@datagrok/bio 2.22.5 → 2.22.6

package/files/tests/to-atomic-level-pt-fasta-2.mol

@@ -1,45 +1,48 @@
 
-Datagrok macromolecule handler
+Actelion Java MolfileCreator 2.0
 
-  0  0  0  0  0  0            999 V3000
+  0  0  0  0  0  0              0 V3000
 M  V30 BEGIN CTAB
 M  V30 COUNTS 17 16 0 0 0
 M  V30 BEGIN ATOM
-M  V30 1 C 1.2991 -2.25  0.000000 0
-M  V30 2 C 1.2991 -0.75  0.000000 0
-M  V30 3 N 0 0  0.000000 0
-M  V30 4 C 2.5981 0  0.000000 0
-M  V30 5 O 3.8971 -0.75  0.000000 0
-M  V30 6 N 7.7941 9  0.000000 0
-M  V30 7 C 6.4951 8.2501  0.000000 0
-M  V30 8 N 5.196 9  0.000000 0
-M  V30 9 N 6.4951 6.7501  0.000000 0
-M  V30 10 C 5.1961 6  0.000000 0
-M  V30 11 C 5.1961 4.5  0.000000 0
-M  V30 12 C 3.8971 3.75  0.000000 0
-M  V30 13 C 3.8971 2.25  0.000000 0
-M  V30 14 N 2.5981 1.5  0.000000 0
-M  V30 15 C 5.1962 1.5  0.000000 0
-M  V30 16 O 6.4952 2.25  0.000000 0
-M  V30 17 O 5.1962 -0.0001 0.000000 0
+M  V30 1 C 1.2991 -2.25 0 0
+M  V30 2 C 1.2991 -0.75 0 0 CFG=2
+M  V30 3 N 0 0 0 0
+M  V30 4 C 2.5981 0 0 0
+M  V30 5 O 3.8971 -0.75 0 0
+M  V30 6 N 7.7941 9 0 0
+M  V30 7 C 6.4951 8.2501 0 0
+M  V30 8 N 5.196 9 0 0
+M  V30 9 N 6.4951 6.7501 0 0
+M  V30 10 C 5.1961 6 0 0
+M  V30 11 C 5.1961 4.5 0 0
+M  V30 12 C 3.8971 3.75 0 0
+M  V30 13 C 3.8971 2.25 0 0 CFG=2
+M  V30 14 N 2.5981 1.5 0 0
+M  V30 15 C 5.1962 1.5 0 0
+M  V30 16 O 6.4952 2.25 0 0
+M  V30 17 O 5.1962 -0.0001 0 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
-M  V30 1 1 2 1 CFG=3 
-M  V30 2 1 2 3 
+M  V30 1 1 2 1 CFG=3
+M  V30 2 1 2 3
 M  V30 3 1 2 4
-M  V30 4 2 4 5 
+M  V30 4 2 4 5
 M  V30 5 1 4 14
-M  V30 6 2 6 7 
-M  V30 7 1 7 8 
-M  V30 8 1 7 9 
-M  V30 9 1 9 10 
-M  V30 10 1 10 11 
-M  V30 11 1 11 12 
-M  V30 12 1 13 12 CFG=1 
-M  V30 13 1 13 14 
+M  V30 6 2 6 7
+M  V30 7 1 7 8
+M  V30 8 1 7 9
+M  V30 9 1 9 10
+M  V30 10 1 10 11
+M  V30 11 1 11 12
+M  V30 12 1 13 12 CFG=1
+M  V30 13 1 13 14
 M  V30 14 1 13 15
-M  V30 15 2 15 16 
+M  V30 15 2 15 16
 M  V30 16 1 15 17
 M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEABS ATOMS=(2 2 13)
+M  V30 END COLLECTION
 M  V30 END CTAB
 M  END

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.22.5",
+  "version": "2.22.6",
   "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",
@@ -44,7 +44,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.54.5",
+    "@datagrok-libraries/bio": "^5.54.6",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.4",
     "@datagrok-libraries/ml": "^6.10.4",
@@ -73,7 +73,7 @@
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^8.8.1",
     "@typescript-eslint/parser": "^8.8.1",
-    "datagrok-tools": "^4.14.37",
+    "datagrok-tools": "^4.14.40",
     "eslint": "^8.57.1",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-rxjs": "^5.0.3",

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

@@ -78,6 +78,7 @@ category('toAtomicLevel', async () => {
       const inputPath = testData.inPath;
 
       sourceDf[testName] = DG.DataFrame.fromCsv((await fileSource.readAsText(testData.inPath)).replace(/\n$/, ''));
+      sourceDf[testName].name = testData.inPath.split('/').pop()!;
       await grok.data.detectSemanticTypes(sourceDf[testName]);
       targetDf[testName] = DG.DataFrame.fromCsv((await fileSource.readAsText(testData.outPath)).replace(/\n$/, ''));
     }
@@ -93,6 +94,7 @@ category('toAtomicLevel', async () => {
     // await toAtomicLevel(source, inputCol, false);
     await grok.functions.call('Bio:toAtomicLevel', {table: source, seqCol: inputCol, nonlinear: false});
     const obtainedCol = source.getCol(outputColName);
+    // DG.Utils.download(source.name.endsWith('.csv') ? source.name : source.name + '.csv', source.toCsv());
     const expectedCol = target.getCol(outputColName);
     const obtainedArray: string[] = wu(obtainedCol.values()).map((mol) => polishMolfile(mol)).toArray();
     const expectedArray: string[] = wu(expectedCol.values()).map((mol) => polishMolfile(mol)).toArray();
@@ -218,6 +220,8 @@ PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.Thr_PO3H2.Aca.Tyr
     seqCol.setTag(bioTAGS.alphabet, ALPHABET.PT);
     const sh = seqHelper.getSeqHandler(seqCol);
     const resCol = (await _testToAtomicLevel(srcDf, 'seq', monomerLibHelper))!;
+    // DG.Utils.download('molfile.mol', polishMolfile(resCol.get(0)));
+
     expect(polishMolfile(resCol.get(0)), polishMolfile(tgtMol));
   });