@datagrok/bio 2.27.4 → 2.27.6

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.27.4",
+  "version": "2.27.6",
   "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": "^5.64.0",
+    "@datagrok-libraries/bio": "^5.64.1",
     "@datagrok-libraries/chem-meta": "^1.2.9",
     "@datagrok-libraries/math": "^1.2.6",
     "@datagrok-libraries/ml": "^6.10.11",

package/src/tests/detectors-tests.ts

@@ -467,7 +467,7 @@ MWRSWY-CKHPMWRSWY-CKHP`;
     // collapse what used to be N distinct triple-tokens into a smaller union
     // of {sugar(s), bases, phosphate(s)} symbols.
     await _testDf(readSamples(Samples.testHelmCsv), {
-      'HELM string': new PosCol(NOTATION.HELM, null, null, 8, true),
+      'HELM string': new PosCol(NOTATION.HELM, null, null, 7, true),
     }, seqHelper);
   });
 

package/src/tests/projects-tests.ts

@@ -25,6 +25,7 @@ category('projects', () => {
 
   async function saveAndOpenProject(tv: DG.TableView, dataSync?: boolean): Promise<void> {
     const project = DG.Project.create();
+    project.name = 'Test project';
     const tableInfo = tv.dataFrame.getTableInfo();
     if (dataSync) {
       //@ts-ignore

package/src/tests/splitters-test.ts

@@ -73,8 +73,8 @@ category('splitters', async () => {
       ['P', 'R', 'U', 'P', 'R', 'T'],
     ],
     testHelm3: [
-      'RNA1{P.R(U).P.R(T)}$$$$', // invalid helm, but oh well,
-      ['P', 'R(U)', 'P', 'R', 'T'],
+      'RNA1{P.R(U).P.R(T)}$$$$',
+      ['P', 'R', 'U', 'P', 'R', 'T'],
     ],
   };
 

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

@@ -167,11 +167,11 @@ export class MonomerLibBase implements IMonomerLibBase {
 
     /** Get or create {@link Monomer} object (in case it is missing in monomer library current config) */
     let m: Monomer | null = this.getMonomer(pt, elem);
-    if (m && biotype == HelmTypes.LINKER && m[REQ.RGROUPS].length != 2) {
+    if (m && biotype == HelmTypes.LINKER && (m[REQ.RGROUPS]?.length ?? 0) < 2) {
       // Web Editor expects null
       return null;
     }
-    if (m && biotype == HelmTypes.SUGAR && m[REQ.RGROUPS].length != 3) {
+    if (m && biotype == HelmTypes.SUGAR && (m[REQ.RGROUPS]?.length ?? 0) < 3) {
       // Web Editor expects null
       return null;
     }

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

@@ -491,7 +491,7 @@ export class MonomerManager implements IMonomerManager {
     ui.tooltip.bind(deleteButton, () =>
       `${(this.tv?.dataFrame?.selection?.trueCount ?? 0) > 0 ? 'Delete selected monomers' : 'Delete monomer'}`);
 
-    const downloadButton = ui.iconFA('arrow-to-bottom', async () => {
+    const downloadAsJson = async () => {
       const libName = this.libInput.value;
       if (!libName)
         return grok.shell.error('No library selected');
@@ -508,6 +508,61 @@ export class MonomerManager implements IMonomerManager {
       if (!lib)
         return grok.shell.error(`Library ${libName} is empty`);
       DG.Utils.download(libName!, lib!, 'text/plain');
+    };
+
+    const downloadAsCsv = async () => {
+      const libName = this.libInput.value;
+      if (!libName)
+        return grok.shell.error('No library selected');
+      const df = this.tv?.dataFrame;
+      if (!df)
+        return grok.shell.error('No monomer table loaded');
+      const monomerCol = df.col(MONOMER_DF_COLUMN_NAMES.MONOMER);
+      const rgroupsCol = df.col(MONOMER_DF_COLUMN_NAMES.R_GROUPS);
+      if (!monomerCol || !rgroupsCol)
+        return grok.shell.error('Monomer or R-groups column not found');
+
+      const filtered = df.clone(df.filter);
+      const filteredMonomerCol = filtered.col(MONOMER_DF_COLUMN_NAMES.MONOMER)!;
+      const filteredRgroupsCol = filtered.col(MONOMER_DF_COLUMN_NAMES.R_GROUPS)!;
+      const cappedColName = filtered.columns.getUnusedName('Capped Molecule');
+      const cappedCol = filtered.columns.addNewString(cappedColName);
+      cappedCol.semType = DG.SEMTYPE.MOLECULE;
+
+      for (let i = 0; i < filtered.rowCount; i++) {
+        const smiles = filteredMonomerCol.get(i) as string | null;
+        if (!smiles) continue;
+        let rgroups: RGroup[] = [];
+        try {
+          const raw = filteredRgroupsCol.get(i) as string | null;
+          rgroups = raw ? JSON.parse(raw) : [];
+        } catch (_e) {
+          rgroups = [];
+        }
+        try {
+          cappedCol.set(i, capSmiles(smiles, rgroups), false);
+        } catch (e) {
+          console.error(`Error capping monomer at row ${i}`, e);
+        }
+      }
+
+      const orderedNames = filtered.columns.names();
+      const monomerIdx = orderedNames.indexOf(MONOMER_DF_COLUMN_NAMES.MONOMER);
+      if (monomerIdx >= 0) {
+        const reordered = orderedNames.filter((n) => n !== cappedColName);
+        reordered.splice(monomerIdx + 1, 0, cappedColName);
+        filtered.columns.setOrder(reordered);
+      }
+
+      const csvName = libName.toLowerCase().endsWith('.json') ? libName.replace(/\.json$/i, '.csv') : `${libName}.csv`;
+      DG.Utils.download(csvName, filtered.toCsv(), 'text/csv');
+    };
+
+    const downloadButton = ui.iconFA('arrow-to-bottom', () => {
+      DG.Menu.popup()
+        .item('JSON', () => { downloadAsJson(); })
+        .item('CSV', () => { downloadAsCsv(); })
+        .show();
     }, 'Download Monomer Library');
 
     ribbons.push([newMonomerButton, editButton, fixAllMonomersIcon, deleteButton, downloadButton]);