@datagrok/bio 2.22.9 → 2.22.10

package/package.json

@@ -5,7 +5,7 @@
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
   },
-  "version": "2.22.9",
+  "version": "2.22.10",
   "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",

package/src/package.g.ts

@@ -19,6 +19,12 @@ export function sequenceTooltip(col: DG.Column) : any {
   return PackageFunctions.sequenceTooltip(col);
 }
 
+//input: string library 
+//output: string result
+export async function standardiseMonomerLibrary(library: string) : Promise<string> {
+  return await PackageFunctions.standardiseMonomerLibrary(library);
+}
+
 //output: object monomerLib
 export function getBioLib() : any {
   return PackageFunctions.getBioLib();

package/src/package.ts

@@ -70,7 +70,7 @@ import {GetRegionFuncEditor} from './utils/get-region-func-editor';
 import {sequenceToMolfile} from './utils/sequence-to-mol';
 import {detectMacromoleculeProbeDo} from './utils/detect-macromolecule-probe';
 import {getMolColumnFromHelm} from './utils/helm-to-molfile/utils';
-import {MonomerManager} from './utils/monomer-lib/monomer-manager/monomer-manager';
+import {MonomerManager, standardizeMonomerLibrary} from './utils/monomer-lib/monomer-manager/monomer-manager';
 import {calculateScoresWithEmptyValues} from './utils/calculate-scores';
 import {SeqHelper} from './utils/seq-helper/seq-helper';
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
@@ -98,7 +98,6 @@ function getDecoratorFunc() {
 if (!grok.decorators)
   (grok as any).decorators = {};
 
-
 const decorators = [
   'func', 'init', 'param', 'panel', 'editor', 'demo', 'app',
   'appTreeBrowser', 'fileHandler', 'fileExporter', 'model', 'viewer', 'filter', 'cellRenderer', 'autostart',
@@ -139,6 +138,11 @@ export class PackageFunctions {
     return resWidget;
   }
 
+  @grok.decorators.func({})
+  static async standardiseMonomerLibrary(library: string): Promise<string> {
+    return await standardizeMonomerLibrary(library);
+  }
+
   // Keep for backward compatibility
   @grok.decorators.func({outputs: [{type: 'object', name: 'monomerLib'}]})
   static getBioLib(): IMonomerLib {

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

@@ -49,14 +49,29 @@ export const MONOMER_DF_COLUMNS = {
   [MONOMER_DF_COLUMN_NAMES.SOURCE]: DG.COLUMN_TYPE.STRING,
 } as const;
 
-export function getMonomersDataFrame(activeMonomerLib: IMonomerLib) {
+export async function standardiseMonomers(monomers: Monomer[]) {
+  const df = getMonomersDataFrame(monomers);
+  if (monomers.length !== df.rowCount)
+    throw new Error(`Monomers length ${monomers.length} does not match dataframe row count ${df.rowCount}`);
+  const fixedMonomers = await Promise.all(new Array(monomers.length).fill(null).map(async (_, i) => monomerFromDfRow(df.rows.get(i))));
+  return fixedMonomers;
+}
+
+/** Standardizes the monomer library
+ * warning: throws error if the library is not valid or has invalid monomers
+ */
+export async function standardizeMonomerLibrary(libraryString: string) {
+  const library: Monomer[] = JSON.parse(libraryString);
+  if (!library || !Array.isArray(library) || library.length === 0)
+    throw new Error('Invalid library format, expected an array of monomers');
+  const fixedMonomers = await standardiseMonomers(library);
+  const fixedLibrary = fixedMonomers.map((m) => ({...m, lib: undefined, wem: undefined}));
+  const libraryStringFixed = JSON.stringify(fixedLibrary, null, 2);
+  return libraryStringFixed;
+}
+
+export function getMonomersDataFrame(monomers: Monomer[]) {
   try {
-    const ploymerTypes = activeMonomerLib.getPolymerTypes();
-    const monomers = ploymerTypes.flatMap((polymerType) => {
-      return activeMonomerLib!.getMonomerSymbolsByType(polymerType).map((symbol) => {
-        return activeMonomerLib!.getMonomer(polymerType, symbol)!;
-      });
-    });
     const df = DG.DataFrame.create(monomers.length);
 
     const uniqueRgroupNamesSet = new Set<string>();
@@ -437,7 +452,14 @@ export class MonomerManager implements IMonomerManager {
         grok.shell.error(`Library ${fileName} not found`);
         return DG.DataFrame.create();
       }
-      const df = getMonomersDataFrame(this.activeMonomerLib);
+
+      const ploymerTypes = this.activeMonomerLib.getPolymerTypes();
+      const monomers = ploymerTypes.flatMap((polymerType) => {
+        return this.activeMonomerLib!.getMonomerSymbolsByType(polymerType).map((symbol) => {
+          return this.activeMonomerLib!.getMonomer(polymerType, symbol)!;
+        });
+      });
+      const df = getMonomersDataFrame(monomers);
       return df;
     } catch (e) {
       grok.shell.error('Error creating monomers dataframe');