@datagrok/peptides 1.27.9 → 1.27.11

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.27.9",
+  "version": "1.27.11",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -13,10 +13,11 @@
     "directory": "packages/Peptides"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.63.6",
+    "@datagrok-libraries/bio": "^6.0.2",
     "@datagrok-libraries/math": "^1.2.6",
-    "@datagrok-libraries/ml": "^6.10.7",
+    "@datagrok-libraries/ml": "^6.10.15",
     "@datagrok-libraries/statistics": "^1.2.12",
+    "@datagrok-libraries/test": "^1.3.1",
     "@datagrok-libraries/tutorials": "^1.7.4",
     "@datagrok-libraries/utils": "^4.6.9",
     "@webgpu/types": "^0.1.40",
@@ -24,18 +25,16 @@
     "datagrok-api": "^1.26.0",
     "file-loader": "^6.2.0",
     "rxjs": "^6.5.5",
-    "uuid": "^10.0.0",
-    "wu": "^2.1.0",
-    "@datagrok-libraries/test": "^1.1.0"
+    "uuid": "^11.1.1",
+    "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.16",
-    "@datagrok-libraries/js-draw-lite": "^0.0.5",
     "@datagrok/bio": "^2.26.4",
     "@datagrok/chem": "^1.17.1",
     "@datagrok/dendrogram": "^1.2.33",
     "@datagrok/eda": "^1.3.1",
     "@datagrok/helm": "^2.13.0",
+    "@playwright/test": "^1.48.0",
     "@types/uuid": "^10.0.0",
     "@types/wu": "^2.1.44",
     "@typescript-eslint/eslint-plugin": "^8.8.1",
@@ -83,6 +82,8 @@
   ],
   "category": "Bioinformatics",
   "overrides": {
-    "datagrok-api": "$datagrok-api"
-  }
+    "datagrok-api": "$datagrok-api",
+    "uuid": "^11.1.1"
+  },
+  "playwrightTests": "playwright"
 }

package/src/package-api.ts

@@ -67,6 +67,13 @@ export namespace funcs {
     return await grok.functions.call('Peptides:ClusterMaxActivity', {});
   }
 
+  /**
+  Generates new candidate peptides from monomer-position statistics, ranked by predicted activity
+  */
+  export async function peptideGeneration(): Promise<any> {
+    return await grok.functions.call('Peptides:PeptideGeneration', {});
+  }
+
   export async function manualAlignment(_monomer: string ): Promise<any> {
     return await grok.functions.call('Peptides:ManualAlignment', { _monomer });
   }

package/src/package.g.ts

@@ -88,6 +88,16 @@ export function clusterMaxActivity() : any {
   return PackageFunctions.clusterMaxActivity();
 }
 
+//name: Peptide Generation
+//description: Generates new candidate peptides from monomer-position statistics, ranked by predicted activity
+//tags: viewer
+//output: viewer result
+//meta.role: viewer
+//meta.icon: files/icons/peptide-sar-vertical-viewer.svg
+export function peptideGeneration() : any {
+  return PackageFunctions.peptideGeneration();
+}
+
 //name: Manual Alignment
 //tags: widgets, panel
 //input: string _monomer { semType: Monomer }

package/src/package.ts

@@ -19,6 +19,7 @@ import {LSTPieChartRenderer} from './utils/cell-renderer';
 import {PeptideUtils} from './peptideUtils';
 import {SequencePositionStatsViewer} from './viewers/position-statistics-viewer';
 import {MutationCliffsViewer} from './viewers/mutation-cliffs-viewer';
+import {PeptideGenerationViewer} from './viewers/peptide-generation-viewer';
 
 let monomerWorks: MonomerWorks | null = null;
 let treeHelper: ITreeHelper;
@@ -240,6 +241,18 @@ export class PackageFunctions {
   }
 
 
+  @grok.decorators.func({
+    name: 'Peptide Generation',
+    description: 'Generates new candidate peptides from monomer-position statistics, ranked by predicted activity',
+    outputs: [{type: 'viewer', name: 'result'}],
+    meta: {role: 'viewer', icon: 'files/icons/peptide-sar-vertical-viewer.svg'},
+    tags: ['viewer'],
+  })
+  static peptideGeneration(): DG.Viewer {
+    return new PeptideGenerationViewer();
+  }
+
+
   @grok.decorators.panel({
     name: 'Manual Alignment',
     meta: {role: 'widgets'},

package/src/tests/viewers.ts

@@ -13,6 +13,9 @@ import {PositionHeight} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {TEST_COLUMN_NAMES} from './utils';
 import {showTooltip} from '../utils/tooltips';
 import {PeptideUtils} from '../peptideUtils';
+import {GEN_COLUMN_NAMES, PEPTIDE_GENERATION_PROPS, PEPTIDE_GENERATION_VIEWER_NAME,
+  PeptideGenerationViewer} from '../viewers/peptide-generation-viewer';
+import {ACTIVITY_TARGET} from '../utils/constants';
 
 // category('Viewers: Basic', () => {
 //   let df: DG.DataFrame;
@@ -195,3 +198,56 @@ category('Viewers: Logo Summary Table', () => {
     expect(tooltipElement !== null, true, `Tooltip is not shown for cluster '${cluster}'`);
   });
 }, {clear: false});
+
+category('Viewers: Peptide Generation', () => {
+  let df: DG.DataFrame;
+  let genViewer: PeptideGenerationViewer;
+
+  before(async () => {
+    await PeptideUtils.loadComponents();
+    df = DG.DataFrame.fromCsv(await _package.files.readAsText('tests/HELM_small.csv'));
+    const sequenceCol = df.getCol(TEST_COLUMN_NAMES.SEQUENCE);
+    sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
+    sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+    genViewer = await df.plot.fromType(PEPTIDE_GENERATION_VIEWER_NAME, {
+      [PEPTIDE_GENERATION_PROPS.SEQUENCE]: TEST_COLUMN_NAMES.SEQUENCE,
+      [PEPTIDE_GENERATION_PROPS.ACTIVITY]: TEST_COLUMN_NAMES.ACTIVITY,
+    }) as PeptideGenerationViewer;
+    await delay(500);
+  });
+
+  after(async () => await delay(1000));
+
+  test('Generates peptides', async () => {
+    const peptideCount = 10;
+    genViewer.getProperty(PEPTIDE_GENERATION_PROPS.PEPTIDE_COUNT)!.set(genViewer, peptideCount);
+    genViewer.getProperty(PEPTIDE_GENERATION_PROPS.EXCLUDE_EXISTING)!.set(genViewer, false);
+    const resultDf = genViewer.generatePeptides();
+    expect(resultDf.rowCount > 0, true, 'Peptide Generation produced no peptides');
+    expect(resultDf.rowCount <= peptideCount, true,
+      `Peptide Generation produced more than the requested ${peptideCount} peptides`);
+    for (const colName of Object.values(GEN_COLUMN_NAMES)) {
+      expect(resultDf.col(colName) !== null, true,
+        `Generated dataframe is missing the '${colName}' column`);
+    }
+    expect(resultDf.getCol(GEN_COLUMN_NAMES.PEPTIDE).semType, DG.SEMTYPE.MACROMOLECULE,
+      'Generated peptide column is not a Macromolecule');
+    // Per-position basis columns are appended after the fixed statistics columns.
+    expect(resultDf.columns.length > Object.values(GEN_COLUMN_NAMES).length, true,
+      'Generated dataframe is missing the per-position basis columns');
+  });
+
+  test('Respects High/Low target', async () => {
+    genViewer.getProperty(PEPTIDE_GENERATION_PROPS.EXCLUDE_EXISTING)!.set(genViewer, false);
+    genViewer.getProperty(PEPTIDE_GENERATION_PROPS.ACTIVITY_TARGET)!.set(genViewer, ACTIVITY_TARGET.HIGH);
+    const highDf = genViewer.generatePeptides();
+    const highMax = highDf.getCol(GEN_COLUMN_NAMES.PREDICTED).stats.max;
+
+    genViewer.getProperty(PEPTIDE_GENERATION_PROPS.ACTIVITY_TARGET)!.set(genViewer, ACTIVITY_TARGET.LOW);
+    const lowDf = genViewer.generatePeptides();
+    const lowMin = lowDf.getCol(GEN_COLUMN_NAMES.PREDICTED).stats.min;
+
+    expect(highMax >= lowMin, true,
+      'High-target peptides should reach at least as high a predicted activity as the Low-target minimum');
+  });
+});