@datagrok/bio 2.0.29 → 2.0.30

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.0.29",
+  "version": "2.0.30",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",

package/scripts/admet-requirements.txt

@@ -0,0 +1,7 @@
+numpy==1.16.6
+pandas==0.24.2
+python-dateutil==2.8.2
+pytz==2022.5
+scikit-learn==0.17.1
+scipy==1.2.3
+six==1.16.0

package/src/package.ts

@@ -34,9 +34,11 @@ import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter'
 import * as C from './utils/constants';
 import {SequenceSimilarityViewer} from './analysis/sequence-similarity-viewer';
 import {SequenceDiversityViewer} from './analysis/sequence-diversity-viewer';
-import {substructureSearchDialog} from './substructure-search/substructure-search';
+import {invalidateMols, MONOMERIC_COL_TAGS, substructureSearchDialog} from './substructure-search/substructure-search';
 import {saveAsFastaUI} from './utils/save-as-fasta';
 import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
+import { getMonomericMols } from './calculations/monomerLevelMols';
+import { delay } from '@datagrok-libraries/utils/src/test';
 
 //tags: init
 export async function initBio() {
@@ -205,13 +207,35 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column,
 //input: dataframe table
 //input: column macroMolecule { semType: Macromolecule }
 //input: string methodName { choices:["UMAP", "t-SNE", "SPE"] }
-//input: string similarityMetric { choices:["Levenshtein", "Tanimoto"] }
+//input: string similarityMetric { choices:["Tanimoto", "Asymmetric", "Cosine", "Sokal"] }
 //input: bool plotEmbeddings = true
 export async function sequenceSpaceTopMenu(table: DG.DataFrame, macroMolecule: DG.Column, methodName: string,
-  similarityMetric: string = 'Levenshtein', plotEmbeddings: boolean): Promise<DG.Viewer | undefined> {
-  if (!checkInputColumnUi(macroMolecule, 'Activity Cliffs'))
+  similarityMetric: string = 'Tanimoto', plotEmbeddings: boolean): Promise<DG.Viewer | undefined> {
+  //delay is required for initial function dialog to close before starting invalidating of molfiles. Otherwise dialog is freezing
+  await delay(10);
+  if (!checkInputColumnUi(macroMolecule, 'Sequence space'))
     return;
-  const encodedCol = encodeMonomers(macroMolecule);
+
+  if (macroMolecule.version !== macroMolecule.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
+    await invalidateMols(macroMolecule, false);
+  const embedColsNames = getEmbeddingColsNames(table);
+
+  await grok.functions.call('Chem:getChemSpaceEmbeddings', {
+    table: table,
+    col: macroMolecule.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS],
+    methodName: methodName,
+    similarityMetric: similarityMetric,
+    xAxis: embedColsNames[0],
+    yAxis: embedColsNames[1]
+  });
+
+  if (plotEmbeddings) {
+    return grok.shell
+      .tableView(table.name)
+      .scatterPlot({x: embedColsNames[0], y: embedColsNames[1], title: 'Sequence space'});
+  };
+
+/*   const encodedCol = encodeMonomers(macroMolecule);
   if (!encodedCol)
     return;
   const embedColsNames = getEmbeddingColsNames(table);
@@ -237,8 +261,7 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, macroMolecule: D
       if (v.name === table.name)
         sp = (v as DG.TableView).scatterPlot({x: embedColsNames[0], y: embedColsNames[1], title: 'Sequence space'});
     }
-  }
-  return sp;
+  } */
 };
 
 //top-menu: Bio | To Atomic Level...

package/src/substructure-search/substructure-search.ts

@@ -6,10 +6,11 @@ import * as bio from '@datagrok-libraries/bio';
 import * as C from '../utils/constants';
 import {getMonomericMols} from '../calculations/monomerLevelMols';
 import {updateDivInnerHTML} from '../utils/ui-utils';
+import { delay } from '@datagrok-libraries/utils/src/test';
 
 export const MONOMER_MOLS_COL = 'monomeric-mols';
 
-const enum MONOMERIC_COL_TAGS {
+export const enum MONOMERIC_COL_TAGS {
   MONOMERIC_MOLS = 'monomeric-mols',
   LAST_INVALIDATED_VERSION = 'last-invalidated-version',
   MONOMERS_DICT = 'monomers-dict'
@@ -99,7 +100,7 @@ function prepareSubstructureRegex(substructure: string, separator: string) {
 
 export async function helmSubstructureSearch(substructure: string, col: DG.Column): Promise<DG.BitSet> {
   if (col.version !== col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION])
-    await invalidateHelmMols(col);
+    await invalidateMols(col, true);
   const substructureCol = DG.Column.string('helm', 1).init((i) => substructure);
   substructureCol.setTag(DG.TAGS.UNITS, bio.NOTATION.HELM);
   const substructureMolsCol =
@@ -112,10 +113,13 @@ export async function helmSubstructureSearch(substructure: string, col: DG.Colum
   return matchesCol.get(0);
 }
 
-export async function invalidateHelmMols(col: DG.Column) {
+export async function invalidateMols(col: DG.Column, pattern: boolean) {
+  const progressBar = DG.TaskBarProgressIndicator.create(`Invalidating molfiles for ${col.name}`);
+  await delay(10);
   const monomersDict = new Map();
-  const monomericMolsCol = await getMonomericMols(col, true, monomersDict);
+  const monomericMolsCol = await getMonomericMols(col, pattern, monomersDict);
   col.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS] = monomericMolsCol;
   col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT] = monomersDict;
   col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION] = col.version;
+  progressBar.close();
 }

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

@@ -207,12 +207,12 @@ export class HelmFilter extends BioFilterBase {
     await ui.tools.waitForElementInDom(this._filterPanel);
     this.updateFilterPanel();
     this._filterPanel.addEventListener('click', (event: MouseEvent) => {
+      const {editorDiv, webEditor} = this.helmEditor.createWebEditor(this.helmSubstructure);
       //@ts-ignore
       ui.dialog({showHeader: false, showFooter: true})
-        .add(this.helmEditor.editorView)
+        .add(editorDiv)
         .onOK(() => {
-          const helmString = this.helmEditor
-            .webEditor.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
+          const helmString = webEditor.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
           this.helmSubstructure = helmString;
           this.updateFilterPanel(this.substructure);
           setTimeout(() => { this.onChanged.next(); }, 10);