  if (semType)
-    col.semType = semType;
-
-  if (col.semType === DG.SEMTYPE.MACROMOLECULE) {
-    const msg = `Negative test detected semType='${col.semType}', units='${col.meta.units}'.`;
-    throw new Error(msg);
-  }
-}
-
 export async function _testPosList(list: string[], units: NOTATION,
   aligned: ALIGNMENT, alphabet: ALPHABET, alphabetSize: number, alphabetIsMultichar: boolean,
   separator: string | null = null
@@ -556,35 +536,6 @@ export async function _testPosList(list: string[], units: NOTATION,
   }
 }
 
-export async function _testPos(
-  readDf: DfReaderFunc, colName: string, units: string, aligned: string | null,
-  alphabet: string | null, alphabetSize: number, alphabetIsMultichar?: boolean,
-  separator: string | null = null,
-) {
-  const df: DG.DataFrame = await readDf();
-  const col: DG.Column = df.col(colName)!;
-  const semType: string = await grok.functions
-    .call('Bio:detectMacromolecule', {col: col}) as unknown as string;
-  if (semType)
-    col.semType = semType;
-
-  expect(col.semType, DG.SEMTYPE.MACROMOLECULE);
-  expect(col.meta.units, units);
-  expect(col.getTag(bioTAGS.aligned), aligned);
-  expect(col.getTag(bioTAGS.alphabet), alphabet);
-  if (separator)
-    expect(col.getTag(bioTAGS.separator), separator);
-
-  const sh = SeqHandler.forColumn(col);
-  expect(sh.getAlphabetSize(), alphabetSize);
-  expect(sh.getAlphabetIsMultichar(), alphabetIsMultichar);
-  if (!sh.isHelm()) {
-    expect(sh.aligned, aligned);
-    expect(sh.alphabet, alphabet);
-  }
-}
-
-
 export async function _testDf(readDf: DfReaderFunc, posCols: { [colName: string]: PosCol }): Promise<void> {
   const df: DG.DataFrame = await readDf();
   const errList: string[] = [];

package/src/tests/detectors-weak-and-likely-tests.ts

@@ -4,8 +4,8 @@ import * as DG from 'datagrok-api/dg';
 
 import {category, test} from '@datagrok-libraries/utils/src/test';
 import {ALIGNMENT, ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {_testNeg, _testPos} from './detectors-tests';
-import {DfReaderFunc} from './types';
+
+import {_testNeg, _testPos, DfReaderFunc} from './utils/detectors-utils';
 
 
 category('detectors:weak-and-likely', () => {

package/src/tests/monomer-libraries-tests.ts

@@ -2,12 +2,16 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import {test, after, before, category, expect} from '@datagrok-libraries/utils/src/test';
+import {test, after, before, category, expect, expectObject} from '@datagrok-libraries/utils/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {expectMonomerLib} from '@datagrok-libraries/bio/src/tests/monomer-lib-tests';
+import {MonomerTypes, PolymerTypes} from '@datagrok-libraries/bio/src/helm/consts';
+import {Monomer} from '@datagrok-libraries/bio/src/types/index';
+
+import {monomerLibForTestsSummary} from '../utils/monomer-lib/consts';
 
 
 category('monomerLibraries', () => {
@@ -35,13 +39,12 @@ category('monomerLibraries', () => {
   });
 
   test('forTests', async () => {
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true); // test defaultLib
+    await monomerLibHelper.loadMonomerLibForTests(); // test defaultLib
 
     // Currently default monomer lib set is of all files at LIB_PATH (at least HELMCoreLibrary.json)
     const currentMonomerLib = monomerLibHelper.getMonomerLib();
     // HELMCoreLibrary.json checks
-    expectMonomerLib(currentMonomerLib);
+    expectMonomerLib(currentMonomerLib, monomerLibForTestsSummary);
   });
 
   test('empty', async () => {
@@ -62,4 +65,26 @@ category('monomerLibraries', () => {
     const polymerTypes = currentMonomerLib.getPolymerTypes();
     expect(polymerTypes.length === 0, true);
   });
+
+  test('override', async () => {
+    const overMon: Monomer = {
+      symbol: 'over1',
+      name: 'Test override monomer 1',
+      molfile: '',
+      author: 'Test Author',
+      id: 0,
+      rgroups: [],
+      smiles: '',
+      polymerType: PolymerTypes.PEPTIDE,
+      monomerType: MonomerTypes.BACKBONE,
+      createDate: null,
+    };
+    const monomerLib = monomerLibHelper.getMonomerLib();
+    const absentOverrideMonomer = monomerLib.getMonomer(overMon.polymerType, overMon.symbol);
+    expect(absentOverrideMonomer === null, true, `Unexpectedly found monomer '${overMon.symbol}' `);
+
+    const overriddenMonomerLib = monomerLib.override({[overMon.polymerType]: {[overMon.symbol]: overMon}});
+    const resOverMon = overriddenMonomerLib.getMonomer(overMon.polymerType, overMon.symbol);
+    expectObject(resOverMon as any, overMon);
+  });
 });

package/src/tests/pepsea-tests.ts

@@ -63,5 +63,5 @@ category('PepSeA', () => {
       logger.error(errMsg, undefined, errStack);
     }
     expect(logger.errorList[0].message, pepseaErrorError);
-  },{skipReason: 'GROK-16699'});
+  });
 });

package/src/tests/renderers-monomer-placer-tests.ts

@@ -10,7 +10,7 @@ import {monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
@@ -24,9 +24,7 @@ category('renderers: monomerPlacer', () => {
     libHelper = await getMonomerLibHelper();
     libSettings = await getUserLibSettings();
 
-    await setUserLibSettingsForTests();
-    await libHelper.awaitLoaded();
-    await libHelper.loadMonomerLib(true);
+    await libHelper.loadMonomerLibForTests();
   });
 
   after(async () => {

package/src/tests/scoring.ts

@@ -10,7 +10,7 @@ import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monom
 
 import {getMonomerLibHelper, sequenceIdentityScoring, sequenceSimilarityScoring} from '../package';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
@@ -41,8 +41,7 @@ PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
 
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {

package/src/tests/seq-handler-get-helm-tests.ts

@@ -5,9 +5,8 @@ import * as DG from 'datagrok-api/dg';
 import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
 category('SeqHandler: getHelm', () => {
@@ -19,8 +18,7 @@ category('SeqHandler: getHelm', () => {
     userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {

package/src/tests/substructure-filters-tests.ts

@@ -8,7 +8,7 @@ import wu from 'wu';
 import {after, before, category, test, expect, delay, testEvent, awaitCheck} from '@datagrok-libraries/utils/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
@@ -36,8 +36,7 @@ category('bio-substructure-filters', async () => {
     userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
   });
 
   after(async () => {

package/src/tests/to-atomic-level-tests.ts

@@ -12,7 +12,7 @@ import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
-  getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+  getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
@@ -68,9 +68,7 @@ category('toAtomicLevel', async () => {
     monomerLibHelper = await getMonomerLibHelper();
     userLibSettings = await getUserLibSettings();
     // Clear settings to test default
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadMonomerLib(true);
+    await monomerLibHelper.loadMonomerLibForTests();
 
     monomerLib = monomerLibHelper.getMonomerLib();
 

package/src/tests/to-atomic-level-ui-tests.ts

@@ -5,7 +5,7 @@ import {after, before, category, expect, expectArray, test} from '@datagrok-libr
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {sequenceToMolfile} from '../utils/sequence-to-mol';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
@@ -31,9 +31,7 @@ category('toAtomicLevel-ui', () => {
     userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await setUserLibSettingsForTests();
-    await monomerLibHelper.awaitLoaded();
-    await monomerLibHelper.loadMonomerLib(true); // load default libraries
+    await monomerLibHelper.loadMonomerLibForTests(); // load default libraries
 
     monomerLib = monomerLibHelper.getMonomerLib();
   });
@@ -91,7 +89,7 @@ category('toAtomicLevel-ui', () => {
     test(`${testName}-nonlinear`, async () => {
       const seqCol = await getSeqCol(testData);
       await _testToAtomicLevelFunc(seqCol, true, testData.tgt);
-    }, {skipReason: 'To publish HelmHelper.removeGaps dependency'});
+    });
   }
 
   async function _testToAtomicLevelFunc(

package/src/tests/types.ts

@@ -2,6 +2,4 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-export type DfReaderFunc = () => Promise<DG.DataFrame>;
-
 export type ConverterFunc = (srcCol: DG.Column) => DG.Column;

package/src/tests/utils/detectors-utils.ts

@@ -0,0 +1,63 @@
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+
+import {ALIGNMENT, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {expect} from '@datagrok-libraries/utils/src/test';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+
+export type DetectorTestData = { [testName: string]: { csv: string, neg?: string[], pos?: { [colName: string]: PosCol } } };
+
+export type DfReaderFunc = () => Promise<DG.DataFrame>;
+
+export class PosCol {
+  constructor(
+    public readonly units: NOTATION,
+    public readonly aligned: ALIGNMENT | null,
+    public readonly alphabet: string | null,
+    public readonly alphabetSize: number,
+    public readonly alphabetIsMultichar?: boolean,
+    public readonly separator?: string,
+  ) { };
+}
+
+export async function _testNeg(readDf: DfReaderFunc, colName: string) {
+  const df: DG.DataFrame = await readDf();
+  const col: DG.Column = df.getCol(colName)!;
+  const semType: string = await grok.functions
+    .call('Bio:detectMacromolecule', {col: col}) as unknown as string;
+  if (semType)
+    col.semType = semType;
+
+  if (col.semType === DG.SEMTYPE.MACROMOLECULE) {
+    const msg = `Negative test detected semType='${col.semType}', units='${col.meta.units}'.`;
+    throw new Error(msg);
+  }
+}
+
+export async function _testPos(
+  readDf: DfReaderFunc, colName: string, units: string, aligned: string | null,
+  alphabet: string | null, alphabetSize: number, alphabetIsMultichar?: boolean,
+  separator: string | null = null,
+) {
+  const df: DG.DataFrame = await readDf();
+  const col: DG.Column = df.col(colName)!;
+  const semType: string = await grok.functions
+    .call('Bio:detectMacromolecule', {col: col}) as unknown as string;
+  if (semType)
+    col.semType = semType;
+
+  expect(col.semType, DG.SEMTYPE.MACROMOLECULE);
+  expect(col.meta.units, units);
+  expect(col.getTag(bioTAGS.aligned), aligned);
+  expect(col.getTag(bioTAGS.alphabet), alphabet);
+  if (separator)
+    expect(col.getTag(bioTAGS.separator), separator);
+
+  const sh = SeqHandler.forColumn(col);
+  expect(sh.getAlphabetSize(), alphabetSize);
+  expect(sh.getAlphabetIsMultichar(), alphabetIsMultichar);
+  if (!sh.isHelm()) {
+    expect(sh.aligned, aligned);
+    expect(sh.alphabet, alphabet);
+  }
+}

package/src/utils/monomer-lib/consts.ts

@@ -0,0 +1,18 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {MonomerLibSummaryType} from '@datagrok-libraries/bio/src/types/index';
+
+export const LIB_PATH = 'System:AppData/Bio/monomer-libraries/';
+export const SETS_PATH: string = 'System:AppData/Bio/monomer-sets/';
+
+export const HELM_JSON_SCHEMA_PATH = 'System:AppData/Bio/tests/libraries/HELMmonomerSchema.json';
+
+export const LIB_SETTINGS_FOR_TESTS: UserLibSettings =
+  {explicit: ['HELMCoreLibrary.json', 'polytool-lib.json'], exclude: [], duplicateMonomerPreferences: {}};
+
+/** Summary for settings {@link LIB_SETTINGS_FOR_TESTS} */
+export const monomerLibForTestsSummary: MonomerLibSummaryType = {'PEPTIDE': 326, 'RNA': 383, 'CHEM': 0};
+

package/src/utils/monomer-lib/lib-manager.ts

@@ -7,7 +7,7 @@ import {delay} from '@datagrok-libraries/utils/src/test';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
 import {IMonomerLib, IMonomerSet} from '@datagrok-libraries/bio/src/types';
 import {
-  getUserLibSettings, setUserLibSettings, LIB_PATH, SETS_PATH
+  getUserLibSettings, setUserLibSettings,
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 import {
@@ -18,6 +18,7 @@ import {MonomerLib} from './monomer-lib';
 import {MonomerSet} from './monomer-set';
 import {MonomerLibFileManager} from './library-file-manager/file-manager';
 import {MonomerLibFileEventManager} from './library-file-manager/event-manager';
+import {LIB_PATH, LIB_SETTINGS_FOR_TESTS, SETS_PATH} from './consts';
 
 import {_package} from '../../package';
 
@@ -267,6 +268,15 @@ export class MonomerLibManager implements IMonomerLibHelper {
     return invalidNames;
   }
 
+  // -- Settings --
+
+  /** Changes userLibSettings set only HELMCoreLibrary.json, polytool-lib.json */
+  async loadMonomerLibForTests(): Promise<void> {
+    await setUserLibSettings(LIB_SETTINGS_FOR_TESTS);
+    await this.awaitLoaded();
+    await this.loadMonomerLib(true); // load default libraries
+  }
+
   // -- Instance singleton --
   public static async getInstance(): Promise<MonomerLibManager> {
     let res = window.$monomerLibHelperPromise;

package/src/utils/monomer-lib/library-file-manager/file-manager.ts

@@ -8,7 +8,6 @@ import {JSONSchemaType} from 'ajv';
 import {MonomerType, PolymerType} from '@datagrok-libraries/bio/src/helm/types';
 import {IMonomerLib, IMonomerLinkData, IMonomerSet, Monomer} from '@datagrok-libraries/bio/src/types';
 import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
-import {LIB_PATH, SETS_PATH} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {
   HELM_REQUIRED_FIELD as REQ,
 } from '@datagrok-libraries/bio/src/utils/const';
@@ -17,10 +16,10 @@ import {
 } from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 
 import {MonomerLib} from '../monomer-lib';
-import {HELM_JSON_SCHEMA_PATH} from './consts';
 import {MonomerLibFileEventManager} from './event-manager';
 import {MonomerLibFileValidator} from './file-validator';
 import {MonomerSet, MonomerSetPlaceholder} from '../monomer-set';
+import {HELM_JSON_SCHEMA_PATH, LIB_PATH, SETS_PATH} from '../consts';
 
 import {_package} from '../../../package';