@datagrok/sequence-translator 1.7.0 → 1.8.0

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.7.0",
+  "version": "1.8.0",
   "author": {
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
@@ -22,13 +22,13 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.46.0",
+    "@datagrok-libraries/bio": "^5.50.0",
     "@datagrok-libraries/chem-meta": "^1.2.8",
     "@datagrok-libraries/tutorials": "^1.4.3",
     "@datagrok-libraries/utils": "^4.3.7",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
-    "datagrok-api": "^1.21.1",
+    "datagrok-api": "^1.24.0",
     "lodash": "^4.17.21",
     "object-hash": "^3.0.0",
     "openchemlib": "6.0.1",
@@ -42,9 +42,9 @@
     "@datagrok-libraries/helm-web-editor": "^1.1.13",
     "@datagrok-libraries/js-draw-lite": "^0.0.10",
     "@datagrok/bio": "^2.18.0",
-    "@datagrok/helm": "^2.7.0",
     "@datagrok/chem": "^1.13.0",
-    "@types/jquery": "^3.5.14",
+    "@datagrok/helm": "^2.7.0",
+    "@types/jquery": "^3.5.32",
     "@types/js-yaml": "^4.0.5",
     "@types/lodash": "^4.14.202",
     "@types/node-fetch": "^2.6.2",

package/src/polytool/pt-dialog.ts

@@ -10,7 +10,7 @@ import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {getSeqHelper, ISeqHelper, ToAtomicLevelRes} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {MmcrTemps} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
-import {addMonomerHoverLink, buildMonomerHoverLink} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
+import {addMonomerHoverLink} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
 import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 
@@ -68,10 +68,10 @@ export async function polyToolEnumerateChemUI(cell?: DG.Cell): Promise<void> {
 
 export async function polyToolConvertUI(): Promise<void> {
   await _package.initPromise;
-  let dialog: DG.Dialog;
+  let dialog: DG.Dialog | null = null;
   try {
     dialog = await getPolyToolConvertDialog();
-    dialog.show();
+    dialog?.show();
   } catch (err: any) {
     const [errMsg, errStack] = errInfo(err);
     grok.shell.warning('To run PolyTool Conversion, open a dataframe with macromolecules');
@@ -79,25 +79,38 @@ export async function polyToolConvertUI(): Promise<void> {
   }
 }
 
-export async function getPolyToolConvertDialog(srcCol?: DG.Column): Promise<DG.Dialog> {
+export async function getPolyToolConvertDialog(srcCol?: DG.Column): Promise<DG.Dialog | null> {
   const subs: Unsubscribable[] = [];
   const destroy = () => {
     for (const sub of subs) sub.unsubscribe();
   };
   try {
     let srcColVal: DG.Column<string> | undefined = srcCol;
+    const srcColList = grok.shell.t.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
+    const customSrcCols = srcColList.filter((col) => {
+      const sh = _package.seqHelper.getSeqHandler(col);
+      return sh.notation === NOTATION.CUSTOM;
+    });
     if (!srcColVal) {
-      const srcColList = grok.shell.t.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
       if (srcColList.length < 1)
         throw new Error(PT_ERROR_DATAFRAME);
+      
+      if (customSrcCols.length < 1) {
+        const toAtomicLevelFunc = DG.Func.find({package: 'Bio', name: 'toAtomicLevel'})[0];
+        if (toAtomicLevelFunc) {
+          toAtomicLevelFunc.prepare().edit();
+          return null;
+        }
+        grok.shell.warning('Polytool requires a macromolecule column with custom notation. \n\nUse Top menu | Bio | Transform | To Atomic Level.');
+        return null;
+      }
+
       srcColVal = srcColList[0];
     }
     const srcColInput = ui.input.column('Column', {
       table: srcColVal.dataFrame, value: srcColVal,
       filter: (col: DG.Column) => {
-        if (col.semType !== DG.SEMTYPE.MACROMOLECULE) return false;
-        const sh = _package.seqHelper.getSeqHandler(col);
-        return sh.notation === NOTATION.CUSTOM;
+        return customSrcCols.includes(col);
       }
     });
 
@@ -353,6 +366,8 @@ function buildCyclizedMonomerHoverLink(
   const resLink: MonomerHoverLink = {
     targetCol: molCol,
     handler: (seqGridCell: DG.GridCell, cyclizedMonomer: ISeqMonomer | null, targetGridCol: DG.GridColumn): boolean => {
+      if (!seqGridCell || !targetGridCol.grid || !seqCol.dataFrame)
+        return true;
       const grid = targetGridCol.grid;
       const tableRowIdx = seqGridCell.tableRowIndex!;
       const gridRowIdx = seqGridCell.gridRow;
@@ -360,13 +375,13 @@ function buildCyclizedMonomerHoverLink(
       const positionMap = positionMaps[gridRowIdx];
 
       const prev = getMonomerHover();
-      if (!prev || (prev && (prev.dataFrameId != seqCol.dataFrame.id || prev.gridRowIdx != gridRowIdx ||
+      if (!prev || (prev && (prev.dataFrameId != seqCol.dataFrame?.id || prev.gridRowIdx != gridRowIdx ||
         prev.seqColName != seqCol.name || prev.seqPosition != cyclizedMonomer?.position))
       ) {
         if (prev) {
           setMonomerHover(null);
-          prev.gridCell.grid?.invalidate();
-          // prev.gridCell.render();
+          //prev.gridCell.grid?.invalidate();
+          prev.gridCell.render();
         }
         if (!cyclizedMonomer) {
           setMonomerHover(null);
@@ -389,7 +404,6 @@ function buildCyclizedMonomerHoverLink(
 
             const resSubstructList: ISubstruct[] = [];
             const seqMonomerList: number[] = positionMap[cyclizedMonomer.position];
-            console.log(seqMonomerList);
             for (const seqMonomer of seqMonomerList) {
               const monomerMap = molMonomerMap.get(seqMonomer); // single monomer
               if (!monomerMap) return {atoms: [], bonds: [], highlightAtomColors: [], highlightBondColors: []};
@@ -402,8 +416,8 @@ function buildCyclizedMonomerHoverLink(
         });
 
         // TODO: Invalidate targetGridCell
-        grid.invalidate();
-        // targetGridCell.render();
+        //grid.invalidate();
+        targetGridCell.render();
       }
 
       return true;

package/src/polytool/pt-enumerate-seq-dialog.ts

@@ -167,6 +167,9 @@ async function getPolyToolEnumerateDialog(
         resDataRole = (resSeqValue.tags[PolyToolTags.dataRole] as PolyToolDataRole.template) ?? PolyToolDataRole.macromolecule;
       } else {
         const seqCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'seq', [PT_HELM_EXAMPLE]);
+        seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
+        const _tempDf = DG.DataFrame.fromColumns([seqCol]);
+        
         seqCol.meta.units = NOTATION.HELM;
         const sh = seqHelper.getSeqHandler(seqCol);
         resSeqValue = sh.getValue(0);
@@ -184,7 +187,7 @@ async function getPolyToolEnumerateDialog(
     const warningsTextDiv = ui.divText('', {style: {color: 'red'}});
     // #### Inputs
     inputs = {
-      macromolecule: helmHelper.createHelmInput(
+      macromolecule: helmHelper.createHelmInput(                                                     
         'Macromolecule', {
           editable: false,
           editorOptions: {
@@ -192,9 +195,20 @@ async function getPolyToolEnumerateDialog(
               monomerNumbering: MonomerNumberingTypes.continuous,
               getMonomer: (a: HelmAtom | HelmType, name?: string): GetMonomerResType => {
                 const aa: HelmAtom = a as HelmAtom;
+
+
                 if (aa.T === 'ATOM') {
-                  const canonicalSymbol = seqValue.getSplitted().getCanonical(aa.bio!.continuousId - 1);
-                  return monomerLibFuncs.getMonomer(aa.bio!.type, canonicalSymbol);
+                  try {
+                    if (!seqValue.isDna() && !seqValue.isRna()) {
+                      const canonicalSymbol = seqValue.getSplitted().getCanonical(aa.bio!.continuousId - 1);
+                      return monomerLibFuncs.getMonomer(aa.bio!.type, canonicalSymbol);
+                    } else {
+                      const canonicalSymbol = seqValue.getSplittedWithSugarsAndPhosphates().getCanonical(aa.bio!.continuousId - 1);
+                      return monomerLibFuncs.getMonomer(aa.bio!.type, canonicalSymbol);
+                    }
+                  } catch (_) {
+                    return monomerLibFuncs.getMonomer(a, name);
+                  }
                 } else { return monomerLibFuncs.getMonomer(a, name); }
               },
             },
@@ -727,7 +741,7 @@ async function polyToolEnumerateSeq(
           toAtomicLevel.chiralityEngine, toAtomicLevel.highlightMonomers);
         enumeratorResDf.columns.add(talRes.molCol!, false);
         const resMolCol = talRes.molCol!;
-        buildMonomerHoverLink(resHelmCol, resMolCol, monomerLib, helmHelper.seqHelper, rdKitModule);
+        await buildMonomerHoverLink(resHelmCol, resMolCol, monomerLib, helmHelper.seqHelper, rdKitModule, true);
       } else if (dataRole === PolyToolDataRole.template) {
         const talRes = await polyToolConvert(enumCol,
           toAtomicLevel.generateHelm, false, toAtomicLevel.chiralityEngine, false, toAtomicLevel.rules);