@datagrok/bio 1.7.4 → 1.7.5

package/files/samples/sample_SEPARATOR_PT.csv

@@ -0,0 +1,101 @@
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package/package.json

@@ -2,7 +2,7 @@
   "name": "@datagrok/bio",
   "beta": false,
   "friendlyName": "Bio",
-  "version": "1.7.4",
+  "version": "1.7.5",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -11,12 +11,13 @@
   },
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "2.8.1",
+    "@datagrok-libraries/bio": "2.8.3",
     "@datagrok-libraries/utils": "^1.0.0",
     "@datagrok-libraries/ml": "^2.0.10",
     "cash-dom": "latest",
     "datagrok-api": "^1.4.12",
     "dayjs": "latest",
+    "rxjs": "^6.5.5",
     "ts-loader": "^9.2.5",
     "typescript": "^4.4.2",
     "openchemlib": "6.0.1"

package/src/const.ts

@@ -2,3 +2,24 @@ import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
+export const jsonSdfMonomerLibDict = {
+    "monomerType": null, 
+    "smiles": null, 
+    "name": "MonomerName", 
+    "author": null, 
+    "molfile": "molecule", 
+    "naturalAnalog": "MonomerNaturalAnalogCode", 
+    "rgroups": "MonomerCaps",
+    "createDate": null, 
+    "id": null, 
+    "polymerType": "MonomerType", 
+    "symbol": "MonomerCode"
+}
+
+export const RGROUP_FIELD = "rgroups";
+export const CAP_GROUP_SMILES = "capGroupSmiles";
+export const RGROUP_ALTER_ID = "alternateId";
+export const CAP_GROUP_NAME = "capGroupName";
+export const RGROUP_LABEL = "label";
+export const MONOMER_SYMBOL = "symbol";
+export const SDF_MONOMER_NAME = "MonomerName";

package/src/package-test.ts

@@ -9,7 +9,7 @@ import './tests/msa-tests';
 import './tests/sequence-space-test';
 import './tests/activity-cliffs-tests';
 import './tests/splitters-test';
-import './tests/renderer-test';
+import './tests/renderers-test';
 import './tests/convert-test';
 
 export const _package = new DG.Package();

package/src/package.ts

@@ -15,10 +15,9 @@ import {getEmbeddingColsNames, sequenceSpace} from './utils/sequence-space';
 import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {sequenceGetSimilarities, drawTooltip} from './utils/sequence-activity-cliffs';
-import {getMolfilesFromSeq, HELM_CORE_LIB_FILENAME} from './utils/utils';
+import {createJsonMonomerLibFromSdf, getMolfilesFromSeq, HELM_CORE_LIB_FILENAME} from './utils/utils';
 import {getMacroMol} from './utils/atomic-works';
 import {MacromoleculeSequenceCellRenderer} from './utils/cell-renderer';
-import {delay} from '@datagrok-libraries/utils/src/test';
 import {convert} from './utils/convert';
 
 //tags: init
@@ -245,7 +244,15 @@ export async function compositionAnalysis(): Promise<void> {
     return;
   }
 
-  tv.addViewer('WebLogo', {sequenceColumnName: col.name});
+  const wlViewer = tv.addViewer('WebLogo', {sequenceColumnName: col.name});
+  grok.shell.tv.dockManager.dock(wlViewer, DG.DOCK_TYPE.DOWN, null, 'Composition analysis', 0.25);
+}
+
+//top-menu: Bio | Sdf to Json lib...
+//name: sdfToJsonLib
+//input: dataframe table
+export async function sdfToJsonLib(table: DG.DataFrame) {
+  const jsonMonomerLibrary = createJsonMonomerLibFromSdf(table);   
 }
 
 // helper function for importFasta
@@ -325,7 +332,7 @@ export function importFasta(fileContent: string): DG.DataFrame [] {
   ])];
 }
 
-//name: Bio | Convert
+//name: Bio | Convert ...
 //friendly-name: Bio | Convert
 //tags: panel, bio
 //input: column col {semType: Macromolecule}

package/src/tests/{renderer-test.ts → renderers-test.ts}

@@ -1,9 +1,11 @@
-import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
 
 import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {importFasta, multipleSequenceAlignmentAny} from '../package';
+import {readDataframe} from './utils';
+import {convertDo} from '../utils/convert';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
 
 category('renderers', () => {
   let tvList: DG.TableView[];
@@ -23,42 +25,49 @@ category('renderers', () => {
     await _testAfterMsa();
   });
 
+  test('afterConvert', async () => {
+    await _testAfterConvert();
+  });
+
   async function _testAfterMsa() {
     const fastaTxt: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/sample_FASTA.fasta');
     const df: DG.DataFrame = importFasta(fastaTxt)[0];
-    // await grok.data.detectSemanticTypes(df);
-
-    const srcSeqCol: DG.Column | null = df.col('sequence');
-    expect(srcSeqCol !== null, true);
-    console.log('Bio: tests/renderers/afterMsa, src data loaded');
-
     const tv: DG.TableView = grok.shell.addTableView(df);
+    await grok.data.detectSemanticTypes(df);
     console.log('Bio: tests/renderers/afterMsa, table view');
 
-    // await grok.data.detectSemanticTypes(df);
-    console.log('Bio: tests/renderers/afterMsa, detectSemanticTypes');
+    const srcSeqCol: DG.Column | null = df.col('sequence');
+    expect(srcSeqCol !== null, true);
 
     console.log('Bio: tests/renderers/afterMsa, src before test ' +
       `semType="${srcSeqCol!.semType}", units="${srcSeqCol!.getTag(DG.TAGS.UNITS)}", ` +
       `cell.renderer="${srcSeqCol!.getTag('cell.renderer')}"`);
     expect(srcSeqCol!.semType, DG.SEMTYPE.MACROMOLECULE);
     expect(srcSeqCol!.getTag(DG.TAGS.UNITS), 'fasta:SEQ:PT');
-    // TODO: Find the way to check renderer for columns
     expect(srcSeqCol!.getTag('cell.renderer'), 'Macromolecule');
-    console.log('Bio: tests/renderers/afterMsa, src semType tested');
 
     const msaSeqCol: DG.Column | null = await multipleSequenceAlignmentAny(df, srcSeqCol!);
-    console.log('Bio: tests/renderers/afterMsa, msaSeqCol created');
-
     tv.grid.invalidate();
-    console.log('Bio: tests/renderers/afterMsa, tv.grid invalidated');
 
     expect(msaSeqCol!.semType, DG.SEMTYPE.MACROMOLECULE);
     expect(msaSeqCol!.getTag(DG.TAGS.UNITS), 'fasta:SEQ.MSA:PT');
     expect(msaSeqCol!.getTag('cell.renderer'), 'Macromolecule');
-    console.log('Bio: tests/renderers/afterMsa, msa semType tested');
 
     dfList.push(df);
     tvList.push(tv);
   }
+
+  async function _testAfterConvert() {
+    const csv: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/sample_FASTA_PT.csv');
+    const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
+    const tv: DG.TableView = grok.shell.addTableView(df);
+    await grok.data.detectSemanticTypes(df);
+
+    const srcCol: DG.Column = df.col('sequence')!;
+    const tgtCol: DG.Column = await convertDo(srcCol, NOTATION.SEPARATOR, '/');
+    expect(tgtCol.getTag('cell.renderer'), 'Macromolecule');
+
+    tvList.push(tv);
+    dfList.push(df);
+  };
 });

package/src/utils/cell-renderer.ts

@@ -9,6 +9,7 @@ import * as ui from 'datagrok-api/ui';
 
 const lru = new DG.LruCache<any, any>();
 const undefinedColor = 'rgb(100,100,100)';
+const grayColor = '#808080'
 
 function getPalleteByType(paletteType: string): SeqPalette {
   switch (paletteType) {
@@ -81,7 +82,7 @@ function printLeftOrCentered(
     g.fillStyle = color;
     g.globalAlpha = transparencyRate;
     g.fillText(colorPart, x + dx1, y + dy);
-    g.fillStyle = '#808080';
+    g.fillStyle = grayColor;
     g.fillText(grayPart, x + dx2, y + dy);
   }
 
@@ -96,6 +97,22 @@ function printLeftOrCentered(
   }
 }
 
+function findMonomers(helmString: string) {
+  //@ts-ignore
+  const types = Object.keys(org.helm.webeditor.monomerTypeList());
+  const monomers: any = [];
+  const monomer_names: any = [];
+  for (var i = 0; i < types.length; i++) {
+    //@ts-ignore
+    monomers.push(new scil.helm.Monomers.getMonomerSet(types[i]));
+    Object.keys(monomers[i]).forEach(k => {
+      monomer_names.push(monomers[i][k].id);
+    });
+  }
+  const split_string = WebLogo.splitterAsHelm(helmString);
+  return new Set(split_string.filter(val => !monomer_names.includes(val)));
+}
+
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   get name(): string { return 'macromoleculeSequence'; }
 
@@ -125,22 +142,47 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const cell = gridCell.cell;
     const tag = gridCell.cell.column.getTag(DG.TAGS.UNITS);
     if (tag === 'HELM') {
-      const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
-      host.setAttribute('dataformat', 'helm');
-      host.setAttribute('data', gridCell.cell.value);
-      gridCell.element = host;
-      //@ts-ignore
-      const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
-      const formula = canvas.getFormula(true);
-      if (!formula) {
-        gridCell.element = ui.divText(gridCell.cell.value, {style: {color: 'red'}});
-      } else {
+      console.log(findMonomers(cell.value));
+      const monomers = findMonomers(cell.value);
+      if (monomers.size == 0) {
+        const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
+        host.setAttribute('dataformat', 'helm');
+        host.setAttribute('data', gridCell.cell.value);
         gridCell.element = host;
-        const molWeight = Math.round(canvas.getMolWeight() * 100) / 100;
-        const coef = Math.round(canvas.getExtinctionCoefficient(true) * 100) / 100;
-        const molfile = canvas.getMolfile();
-        const result = formula + ', ' + molWeight + ', ' + coef + ', ' + molfile;
-        lru.set(gridCell.cell.value, result);
+        //@ts-ignore
+        const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
+        const formula = canvas.getFormula(true);
+        if (!formula) {
+          gridCell.element = ui.divText(gridCell.cell.value, {style: {color: 'red'}});
+        }
+        return;
+      }
+      if (monomers.size > 0) {
+        w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
+        g.save();
+        g.beginPath();
+        g.rect(x, y, w, h);
+        g.clip();
+        g.font = '12px monospace';
+        g.textBaseline = 'top';
+        let x1 = x;
+        const s: string = cell.value ?? '';
+        let subParts: string[] = WebLogo.splitterAsHelm(s);
+        let color = undefinedColor;
+        subParts.forEach((amino, index) => {
+          if (monomers.has(amino)) {
+            color = 'red';
+          } else {
+            color = grayColor;
+          }
+          g.fillStyle = undefinedColor;
+          let last = false;
+          if (index === subParts.length - 1)
+            last = true;
+          x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0, '/', last);
+        });
+        g.restore();
+        return;
       }
     } else {
       const [type, subtype, paletteType] = gridCell.cell.column.getTag(DG.TAGS.UNITS).split(':');
@@ -176,6 +218,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       });
 
       g.restore();
+      return;
+
     }
   }
 }

package/src/utils/convert.ts

@@ -1,7 +1,14 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
+import * as grok from 'datagrok-api/grok';
+
+import {Subscription} from 'rxjs';
 import {NotationConverter, NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
 
+
+let convertDialog: DG.Dialog | null = null;
+let convertDialogSubs: Subscription[] = [];
+
 /**
  * Converts notations of a Macromolecule column
  *
@@ -22,19 +29,35 @@ export function convert(col: DG.Column): void {
 
   const separatorInput = ui.choiceInput('Choose separator', separatorArray[0], separatorArray);
 
-  ui.dialog('Convert sequence notation')
-    .add(ui.div([
-      ui.h1('Current notation: ' + current),
-      targetNotationInput.root,
-      // TODO: conditional separator input
-      separatorInput.root
-    ]))
-    .onOK(() => {
-      //TODO: create new converted column
-      const targetNotation = targetNotationInput.value as NOTATION;
-      const separator = separatorInput.value!;
-      const newColumn = converter.convert(targetNotation, separator);
-      col.dataFrame.columns.add(newColumn);
-    })
-    .show();
+  if (convertDialog == null) {
+    convertDialog = ui.dialog('Convert sequence notation')
+      .add(ui.div([
+        ui.h1('Current notation: ' + current),
+        targetNotationInput.root,
+        // TODO: conditional separator input
+        separatorInput.root
+      ]))
+      .onOK(async () => {
+        const targetNotation = targetNotationInput.value as NOTATION;
+        const separator: string | null = separatorInput.value;
+
+        await convertDo(col, targetNotation, separator);
+      })
+      .show();
+
+    convertDialogSubs.push(convertDialog.onClose.subscribe((value) => {
+      convertDialogSubs.forEach((s) => {s.unsubscribe(); });
+      convertDialogSubs = [];
+      convertDialog = null;
+    }));
+  }
+}
+
+export async function convertDo(srcCol: DG.Column, targetNotation: NOTATION, separator: string | null): Promise<DG.Column> {
+  const converter = new NotationConverter(srcCol);
+  const newColumn = converter.convert(targetNotation, separator);
+  srcCol.dataFrame.columns.add(newColumn);
+  await grok.data.detectSemanticTypes(srcCol.dataFrame);
+  return newColumn;
 }
+

package/src/utils/utils.ts

@@ -1,6 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import {WebLogo, SplitterFunc} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import * as grok from 'datagrok-api/grok';
+import { CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_SYMBOL, RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME } from '../const';
 
 export const HELM_CORE_LIB_FILENAME = '/samples/HELMCoreLibrary.json';
 export const HELM_CORE_LIB_MONOMER_SYMBOL = 'symbol';
@@ -43,3 +44,37 @@ export function createMomomersMolDict(lib: any[]): { [key: string]: string | any
   });
   return dict;
 }
+
+
+export function createJsonMonomerLibFromSdf(table: DG.DataFrame): any {
+  const resultLib = [];
+  for (let i = 0; i < table.rowCount; i++) {
+    const monomer: { [key: string]: string | any } = {};
+    Object.keys(jsonSdfMonomerLibDict).forEach(key => {
+      if (key === MONOMER_SYMBOL) {
+        const monomerSymbol = table.get(jsonSdfMonomerLibDict[key], i);
+        monomer[key] = monomerSymbol === '.' ? table.get(SDF_MONOMER_NAME, i) : monomerSymbol;
+      } else if (key === RGROUP_FIELD) {
+        const rgroups = table.get(jsonSdfMonomerLibDict[key], i).split('\n');
+        const jsonRgroups: any[] = [];
+        rgroups.forEach((g: string) => {
+          const rgroup: { [key: string]: string | any } = {};
+          const altAtom = g.substring(g.lastIndexOf("]") + 1);
+          let radicalNum = g.match(/\[R(\d+)\]/)![1];
+          rgroup[CAP_GROUP_SMILES] = altAtom === 'H' ? `[*:${radicalNum}][H]` : `O[*:${radicalNum}]`;
+          rgroup[RGROUP_ALTER_ID] = altAtom === 'H' ? `R${radicalNum}-H` : `R${radicalNum}-OH`;
+          rgroup[CAP_GROUP_NAME] = altAtom === 'H' ? `H` : `OH`;
+          rgroup[RGROUP_LABEL] = `R${radicalNum}`;
+          jsonRgroups.push(rgroup);
+        })
+        monomer[key] = jsonRgroups;
+      } else {
+        if((jsonSdfMonomerLibDict as { [key: string]: string | any })[key]) {
+          monomer[key] = table.get((jsonSdfMonomerLibDict as { [key: string]: string | any })[key], i);
+        }
+      }
+    })
+    resultLib.push(monomer);
+  }
+  return resultLib;
+}

package/{test-Bio-34f75e5127b8-1314754e.html → test-Bio-34f75e5127b8-0507068d.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 1314754e.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 0507068d.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 1314754e.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-13 15:23:55</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">110.181s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 0507068d.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-14 14:09:37</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">110.386s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
 Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long-running test."
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:22:1)
     at Runtime._execModule (/home/runner/work/public/public/packages/Bio/node_modules/jest-runtime/build/index.js:1646:24)