@datagrok/bio 2.12.12 → 2.12.13

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.12.12",
+  "version": "2.12.13",
   "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",
@@ -34,12 +34,12 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.40.6",
-    "@datagrok-libraries/chem-meta": "^1.2.4",
+    "@datagrok-libraries/bio": "^5.40.8",
+    "@datagrok-libraries/chem-meta": "^1.2.5",
+    "@datagrok-libraries/math": "^1.1.1",
     "@datagrok-libraries/ml": "^6.6.0",
     "@datagrok-libraries/tutorials": "^1.3.12",
     "@datagrok-libraries/utils": "^4.2.0",
-    "@datagrok-libraries/math": "^1.1.1",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
@@ -103,7 +103,8 @@
     "All users"
   ],
   "sources": [
-    "css/helm.css"
+    "css/helm.css",
+    "common/openchemlib-full.js"
   ],
   "category": "Bioinformatics",
   "meta": {

package/src/tests/renderers-test.ts

@@ -1,7 +1,11 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
+import * as ui from 'datagrok-api/ui';
 
-import {category, expect, test, delay} from '@datagrok-libraries/utils/src/test';
+import $ from 'cash-dom';
+import {fromEvent} from 'rxjs';
+
+import {category, expect, test, delay, testEvent} from '@datagrok-libraries/utils/src/test';
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -12,6 +16,8 @@ import {multipleSequenceAlignmentUI} from '../utils/multiple-sequence-alignment-
 import {awaitGrid} from './utils';
 import * as C from '../utils/constants';
 
+import {_package} from '../package-test';
+
 category('renderers', () => {
   test('long sequence performance ', async () => {
     await performanceTest(generateLongSequence, 'Long sequences');
@@ -48,6 +54,10 @@ category('renderers', () => {
     await _selectRendererBySemType();
   });
 
+  test('scatterPlotTooltip', async () => {
+    await _testScatterPlotTooltip();
+  });
+
   async function _rendererMacromoleculeFasta() {
     const csv: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/FASTA.csv');
     const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
@@ -197,4 +207,40 @@ category('renderers', () => {
         `view renderer has set to '${renderer}' instead of correct 'MacromoleculeDifference'.`);
     }
   }
+
+  const seqCoordsCsv = `seq,x,y
+ACGGTGTCGT,0,0
+CGGTATCCCT,1,0
+CTCGGCATGC,2,0
+`;
+
+  async function _testScatterPlotTooltip(): Promise<void> {
+    const df = DG.DataFrame.fromCsv(seqCoordsCsv);
+    df.currentRowIdx = 0;
+    const view = grok.shell.addTableView(df);
+    const sp: DG.ScatterPlotViewer = df.plot.scatter({x: 'x', y: 'y'});
+    view.dockManager.dock(sp, DG.DOCK_TYPE.RIGHT, null);
+    await Promise.all([
+      testEvent(sp.onAfterDrawScene, () => {}, () => { sp.invalidateCanvas(); }, 1000),
+      awaitGrid(view.grid, 500)
+    ]);
+
+    const spBcr = sp.root.getBoundingClientRect();
+    const wp = sp.worldToScreen(1, 0);
+    const ev = new MouseEvent('mousemove', {
+      cancelable: true, bubbles: true, view: window, button: 0,
+      clientX: spBcr.left + wp.x, clientY: spBcr.top + wp.y
+    });
+    const spCanvas = $(sp.root).find('canvas').get()[0] as HTMLCanvasElement;
+    await testEvent(fromEvent(spCanvas, 'mousemove'), () => {
+      _package.logger.debug(`Test: event, currentRowIdx=${df.currentRowIdx}`);
+      expect($(ui.tooltip.root).find('div table.d4-row-tooltip-table tr td canvas').length, 1);
+      expect(sp.hitTest(wp.x, wp.y), 1);
+    }, () => {
+      spCanvas.dispatchEvent(ev);
+    }, 500);
+    // TODO: Any error occurred become 'Cannot read properties of null (reading 'get$columns')' because of scatter plot
+    //await testEvent(sp.onAfterDrawScene, () => {}, () => { sp.invalidateCanvas(); }, 200);
+    await awaitGrid(view.grid, 500);
+  }
 });

package/src/utils/cell-renderer.ts

@@ -59,6 +59,31 @@ export function processSequence(subParts: string[]): [string[], boolean] {
   return [text, simplified];
 }
 
+type RendererGridCellTemp = {
+  [mmcrTemps.monomerPlacer]: MonomerPlacer
+}
+
+function getRendererFridCellTempTemp(gridCell: DG.GridCell): RendererGridCellTemp {
+  /** Primarily store/get MonomerPlacer at GridColumn, fallback at (Table) Column for scatter plot tooltip  */
+  let temp: RendererGridCellTemp | null = null;
+
+  let gridCol: DG.GridColumn | null = null;
+  try { gridCol = gridCell.gridColumn; } catch { gridCol = null; }
+  temp = gridCol && gridCol.dart ? gridCol.temp as RendererGridCellTemp : null;
+
+  if (!temp) {
+    let tableCol: DG.Column | null = null;
+    try { tableCol = gridCell.cell.column; } catch { tableCol = null; }
+    if (!tableCol) {
+      const k = 42;
+    }
+    temp = tableCol ? tableCol.temp as RendererGridCellTemp : null;
+  }
+  if (temp === null)
+    throw new Error(`Monomer placer store (GridColumn or Column) not found.`);
+  return temp;
+}
+
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   private padding: number = 5;
 
@@ -82,7 +107,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
     const tableCol: DG.Column = gridCell.cell.column;
     //const tableColTemp: TempType = tableCol.temp;
-    const seqColTemp: MonomerPlacer = gridCell.gridColumn.temp[mmcrTemps.monomerPlacer];
+    const seqColTemp: MonomerPlacer = getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer];
     if (!seqColTemp) return; // Can do nothing without precalculated data
 
     const gridCellBounds: DG.Rect = gridCell.bounds;
@@ -165,7 +190,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         (!isNaN(tagMaxMonomerLength) ? tagMaxMonomerLength : _package.properties?.MaxMonomerLength) ?? 4;
     }
 
-    let seqColTemp: MonomerPlacer = gridCell.gridColumn.temp[mmcrTemps.monomerPlacer];
+    let seqColTemp: MonomerPlacer = getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer];
     if (!seqColTemp) {
       seqColTemp = new MonomerPlacer(grid, tableCol,
         () => {
@@ -192,7 +217,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const _maxIndex = maxLengthWords.length;
 
     // Store updated seqColTemp to the col temp
-    if (seqColTemp.updated) gridCell.gridColumn.temp[mmcrTemps.monomerPlacer] = seqColTemp;
+    if (seqColTemp.updated) getRendererFridCellTempTemp(gridCell)[mmcrTemps.monomerPlacer] = seqColTemp;
 
     g.save();
     try {

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

@@ -1,29 +1,4 @@
 export const HELM_ITEM_SEPARATOR = '|';
 export const HELM_SECTION_SEPARATOR = '$';
-export const HYDROGEN_SYMBOL = 'H';
-export const R_GROUP_ELEMENT_SYMBOL = 'R#';
-
-export const enum V2K_CONST {
-  MAX_ATOM_COUNT = 999,
-  RGP_LINE_START = 'M  RGP',
-  ATOM_ALIAS_LINE_START = 'A  ',
-}
-
-export const enum V3K_CONST {
-  HEADER = `
-     RDKit          2D
-
-  0  0  0  0  0  0  0  0  0  0999 V3000`,
-  BEGIN_CTAB = 'M  V30 BEGIN CTAB',
-  COUNTS_LINE_START = 'M  V30 COUNTS ',
-  COUNTS_LINE_END = ' 0 0 0',
-  BEGIN_ATOM_BLOCK = 'M  V30 BEGIN ATOM',
-  END_ATOM_BLOCK = 'M  V30 END ATOM',
-  BEGIN_BOND_BLOCK = 'M  V30 BEGIN BOND',
-  END_BOND_BLOCK = 'M  V30 END BOND',
-  BEGIN_COLLECTION_BLOCK = 'M  V30 BEGIN COLLECTION',
-  END_COLLECTION_BLOCK = 'M  V30 END COLLECTION',
-  END_CTAB = 'M  V30 END CTAB',
-  END = 'M  END\n',
-}
 
+export const HYDROGEN_SYMBOL = 'H';

package/src/utils/helm-to-molfile/converter/mol-atoms.ts

@@ -1,4 +1,4 @@
-import {R_GROUP_ELEMENT_SYMBOL} from './const';
+import {R_GROUP_ELEMENT_SYMBOL} from '@datagrok-libraries/chem-meta/src/formats/molfile-const';
 
 export abstract class MolfileAtoms {
   protected coordinates: {x: number, y: number}[] = [];

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

@@ -1,5 +1,5 @@
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
-import {V2K_CONST, V3K_CONST} from './const';
+import {V3K_CONST} from '@datagrok-libraries/chem-meta/src/formats/molfile-const';
 import {Helm} from './helm';
 import {MonomerWrapper} from './monomer-wrapper';
 
@@ -44,7 +44,6 @@ export class Polymer {
   }
 
   compileToMolfile(): string {
-    const molfileHeader = '\nDatagrok\n';
     const atomLines: string[] = [];
     const bondLines: string[] = [];
 
@@ -73,8 +72,8 @@ export class Polymer {
   }
 
   private getV3KHeader(atomCount: number, bondCount: number): string {
-    const countsLine = `${V3K_CONST.COUNTS_LINE_START}${atomCount} ${bondCount}${V3K_CONST.COUNTS_LINE_END}`;
-    return `${V3K_CONST.HEADER}\n${V3K_CONST.BEGIN_CTAB}\n${countsLine}`;
+    const countsLine = `${V3K_CONST.COUNTS_LINE_START}${atomCount} ${bondCount}${V3K_CONST.COUNTS_LINE_DUMMY_END}`;
+    return `${V3K_CONST.DUMMY_HEADER}\n${V3K_CONST.BEGIN_CTAB}\n${countsLine}`;
   }
 
   private getV3KAtomBlock(atomLines: string[]): string {

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

@@ -1,9 +1,5 @@
 import {HELM_REQUIRED_FIELD} from '@datagrok-libraries/bio/src/utils/const';
 
-export const enum HELM_WRAPPER {
-  LEFT = 'PEPTIDE1{',
-  RIGHT = '}$$$$',
-}
 export const ALL_MONOMERS = '<All>';
 
 export const enum TRANSFORMATION_TYPE {

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

@@ -6,12 +6,15 @@ import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {ALIGNMENT, ALPHABET} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
-import {HELM_WRAPPER} from './const';
 import {getMolColumnFromHelm} from '../helm-to-molfile/utils';
 
 export const RULES_PATH = 'System:AppData/Bio/polytool-rules/';
 export const RULES_STORAGE_NAME = 'Polytool';
 
+const enum HELM_WRAPPER {
+  LEFT = 'PEPTIDE1{',
+  RIGHT = '}$$$$',
+}
 
 type ConnectionData = {
   allPos1: number[],
@@ -43,19 +46,8 @@ class TransformationCommon {
     this.helmColumn = helmColumn;
   }
 
-  protected hasTerminals(helm: string): boolean {
-    let isLinkable = false;
-    if (helm.includes('(1)'))
-      isLinkable = true;
-    if (helm.includes('(2)'))
-      isLinkable = true;
-
-    return isLinkable;
-  }
-
-  protected getLinkedPositions(helm: string, rules: Rule[]): [number, number][] {
-    const seq = helm.replace(HELM_WRAPPER.LEFT, '').replace(HELM_WRAPPER.RIGHT, '');
-    const monomers = seq.split('.').map((m) => { return m.replace('[', '').replace(']', ''); });
+  protected getLinkedPositions(monomers: string[], rules: Rule[]): [number, number][] {
+    const monomersNames = monomers.map((m) => { return m.replace('[', '').replace(']', ''); });
     const result: [number, number][] = new Array<[number, number]>(rules.length);
 
     for (let i = 0; i < rules.length; i++) {
@@ -65,14 +57,14 @@ class TransformationCommon {
       let firstEntryIndex = -1;
       let secondEntryIndex = -1;
       const add = `(${rules[i].code})`;
-      for (let j = 0; j < monomers.length; j++) {
-        if (monomers[j].includes(add)) {
+      for (let j = 0; j < monomersNames.length; j++) {
+        if (monomersNames[j].includes(add)) {
           if (firstFound) {
-            if (firstIsFirst && monomers[j] == rules[i].secondMonomer + add) {
+            if (firstIsFirst && monomersNames[j] == rules[i].secondMonomer + add) {
               secondFound = true;
               secondEntryIndex = j;
               break;
-            } else if (!firstIsFirst && monomers[j] == rules[i].firstMonomer + add) {
+            } else if (!firstIsFirst && monomersNames[j] == rules[i].firstMonomer + add) {
               secondFound = true;
               secondEntryIndex = j;
               break;
@@ -83,11 +75,11 @@ class TransformationCommon {
             // secondFound = true;
             // break;
           } else {
-            if (monomers[j] == rules[i].firstMonomer + add) {
+            if (monomersNames[j] == rules[i].firstMonomer + add) {
               firstFound = true;
               firstIsFirst = true;
               firstEntryIndex = j;
-            } else if (monomers[j] == rules[i].secondMonomer + add) {
+            } else if (monomersNames[j] == rules[i].secondMonomer + add) {
               firstFound = true;
               firstIsFirst = false;
               firstEntryIndex = j;
@@ -141,22 +133,42 @@ class TransformationCommon {
     return rules;
   }
 
-  protected getTransformedHelm(helm: string, rules: Rule[]): string {
-    const ruleCount = rules.length;
-    const positions = this.getLinkedPositions(helm, rules);
+  protected getDimeric(helm: string): [string[], [number, number][]] {
+    const seq = helm.replace(HELM_WRAPPER.LEFT, '').replace(HELM_WRAPPER.RIGHT, '');
+    const monomers = seq.split('.');
+    const duplicates: [number, number][] = [];
+
+    for (let i = 0; i < monomers.length; i++) {
+      if (monomers[i].includes('(#2)')) {
+        monomers[i] = monomers[i].replace('(#2)', '');
+        const duplicateStart = i + 1;
+        let duplicateFinish = 0;
+        for (let j = duplicateStart + 1; j < monomers.length; j++) {
+          if (monomers[j].includes('}')) {
+            duplicateFinish = j; break;
+          }
+        }
+        monomers[duplicateStart] = monomers[duplicateStart].replace('{', '');
+        monomers[duplicateFinish] = monomers[duplicateFinish].replace('}', '');
+        duplicates.push([duplicateStart, duplicateFinish]);
+      }
+    }
 
+    return [monomers, duplicates];
+  }
+
+  protected getAllCycles(rules: Rule[], monomers: string [], positions: [number, number][]) :
+  [string [], number [], number [], number [], number []] {
     const allPos1: number [] = [];
     const allPos2: number [] = [];
     const allAttaches1: number [] = [];
     const allAttaches2: number [] = [];
+    const ruleCount = rules.length;
 
     for (let i = 0; i < ruleCount; i++) {
       if (positions[i][0] == -1)
         continue;
 
-      //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(']', '');
 
@@ -167,31 +179,97 @@ class TransformationCommon {
       allPos2.push(positions[i][1] + 1);
       allAttaches1.push(rules[i].firstR);
       allAttaches2.push(rules[i].secondR);
+    }
 
-      helm = HELM_WRAPPER.LEFT;
-      for (let i = 0; i < monomers.length; i++) {
-        if (i != monomers.length - 1)
-          helm = helm + monomers[i] + '.';
-        else
-          helm = helm + monomers[i];
-      }
-      helm = helm + HELM_WRAPPER.RIGHT;
+    return [monomers, allPos1, allPos2, allAttaches1, allAttaches2];
+  }
+
+  protected getHelmCycle(source: ConnectionData, polFirst: number, poSecond: number): string {
+    let cycled = '';
+
+    for (let i = 0; i < source.allPos1.length; i++) {
+      if (i == 0)
+        cycled += `PEPTIDE${polFirst},PEPTIDE${poSecond},`;
+      else
+        cycled += `|PEPTIDE${polFirst},PEPTIDE${poSecond},`;
+      cycled += `${source.allPos1[i]}:R${source.allAttaches1[i]}-${source.allPos2[i]}:R${source.allAttaches2[i]}`;
     }
+    return cycled;
+  }
+
+  //"PEPTIDE1{[(#2)Succ].[{R].F.[Dab(2)].T.G.H.F.G.A.A.Y.P.[E(2)].[NH2}]}$$$$"
+  protected getTransformedHelm(helm: string, rules: Rule[]): string {
+    const [monomers, duplicates] = this.getDimeric(helm);
+    const positions = this.getLinkedPositions(monomers, rules);
+    const [monomersCycled, allPos1, allPos2, allAttaches1, allAttaches2] =
+      this.getAllCycles(rules, monomers, positions);
+
+    helm = 'PEPTIDE1{';
+    for (let i = 0; i < monomersCycled.length; i++)
+      helm += i != monomersCycled.length - 1 ? monomersCycled[i] + '.' : monomersCycled[i];
+
+    helm += '}';
+
+    const dimerCodes = new Array<string>(duplicates.length);
+    const cycleCodes = new Array<string>(duplicates.length);
+    for (let i = 0; i < duplicates.length; i++) {
+      let helmAdd = `|PEPTIDE${i + 2}{`;
+      const lengthAdd = duplicates[i][1] - duplicates[i][0];
+      //const monomersAdd = new Array<string>(lengthAdd);
+      const allPosAdd1: number [] = [];
+      const allPosAdd2: number [] = [];
+      const allAttachesAdd1: number [] = [];
+      const allAttachesAdd2: number [] = [];
+
+      for (let j = 0; j <= lengthAdd; j ++) {
+        const index = j + duplicates[i][0];
+        helmAdd += j != lengthAdd ? monomersCycled[index] + '.' : monomersCycled[index];
+      }
+
+      helmAdd += '}';
+
+      for (let j = 0; j < allPos1.length; j++) {
+        if (allPos1[j] - 1 >= duplicates[i][0] && allPos1[j] - 1 <= duplicates[i][1]) {
+          allPosAdd1.push(allPos1[j] - duplicates[i][0]);
+          allPosAdd2.push(allPos2[j] - duplicates[i][0]);
+          allAttachesAdd1.push(allAttaches1[j]);
+          allAttachesAdd2.push(allAttaches1[j]);
+        }
+      }
 
+      const addCyclysation = this.getHelmCycle({
+        allPos1: allPosAdd1,
+        allPos2: allPosAdd2,
+        allAttaches1: allAttachesAdd1,
+        allAttaches2: allAttachesAdd2}, i + 2, i + 2);
+
+      dimerCodes[i] = helmAdd;
+      cycleCodes[i] = this.getHelmCycle({
+        allPos1: [duplicates[i][0]],
+        allPos2: [1],
+        allAttaches1: [1],
+        allAttaches2: [1]}, 1, i + 2);
+      cycleCodes.push(addCyclysation);
+    }
 
-    const cycledHelm = getHelmCycle(helm, {allPos1, allPos2, allAttaches1, allAttaches2});
+    for (let i = 0; i < dimerCodes.length; i++)
+      helm += dimerCodes[i];
 
-    return cycledHelm;
+    helm += '$';
+    const mainCyclysation = this.getHelmCycle({allPos1, allPos2, allAttaches1, allAttaches2}, 1, 1);
+    helm += mainCyclysation;
+    for (let i = 0; i < cycleCodes.length; i++) {
+      helm += '|';
+      helm += cycleCodes[i];
+    }
+    helm += '$$$';
+    return helm;
   }
 
   transform(rulesTables: DG.DataFrame[]): string[] {
     const rules = this.getRules(rulesTables);
     const resultList = this.helmColumn.toList().map((helm: string) => {
-      if (this.hasTerminals(helm))
-        return this.getTransformedHelm(helm, rules);
-
-      console.log(helm);
-      return helm;
+      return this.getTransformedHelm(helm, rules);
     });
     return resultList;
   }
@@ -205,21 +283,6 @@ class PolymerTransformation {
   }
 }
 
-function getHelmCycle(helm: string, source: ConnectionData): string {
-  let cycled = helm.replace(HELM_WRAPPER.RIGHT, '}$');
-
-  for (let i = 0; i < source.allPos1.length; i++) {
-    if (i == 0)
-      cycled += 'PEPTIDE1,PEPTIDE1,';
-    else
-      cycled += '|PEPTIDE1,PEPTIDE1,';
-    cycled += `${source.allPos1[i]}:R${source.allAttaches1[i]}-${source.allPos2[i]}:R${source.allAttaches2[i]}`;
-  }
-
-  cycled += '$$$';
-  return cycled;
-}
-
 export async function addTransformedColumn(
   molColumn: DG.Column<string>, addHelm: boolean, ruleFiles: string[], chiralityEngine?: boolean
 ): Promise<void> {

package/webpack.config.js

@@ -2,11 +2,12 @@ const path = require('path');
 const FuncGeneratorPlugin = require('datagrok-tools/plugins/func-gen-plugin');
 const packageName = path.parse(require('./package.json').name).name.toLowerCase().replace(/-/g, '');
 
+const mode = 'development';
 module.exports = {
   cache: {
     type: 'filesystem',
   },
-  mode: 'development',
+  mode: mode,
   entry: {
     package: ['./src/package.ts'],
     test: {
@@ -29,12 +30,12 @@ module.exports = {
   plugins: [
     new FuncGeneratorPlugin({outputPath: './src/package.g.ts'}),
   ],
-  devtool: 'source-map',
+  devtool: mode === 'development' ? 'source-map' : 'inline-source-map',
   externals: {
     'datagrok-api/dg': 'DG',
     'datagrok-api/grok': 'grok',
     'datagrok-api/ui': 'ui',
-    'openchemlib/full.js': 'OCL',
+    'openchemlib/full': 'OCL',
     'rxjs': 'rxjs',
     'rxjs/operators': 'rxjs.operators',
     'cash-dom': '$',