@datagrok/bio 2.20.4 → 2.20.5

package/files/tests/libraries/HELMmonomerSchema.json

@@ -85,12 +85,10 @@
     "symbol",
     "name",
     "molfile",
-    "author",
     "id",
     "rgroups",
     "smiles",
     "polymerType",
-    "monomerType",
-    "createDate"
+    "monomerType"
   ]
 }

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.20.4",
+  "version": "2.20.5",
   "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",
@@ -65,7 +65,7 @@
     "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.13",
+    "@datagrok-libraries/helm-web-editor": "^1.1.14",
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@datagrok/chem": "^1.13.0",
     "@datagrok/dendrogram": "^1.2.33",

package/src/package.ts

@@ -543,7 +543,6 @@ export async function macromoleculePreprocessingFunction(
 }
 
 //name: Helm Fingerprints
-//tags: dim-red-preprocessing-function
 //meta.supportedSemTypes: Macromolecule
 //meta.supportedTypes: string
 //meta.supportedUnits: helm
@@ -581,7 +580,6 @@ export async function helmPreprocessingFunction(
 //input: object options {optional: true}
 //input: bool clusterEmbeddings = true { optional: true }
 //input: bool isDemo {optional: true}
-//output: viewer result
 //editor: Bio:SequenceSpaceEditor
 export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Column,
   methodName: DimReductionMethods, similarityMetric: BitArrayMetrics | MmDistanceFunctionsNames,

package/src/tests/sequence-space-utils.ts

@@ -11,6 +11,7 @@ export async function _testSequenceSpaceReturnsResult(
 ) {
   // await grok.data.detectSemanticTypes(df);
   const col: DG.Column = df.getCol(colName);
+  df.name = 'seqSpaceDf';
   const semType: string = await grok.functions.call('Bio:detectMacromolecule', {col: col});
   if (semType)
     col.semType = semType;
@@ -18,12 +19,14 @@ export async function _testSequenceSpaceReturnsResult(
   const preprocessingFunc = DG.Func.find({package: 'Bio', name: 'macromoleculePreprocessingFunction'})[0];
   if (!preprocessingFunc)
     throw new Error('Preprocessing function not found');
-  const sp = await grok.functions.call('Bio:sequenceSpaceTopMenu', {
+  await grok.functions.call('Bio:sequenceSpaceTopMenu', {
     table: df, molecules: df.col(colName)!,
     methodName: algorithm, similarityMetric: MmDistanceFunctionsNames.LEVENSHTEIN,
     plotEmbeddings: true, preprocessingFunction: preprocessingFunc, options: {[BYPASS_LARGE_DATA_WARNING]: true}
   });
   // const sp = await sequenceSpaceTopMenu(df, df.col(colName)!, algorithm, MmDistanceFunctionsNames.LEVENSHTEIN, true,
   //   preprocessingFunc, {[BYPASS_LARGE_DATA_WARNING]: true});
-  expect(sp != null, true);
+  const tv = grok.shell.tableView(df.name);
+  const sp = Array.from(tv?.viewers ?? [])[1];
+  expect(sp != null);
 }

package/src/utils/helm-to-molfile/converter/converter.ts

@@ -109,7 +109,7 @@ export class HelmToMolfileConverter implements IHelmToMolfileConverter {
   public convertToMolfileV3KColumn(helmCol: DG.Column<string>): DG.Column<string> {
     const df = helmCol.dataFrame;
     const molfileList = this.convertToMolfileV3K(helmCol.toList()).map((mwm) => mwm.molfile);
-    const molColName = getUnusedColName(df, `molfileV2K(${helmCol.name})`);
+    const molColName = getUnusedColName(df, `molfileV3K(${helmCol.name})`);
     const molfileColumn = DG.Column.fromList('string', molColName, molfileList);
     return molfileColumn;
   }

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

@@ -54,7 +54,7 @@ export class MonomerLibFileValidator {
           `Bio: Monomer Library File Validator file ${fileName}, monomer '${name}' violating JSON schema:`,
           monomer,
           '\nError reason: ',
-          this.validateMonomerSchema.errors,
+          JSON.stringify(this.validateMonomerSchema.errors ?? {}),
           `\nThere may be other errors in ${fileName} since the validation is stopped after the first error.`,
           ' Please, verify that the monomer library file satisfies the JSON schema'
         );

package/src/utils/seq-helper/seq-helper.ts

@@ -89,11 +89,16 @@ export class SeqHelper implements ISeqHelper {
     //#endregion From HelmToMolfileConverter
     const helmList = helmCol.toList();
     const molList = new Array<string>(helmCol.length);
+    // this function is paralelized and in threads, so will not block the UI. OFC, we prefer to use it.
+    // if not found, we will use the default one running in main thread...
     const beautifyMolsChemFunc = DG.Func.find({package: 'Chem', name: 'beautifyMols'})[0];
-    // both options set to false, ugly molfiles
+    // similarly, OCL Function is also paralelized and in threads, so will not block the UI.
+    const OCLFunc = DG.Func.find({package: 'Chem', name: 'convertToV3KViaOCL'})[0];
+
+    // depending on the function found, we will use it or not. if not, use internal OCL and beautification
     for (let i = 0; i < helmCol.length; i++) {
       molList[i] = (this.helmToAtomicLevelSingle(helmList[i], converter,
-        chiralityEngine, !beautifyMolsChemFunc)).molfile;
+        chiralityEngine && !OCLFunc, !beautifyMolsChemFunc)).molfile;
     }
     // need to beautify the molfiles
     if (beautifyMolsChemFunc) {
@@ -103,6 +108,15 @@ export class SeqHelper implements ISeqHelper {
           beautifiedMols[i] && (molList[i] = beautifiedMols[i]);
       }
     }
+    // handle OCL
+    if (chiralityEngine && OCLFunc) {
+      const oclMols = await OCLFunc.apply({mols: molList});
+      if (oclMols && Array.isArray(oclMols) && oclMols.length === helmCol.length) {
+        for (let i = 0; i < helmCol.length; i++)
+          oclMols[i] && (molList[i] = oclMols[i]);
+      } else
+        grok.shell.warning('OCL function returned an unexpected result');
+    }
     //const molHlList = molfilesV3K.map((item: MolfileWithMap) => getMolHighlight(item.monomers.values(), monomerLib));
 
     const molCol = DG.Column.fromStrings(molColName, molList);