@datagrok/bio 1.11.4 → 2.0.1

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "1.11.4",
+  "version": "2.0.1",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -70,11 +70,7 @@
     "Developers"
   ],
   "sources": [
-    "css/helm.css",
-    "https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js",
-    "helm/JSDraw/Scilligence.JSDraw2.Lite.js",
-    "helm/JSDraw/Scilligence.JSDraw2.Resources.js",
-    "helm/JSDraw/Pistoia.HELM-uncompressed.js"
+    "css/helm.css"
   ],
   "category": "Bioinformatics"
 }

package/src/calculations/fingerprints.ts

@@ -0,0 +1,76 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+const V2000_ATOM_NAME_POS = 31;
+
+export async function getFingerprints(mols: Array<string>, monomers: Array<string>): Promise<Uint8Array[]> {
+  const mod = await grok.functions.call('Chem:getRdKitModule');
+  const fps: Uint8Array[] = [];
+
+  let dict = new Map(); 
+  for(let i = 0; i < monomers.length; i++)
+    dict.set(monomers[i], `R${Math.pow(10,(i + 1))}`);
+
+  mols = changeToV3000(mols, dict);
+
+  for(let i = 0; i< mols.length; i++) {
+    const mol = mod.get_mol(mols[i]);
+    const fp = mol.get_pattern_fp_as_uint8array();
+    fps.push(fp);
+    mol?.delete();
+  }
+
+  return fps;
+}
+
+function changeToV3000(mols: Array<string>, dict: Map<string, string>): Array<string> {
+  for (let i = 0; i < mols.length; i++) {
+    let curPos = 0;
+    let endPos = 0;
+    let molV3000 = `
+    Datagrok macromolecule handler
+
+  0  0  0  0  0  0            999 V3000
+M  V30 BEGIN CTAB
+`;
+
+    const mol = mols[i];
+    curPos = mol.indexOf('\n', curPos) + 1;
+    curPos = mol.indexOf('\n', curPos) + 1;
+    curPos = mol.indexOf('\n', curPos) + 1;
+
+    const atomMonomerCounts = parseInt(mol.substring(curPos, curPos + 3));
+    const bondMonomerCounts = parseInt(mol.substring(curPos + 3, curPos + 6));
+
+    molV3000 += `M  V30 COUNTS ${atomMonomerCounts} ${bondMonomerCounts} 0 0 0\n`;
+    molV3000 += 'M  V30 BEGIN ATOM\n';
+
+    for (let atomRowI = 0; atomRowI < atomMonomerCounts; atomRowI++) {
+      curPos = mol.indexOf('\n', curPos) + 1 + V2000_ATOM_NAME_POS;
+      endPos = mol.indexOf(' ', curPos);
+      const monomerName: string = mol.substring(curPos, endPos);
+      molV3000 += `M  V30 ${atomRowI + 1} ${dict.get(monomerName)} 0.000 0.000 0 0\n`;
+    } 
+
+    molV3000 += 'M  V30 END ATOM\n';
+    molV3000 += 'M  V30 BEGIN BOND\n';
+
+    for (let bondRowI = 0; bondRowI < bondMonomerCounts; bondRowI++) {
+      curPos = mol.indexOf('\n', curPos) + 1;
+      const firstMonomer = parseInt(mol.substring(curPos, curPos + 3).trim());
+      const secondMonomer = parseInt(mol.substring(curPos + 3, curPos + 6).trim());
+      const order = parseInt(mol.substring(curPos + 6, curPos + 9).trim());
+
+      molV3000 += `M  V30 ${bondRowI + 1} ${order} ${firstMonomer} ${secondMonomer}\n`;
+    } 
+
+    molV3000 += 'M  V30 END BOND\n';
+    molV3000 += 'M  V30 END CTAB\n';
+    molV3000 += 'M  END';
+    console.log(molV3000);
+    mols[i] = molV3000;
+  }
+
+  return mols;
+}

package/src/package.ts

@@ -32,22 +32,12 @@ import {
 
 import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
 import * as C from './utils/constants';
+import {getFingerprints} from './calculations/fingerprints'
 
 //tags: init
 export async function initBio() {
 }
 
-//name: testManySequencesPerformance
-export function testManySequencesPerformance(): void {
-  performanceTest(generateManySequences, 'Many sequences');
-}
-
-//name: testLongSequencesPerformance
-export function testLongSequencesPerformance(): void {
-  performanceTest(generateLongSequence, 'Long sequences');
-}
-
-
 //name: fastaSequenceCellRenderer
 //tags: cellRenderer
 //meta.cellType: Sequence
@@ -457,7 +447,23 @@ export function splitToMonomers(col: DG.Column<string>): void {
   for (const tempCol of tempDf.columns) {
     const newCol = originalDf.columns.add(tempCol);
     newCol.semType = C.SEM_TYPES.MONOMER;
-    // newCol.setTag(DG.TAGS.CELL_RENDERER, C.SEM_TYPES.MONOMER);
+    newCol.setTag(DG.TAGS.CELL_RENDERER, C.SEM_TYPES.MONOMER);
     newCol.setTag(C.TAGS.ALPHABET, col.getTag(C.TAGS.ALPHABET));
   }
+  grok.shell.tv.grid.invalidate();
+}
+
+//name: Bio: getHelmMonomers
+//input: column col {semType: Macromolecule}
+export function getHelmMonomers(seqCol: DG.Column<string>): string[] {
+  const stats = WebLogo.getStats(seqCol, 1, WebLogo.splitterAsHelm);
+  return Object.keys(stats.freq);
+}
+
+export async function macromoleculesFingerprints(mcol: DG.Column): Promise<Uint8Array[]> {
+  grok.functions.call('Chem:getRdKitModule');
+  const monomers = getHelmMonomers(mcol);
+  const mols = await grok.functions.call('HELM:getMolFiles', {mcol : mcol});
+
+  return getFingerprints(mols.toList(), monomers);
 }

package/src/tests/renderers-test.ts

@@ -6,6 +6,7 @@ import {importFasta, multipleSequenceAlignmentAny} from '../package';
 import {convertDo} from '../utils/convert';
 import {ALPHABET, NOTATION, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {SEM_TYPES, TAGS} from '../utils/constants';
+import {generateLongSequence, generateManySequences, performanceTest} from './test-sequnces-generators';
 
 category('renderers', () => {
   let tvList: DG.TableView[];
@@ -22,6 +23,14 @@ category('renderers', () => {
     tvList.forEach((tv: DG.TableView) => tv.close());
   });
 
+  test('long sequence performance ', async () => {
+    performanceTest(generateLongSequence, 'Long sequences');
+  });
+
+  test('many sequence performance', async () => {
+    performanceTest(generateManySequences, 'Many sequences');
+  });
+
   test('afterMsa', async () => {
     await _testAfterMsa();
   });

package/src/utils/cell-renderer.ts

@@ -196,7 +196,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 }
 
 export class MonomerCellRenderer extends DG.GridCellRenderer {
-  get name(): string {return 'MonomerCR';}
+  get name(): string {return C.SEM_TYPES.MONOMER;}
 
   get cellType(): string {return C.SEM_TYPES.MONOMER;}
 
@@ -217,21 +217,17 @@ export class MonomerCellRenderer extends DG.GridCellRenderer {
    */
   render(
     g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
-    cellStyle: DG.GridCellStyle): void {
-    y -= 2;
-    g.save();
-    g.beginPath();
-    g.rect(x, y, w, h);
-    g.clip();
+    _cellStyle: DG.GridCellStyle): void {
     g.font = `12px monospace`;
-    g.textBaseline = 'top';
+    g.textBaseline = 'middle';
+    g.textAlign = 'center';
 
-    const palette = getPaletteByType(gridCell.tableColumn!.tags[C.TAGS.ALPHABET]);
-    const s: string = gridCell.cell.value ? gridCell.cell.value : '-';
+    const palette = getPaletteByType(gridCell.cell.column.getTag(C.TAGS.ALPHABET));
+    const s: string = gridCell.cell.value || '-';
     const color = palette.get(s);
 
-    printLeftOrCentered(x, y, w, h, g, s, color, 0, false);
-    g.restore();
+    g.fillStyle = color;
+    g.fillText(s, x + (w / 2), y - (h / 2), w);
   }
 }
 

package/{test-Bio-a3ba57cf36f3-42effe59.html → test-Bio-c5a05867bf79-5c91e1fb.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=a3ba57cf36f3. Commit 42effe59.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=c5a05867bf79. Commit 5c91e1fb.</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=a3ba57cf36f3. Commit 42effe59.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-09 08:55:59</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">8.833s</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">0.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Unknown server alias. Please add it to /home/runner/.grok/config.yaml
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=c5a05867bf79. Commit 5c91e1fb.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-14 12:47:46</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">7.679s</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">0.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Unknown server alias. Please add it to /home/runner/.grok/config.yaml
     at getDevKey (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:48:13)
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:57:15)
     at Generator.next (&lt;anonymous&gt;)