@datagrok/bio 2.18.1 → 2.18.3

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.18.1",
+  "version": "2.18.3",
   "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": "^5.47.1",
+    "@datagrok-libraries/bio": "^5.48.1",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.4",
     "@datagrok-libraries/ml": "^6.7.6",

package/src/tests/renderers-test.ts

@@ -65,7 +65,7 @@ category('renderers', () => {
 
   test('scatterPlotTooltip', async () => {
     await _testScatterPlotTooltip();
-  });
+  }, {skipReason: 'GROK-17450'});
 
   async function _rendererMacromoleculeFasta() {
     const csv: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/FASTA.csv');

package/src/utils/monomer-cell-renderer.ts

@@ -15,8 +15,6 @@ const Tags = new class {
   tooltipHandlerTemp = 'tooltip-handler.Monomer';
 }();
 
-const svgMolOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
-
 export class MonomerCellRendererBack extends CellRendererWithMonomerLibBackBase {
   constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column) {
     super(gridCol, tableCol);

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

@@ -25,6 +25,12 @@ const monomerRe = /[\w()]+/;
 //** Do not mess with monomer symbol with parenthesis enclosed in square brackets */
 const ambMonomerRe = RegExp(String.raw`\(${monomerRe}(,${monomerRe})+\)`);
 
+const drawMoleculeCall = (s: string) => {
+  const canvas = ui.canvas(250, 250);
+  grok.chem.canvasMol(0, 0, 250, 250, canvas, s);
+  return canvas;
+};
+
 export type MonomerLibDataType = { [polymerType: string]: { [monomerSymbol: string]: Monomer } };
 
 const whiteColorV = new Vector([255.0, 255.0, 255.0]);
@@ -189,10 +195,10 @@ export class MonomerLibBase implements IMonomerLibBase {
       const chemOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
       let structureEl: HTMLElement;
       if (monomer.molfile)
-        structureEl = grok.chem.svgMol(monomer.molfile, undefined, undefined, chemOptions);
+        structureEl = drawMoleculeCall(monomer.molfile);
       else if (monomer.smiles) {
         structureEl = ui.divV([
-          grok.chem.svgMol(monomer.smiles, undefined, undefined, chemOptions),
+          drawMoleculeCall(monomer.smiles),
           ui.divText('from smiles', {style: {fontSize: 'smaller'}}),
         ]);
       } else {
@@ -271,13 +277,12 @@ export class MonomerLibBase implements IMonomerLibBase {
       }
 
       const naSymbol: string | undefined = monomer[OPT.NATURAL_ANALOG];
-      if (!res && naSymbol) {
+      if (!res && naSymbol)
         return this.getMonomerColors(biotype, naSymbol);
-      }
     }
 
     if (!res)
-      res = {textColor: "#202020", lineColor: "#202020", backgroundColor: "#A0A0A0"};
+      res = {textColor: '#202020', lineColor: '#202020', backgroundColor: '#A0A0A0'};
 
     return {
       textcolor: res.text ?? res.textColor,

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

@@ -97,6 +97,8 @@ export class DuplicateMonomerManager {
       DuplicateMonomerManager._instance = new DuplicateMonomerManager();
       await DuplicateMonomerManager._instance.refresh();
       const libManager = await MonomerLibManager.getInstance();
+      // reason: subscription happens only once, and is needed throught the lifetime of the app
+      // eslint-disable-next-line rxjs/no-async-subscribe, rxjs/no-ignored-subscription
       libManager.getMonomerLib().onChanged.subscribe(async () => await DuplicateMonomerManager._instance.refresh());
     }
     DuplicateMonomerManager._instance.refresh();

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

@@ -1087,12 +1087,24 @@ function monomerFromDfRow(dfRow: DG.Row): Monomer {
     if (typeof metaJSON[key] === 'object')
       metaJSON[key] = JSON.stringify(metaJSON[key]);
   }
+  const smiles = dfRow.get(MONOMER_DF_COLUMN_NAMES.MONOMER);
+  if (!smiles)
+    throw new Error('Monomer SMILES is empty');
+  let molfile = '';
+
+  try {
+    molfile = grok.chem.convert(smiles, DG.chem.Notation.Smiles, DG.chem.Notation.MolBlock);
+    molfile = getCorrectedMolBlock(molfile);
+  } catch (e) {
+    grok.shell.error(`Error converting SMILES to molfile, \n ${smiles}`);
+    console.error(e);
+  }
 
   return {
     symbol: dfRow.get(MONOMER_DF_COLUMN_NAMES.SYMBOL),
     name: dfRow.get(MONOMER_DF_COLUMN_NAMES.NAME),
-    molfile: '',
-    smiles: dfRow.get(MONOMER_DF_COLUMN_NAMES.MONOMER),
+    molfile: molfile,
+    smiles: smiles,
     polymerType: dfRow.get(MONOMER_DF_COLUMN_NAMES.POLYMER_TYPE),
     monomerType: dfRow.get(MONOMER_DF_COLUMN_NAMES.MONOMER_TYPE),
     naturalAnalog: dfRow.get(MONOMER_DF_COLUMN_NAMES.NATURAL_ANALOG),