@datagrok/bio 2.11.35 → 2.11.37

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.35",
+  "version": "2.11.37",
   "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/analysis/sequence-diversity-viewer.ts

@@ -40,7 +40,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
         this.tags.forEach((tag) => resCol.setTag(tag, this.moleculeColumn!.getTag(tag)));
         const resDf = DG.DataFrame.fromColumns([resCol]);
         resDf.onCurrentRowChanged.subscribe(
-          (_) => { this.dataFrame.currentRowIdx = this.renderMolIds![resDf.currentRowIdx]; });
+          (_: any) => { this.dataFrame.currentRowIdx = this.renderMolIds![resDf.currentRowIdx]; });
         updateDivInnerHTML(this.root, resDf.plot.grid().root);
         this.computeCompleted.next(true);
       }
@@ -61,7 +61,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
 
   private async computeByMM() {
     const encodedSequences =
-        (await getEncodedSeqSpaceCol(this.moleculeColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;
+      (await getEncodedSeqSpaceCol(this.moleculeColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;
     const distanceMatrixService = new DistanceMatrixService(true, false);
     const distanceMatrixData = await distanceMatrixService.calc(encodedSequences, MmDistanceFunctionsNames.LEVENSHTEIN);
     distanceMatrixService.terminate();

package/src/analysis/sequence-similarity-viewer.ts

@@ -60,7 +60,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
         this.molCol.semType = DG.SEMTYPE.MACROMOLECULE;
         this.tags.forEach((tag) => this.molCol!.setTag(tag, this.moleculeColumn!.getTag(tag)));
         const resDf = DG.DataFrame.fromColumns([this.idxs!, this.molCol!, this.scores!]);
-        resDf.onCurrentRowChanged.subscribe((_) => {
+        resDf.onCurrentRowChanged.subscribe((_: any) => {
           this.dataFrame.currentRowIdx = resDf.col('indexes')!.get(resDf.currentRowIdx);
           setTimeout(() => { this.createPropertyPanel(resDf); }, 1000);
           this.gridSelect = true;

package/src/tests/msa-tests.ts

@@ -81,12 +81,12 @@ MWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHP
   test('isCorrectHelm', async () => {
     await awaitContainerStart();
     await _testMSAOnColumn(helmFromCsv, helmToCsv, NOTATION.HELM, NOTATION.SEPARATOR, undefined, 'mafft');
-  }, {timeout: 60000});
+  }, {timeout: 60000 /* docker */});
 
   test('isCorrectHelmLong', async () => {
     await awaitContainerStart();
     await _testMSAOnColumn(longHelmFromCsv, longHelmToCsv, NOTATION.HELM, NOTATION.SEPARATOR, undefined, 'mafft');
-  }, {timeout: 60000});
+  }, {timeout: 60000 /* docker */});
 
   test('isCorrectSeparator', async () => {
     await _testMSAOnColumn(

package/src/tests/pepsea-tests.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
 import {runPepsea} from '../utils/pepsea';
 import {awaitContainerStart} from './utils';
 
@@ -12,13 +12,16 @@ category('PepSeA', () => {
   "PEPTIDE1{F.L.R.G.Y.[MeF].Y.W.S.N.D.C}$$$$","F.L.R.G.Y.MeF.Y.W.S.N.D.C"
   "PEPTIDE1{F.V.R.G.Y.[MeF].Y.W.S.N.C}$$$$","F.V.R.G.Y.MeF.Y.W.S..N.C"`;
 
-  test('Basic alignment', async () => {
+  before(async () => {
     await awaitContainerStart();
+  });
+
+  test('Basic alignment', async () => {
     const table = DG.DataFrame.fromCsv(testCsv);
     const alignedCol = await runPepsea(table.getCol('HELM'), 'msa(HELM)');
     expect(alignedCol !== null, true, 'PepSeA container has not started');
     const alignedTestCol = table.getCol('MSA');
     for (let i = 0; i < alignedCol!.length; ++i)
       expect(alignedCol!.get(i) == alignedTestCol.get(i), true);
-  }, {timeout: 60000});
+  }, {timeout: 60000 /* docker */});
 });

package/src/tests/similarity-diversity-tests.ts

@@ -28,7 +28,7 @@ async function _testSimilaritySearchViewer() {
   const viewer: SequenceSimilarityViewer = (await moleculesView.dataFrame.plot
     .fromType('Sequence Similarity Search')) as SequenceSimilarityViewer;
   let computeCompleted: boolean = false;
-  viewer.computeCompleted.subscribe((value) => {
+  viewer.computeCompleted.subscribe((value: any) => {
     if (value) computeCompleted = true;
   });
   moleculesView.dockManager.dock(viewer, DG.DOCK_TYPE.RIGHT, null, 'Similarity');
@@ -78,7 +78,7 @@ async function _testDiversitySearchViewer() {
   const viewer: SequenceDiversityViewer = (await moleculesView.dataFrame.plot
     .fromType('Sequence Diversity Search')) as SequenceDiversityViewer;
   let computeCompleted: boolean = false;
-  viewer.computeCompleted.subscribe((value) => {
+  viewer.computeCompleted.subscribe((value: boolean) => {
     if (value) computeCompleted = true;
   });
   moleculesView.dockManager.dock(viewer, DG.DOCK_TYPE.DOWN, null, 'Diversity');

package/src/utils/convert.ts

@@ -102,7 +102,7 @@ export function convert(col?: DG.Column): void {
       })
       .show({x: 350, y: 100});
 
-    convertDialogSubs.push(convertDialog.onClose.subscribe((_value) => {
+    convertDialogSubs.push(convertDialog.onClose.subscribe((_: any) => {
       convertDialogSubs.forEach((s) => { s.unsubscribe(); });
       convertDialogSubs = [];
       convertDialog = null;

package/src/utils/helm-to-molfile.ts

@@ -106,7 +106,9 @@ export class HelmToMolfileConverter {
     return DG.Column.fromStrings(columnName, beautifiedMols.map((mol) => {
       if (mol === null)
         return '';
-      return mol.get_molblock();
+      const molBlock = mol.get_v3Kmolblock();
+      mol!.delete();
+      return molBlock;
     }));
   }
 

package/src/utils/poly-tool/transformation.ts

@@ -9,6 +9,8 @@ import {HELM_WRAPPER} from './const';
 import {getMolColumnFromHelm} from '../helm-to-molfile';
 import {ALIGNMENT, ALPHABET} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
+const RULE_PATH = 'System:AppData/Bio/polytool-rules/';
+
 type ConnectionData = {
   allPos1: number[],
   allPos2: number[],
@@ -17,6 +19,7 @@ type ConnectionData = {
 }
 
 type Rule = {
+  code: number,
   firstMonomer: string,
   secondMonomer: string,
   firstModification: string,
@@ -48,27 +51,58 @@ class TransformationCommon {
     return isLinkable;
   }
 
-  protected getLinkedPositions(helm: string, ruleCount: number): [number, number][] {
+  protected getLinkedPositions(helm: string, rules: Rule[]): [number, number][] {
     const seq = helm.replace(HELM_WRAPPER.LEFT, '').replace(HELM_WRAPPER.RIGHT, '');
-    const monomers = seq.split('.');
-    const result:[number, number][] = new Array<[number, number]>(ruleCount);
+    const monomers = seq.split('.').map((m) => { return m.replace('[', '').replace(']', ''); });
+    const result:[number, number][] = new Array<[number, number]>(rules.length);
 
-    for (let i = 0; i < ruleCount; i++) {
+    for (let i = 0; i < rules.length; i++) {
       let firstFound = false;
+      let secondFound = false;
+      let firstIsFirst = false;
+      let firstEntryIndex = -1;
+      let secondEntryIndex = -1;
+      const add = `(${rules[i].code})`;
       for (let j = 0; j < monomers.length; j++) {
-        if (monomers[j].includes(`(${i + 1})`)) {
+        if (monomers[j].includes(add)) {
           if (firstFound) {
-            result[i][1] = j;
-            break;
+            if (firstIsFirst && monomers[j] == rules[i].secondMonomer + add) {
+              secondFound = true;
+              secondEntryIndex = j;
+              break;
+            } else if (!firstIsFirst && monomers[j] == rules[i].firstMonomer + add) {
+              secondFound = true;
+              secondEntryIndex = j;
+              break;
+            } else {
+              continue;
+            }
+            //result[i][1] = j;
+            // secondFound = true;
+            // break;
           } else {
-            firstFound = true;
-            result[i] = [j, 0];
+            if (monomers[j] == rules[i].firstMonomer + add) {
+              firstFound = true;
+              firstIsFirst = true;
+              firstEntryIndex = j;
+            } else if (monomers[j] == rules[i].secondMonomer + add) {
+              firstFound = true;
+              firstIsFirst = false;
+              firstEntryIndex = j;
+            } else {
+              continue;
+            }
+            //result[i] = [j, 0];
           }
         }
       }
 
-      if (!firstFound)
+      if (!(firstFound && secondFound))
         result[i] = [-1, -1];
+      else if (firstIsFirst)
+        result[i] = [firstEntryIndex, secondEntryIndex];
+      else
+        result[i] = [secondEntryIndex, firstEntryIndex];
     }
 
 
@@ -88,6 +122,7 @@ class TransformationCommon {
 
     for (let i = 0; i < ruleCount; i++) {
       rules[i] = {
+        code: codeCol.get(i),
         firstMonomer: monomer1Col.get(i),
         secondMonomer: monomer2Col.get(i),
         firstModification: modification1Col.get(i),
@@ -102,7 +137,7 @@ class TransformationCommon {
 
   protected getTransformedHelm(helm: string, rules: Rule[]): string {
     const ruleCount = rules.length;
-    const positions = this.getLinkedPositions(helm, ruleCount);
+    const positions = this.getLinkedPositions(helm, rules);
 
     const allPos1: number [] = [];
     const allPos2: number [] = [];
@@ -113,31 +148,19 @@ class TransformationCommon {
       if (positions[i][0] == -1)
         continue;
 
-      helm = helm.replaceAll(`(${i + 1})`, '');
+      //helm = helm.replaceAll(`(${i + 1})`, '');
       const seq = helm.replace(HELM_WRAPPER.LEFT, '').replace(HELM_WRAPPER.RIGHT, '');
       const monomers = seq.split('.');
       const firstMonomer = monomers[positions[i][0]].replace('[', '').replace(']', '');
       const secondMonomer = monomers[positions[i][1]].replace('[', '').replace(']', '');
-      let attach1 = 0;
-      let attach2 = 0;
-      if (firstMonomer === rules[i].firstMonomer && secondMonomer === rules[i].secondMonomer) {
-        monomers[positions[i][0]] = monomers[positions[i][0]].replace(firstMonomer, rules[i].firstModification);
-        monomers[positions[i][1]] = monomers[positions[i][1]].replace(secondMonomer, rules[i].secondModification);
-        attach1 = rules[i].firstR;
-        attach2 = rules[i].secondR;
-      } else if (secondMonomer === rules[i].firstModification && firstMonomer === rules[i].secondModification) {
-        monomers[positions[i][0]] = monomers[positions[i][1]].replace(secondMonomer, rules[i].secondModification);
-        monomers[positions[i][1]] = rules[i].firstModification.replace(firstMonomer, rules[i].firstModification);
-        attach1 = rules[i].secondR;
-        attach2 = rules[i].firstR;
-      } else {
-        continue;
-      }
+
+      monomers[positions[i][0]] = monomers[positions[i][0]].replace(firstMonomer, rules[i].firstModification);
+      monomers[positions[i][1]] = monomers[positions[i][1]].replace(secondMonomer, rules[i].secondModification);
 
       allPos1.push(positions[i][0] + 1);
       allPos2.push(positions[i][1] + 1);
-      allAttaches1.push(attach1);
-      allAttaches2.push(attach2);
+      allAttaches1.push(rules[i].firstR);
+      allAttaches2.push(rules[i].secondR);
 
       helm = HELM_WRAPPER.LEFT;
       for (let i = 0; i < monomers.length; i ++) {
@@ -203,12 +226,15 @@ function getHelmCycle(helm: string, source: ConnectionData): string {
 }
 
 export async function addTransformedColumn(
-  molColumn: DG.Column<string>, rulesTable: DG.DataFrame, addHelm: boolean
+  molColumn: DG.Column<string>, addHelm: boolean
 ): Promise<void> {
   const df = molColumn.dataFrame;
   const uh = UnitsHandler.getOrCreate(molColumn);
   const sourceHelmCol = uh.convert(NOTATION.HELM);
   const pt = PolymerTransformation.getInstance(sourceHelmCol);
+  const fileSource = new DG.FileSource(RULE_PATH);
+  const rulesRaw = await fileSource.readAsText('rules.csv');
+  const rulesTable = DG.DataFrame.fromCsv(rulesRaw);
   const targetList = pt.transform(rulesTable);
   const helmColName = df.columns.getUnusedName('transformed(' + molColumn.name + ')');
   const targetHelmCol = DG.Column.fromList('string', helmColName, targetList);

package/src/utils/poly-tool/ui.ts

@@ -10,6 +10,8 @@ import {addTransformedColumn} from './transformation';
 import * as rxjs from 'rxjs';
 //import {MetaData} from './types';
 
+const RULE_PATH = 'System:AppData/Bio/polytool-rules/';
+
 export function getPolyToolDialog(): DG.Dialog {
   //const monomerLib = MonomerLibManager.instance.getBioLib();
   const targetColumns = grok.shell.t.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
@@ -24,41 +26,19 @@ export function getPolyToolDialog(): DG.Dialog {
   const generateHelmChoiceInput = ui.boolInput('Get HELM', true);
   ui.tooltip.bind(generateHelmChoiceInput.root, 'Add HELM column');
 
-  let rulesTable: DG.DataFrame = DG.DataFrame.create();
+  // let rulesTable: DG.DataFrame = DG.DataFrame.create();
 
   const ruleFileInput = ui.button('ADD RULES', () => {
     DG.Utils.openFile({
       accept: '.csv',
       open: async (selectedFile) => {
         const content = await selectedFile.text();
-        rulesTable = DG.DataFrame.fromCsv(content);
+        // rulesTable = DG.DataFrame.fromCsv(content);
+        await grok.dapi.files.writeAsText(RULE_PATH + `${selectedFile.name}`, content);
         //console.log(df.toCsv());
       },
     });
   });
-  // dialog.addButton(
-  //   'Add',
-  //   () => eventManager.addLibraryFile(),
-  //   undefined,
-  //   'Upload new HELM monomer library'
-  // );
-
-
-  // const ruleFileInput = DG.Utils.openFile({
-  //   accept: '.csv',
-  //   open: async (selectedFile) => {
-  //     const content = await selectedFile.text();
-  //     const name = selectedFile.name;
-  //     const df = DG.DataFrame.fromCsv(content);
-
-  //     console.log(df.toCsv());
-  //   },
-  // });
-
-  //grok.data.files.openTable('Samples:Files/chem/smiles_10K_with_activities.csv')
-  // const file = await loadFileAsText(tableName);
-  // const df = DG.DataFrame.fromCsv(file);
-  // df.name = tableName.replace('.csv', '');
 
   const div = ui.div([
     targetColumnInput,
@@ -74,7 +54,7 @@ export function getPolyToolDialog(): DG.Dialog {
         grok.shell.warning('No marcomolecule column chosen!');
         return;
       }
-      addTransformedColumn(molCol!, rulesTable!, generateHelmChoiceInput.value!);
+      addTransformedColumn(molCol!, generateHelmChoiceInput.value!);
     }
     );
 

package/src/widgets/bio-substructure-filter-helm.ts

@@ -87,7 +87,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
         //   webEditor = undefined;
         // });
       }));
-      this.viewSubs.push(ui.onSizeChanged(this._filterPanel).subscribe((_) => {
+      this.viewSubs.push(ui.onSizeChanged(this._filterPanel).subscribe((_: any) => {
         try {
           if (!!webEditorApp) {
             const helmString = webEditorApp.canvas.getHelm(true)
@@ -110,7 +110,7 @@ export class HelmBioFilter extends BioFilterBase<BioFilterProps> /* implements I
 
   applyProps() {
     if (!this.helmEditor) return; // helmEditor is not created, the filter is not in dom yet
-      this.updateFilterPanel(this.props.substructure);
+    this.updateFilterPanel(this.props.substructure);
   }
 
   get filterPanel() {

package/webpack.config.js

@@ -3,6 +3,9 @@ const FuncGeneratorPlugin = require('datagrok-tools/plugins/func-gen-plugin');
 const packageName = path.parse(require('./package.json').name).name.toLowerCase().replace(/-/g, '');
 
 module.exports = {
+  cache: {
+    type: 'filesystem',
+  },
   mode: 'development',
   entry: {
     package: ['./src/package.ts'],