@datagrok/helm 2.1.9 → 2.1.11

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.1.9",
+  "version": "2.1.11",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
   },
   "description": "Provides support for HELM notation (importing, detecting, rendering, conversion).",
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.22.1",
+    "@datagrok-libraries/bio": "^5.32.3",
     "@datagrok-libraries/utils": "^1.19.1",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.10.2",

package/src/cell-renderer.ts

@@ -6,6 +6,10 @@ import {findMonomers, parseHelm, getParts} from './utils';
 import {printLeftOrCentered} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 
+// Global flag is for replaceAll
+const helmGapStartRe = /\{(\*\.)+/g;
+const helmGapIntRe = /\.(\*\.)+/g;
+const helmGapEndRe = /(\.\*)+\}/g;
 
 export class HelmCellRenderer extends DG.GridCellRenderer {
   get name() { return 'helm'; }
@@ -50,7 +54,7 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
       for (let i = 0; i < allParts.length; ++i) {
         if (monomers.has(allParts[i])) {
           tooltipMessage[i] = ui.divV([
-            ui.divText(`Monomer ${allParts[i]} not found.`),
+            ui.divText(`Monomer '${allParts[i]}' not found.`),
             ui.divText('Open the Context Panel, then expand Manage Libraries')
           ]);
         }
@@ -70,13 +74,15 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
     const grid = gridCell.gridRow !== -1 ? gridCell.grid : undefined;
     const undefinedColor = 'rgb(100,100,100)';
     const grayColor = '#808080';
-    const monomers = findMonomers(gridCell.cell.value);
-    const s: string = gridCell.cell.value ?? '';
+
+    const s: string = !gridCell.cell.value ? '' : gridCell.cell.value
+      .replaceAll(helmGapStartRe, '{').replaceAll(helmGapIntRe, '.').replaceAll(helmGapEndRe, '}');
+    const monomers = findMonomers(s);
     const subParts: string[] = parseHelm(s);
     if (monomers.size == 0 && grid) {
       const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
       host.setAttribute('dataformat', 'helm');
-      host.setAttribute('data', gridCell.cell.value);
+      host.setAttribute('data', s);
       gridCell.element = host;
       //@ts-ignore
       const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
@@ -85,7 +91,7 @@ export class HelmCellRenderer extends DG.GridCellRenderer {
       if (!grid) {
         const r = window.devicePixelRatio;
         h = 28;
-        g.canvas.height = h*r;
+        g.canvas.height = h * r;
         g.canvas.style.height = `${h}px`;
       }
       w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;

package/src/package.ts

@@ -10,7 +10,7 @@ import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
 import {findMonomers} from './utils';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
-import { NOTATION } from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 export const _package = new DG.Package();
 let monomerLib: IMonomerLib | null = null;
@@ -27,10 +27,10 @@ export async function initHelm(): Promise<void> {
       try {
         rewriteLibraries(); // initHelm()
 
-        const monTypeList: string[] = monomerLib.getTypes();
+        const polymerTypeList: string[] = monomerLib.getPolymerTypes();
         const msgStr: string = 'Monomer lib updated:<br />' + (
-          monTypeList.length == 0 ? 'empty' : monTypeList.map((monType) => {
-            return `${monType} ${monomerLib.getMonomerNamesByType(monType).length}`;
+          polymerTypeList.length == 0 ? 'empty' : polymerTypeList.map((polymerType) => {
+            return `${polymerType} ${monomerLib.getMonomerSymbolsByType(polymerType).length}`;
           }).join('<br />'));
 
         grok.shell.info(msgStr);
@@ -45,13 +45,13 @@ export async function initHelm(): Promise<void> {
 
 function rewriteLibraries() {
   org.helm.webeditor.Monomers.clear();
-  monomerLib.getTypes().forEach((type) => {
-    const mms = monomerLib.getMonomerNamesByType(type);
-    mms.forEach((symbol) => {
+  monomerLib.getPolymerTypes().forEach((polymerType) => {
+    const monomerSymbols = monomerLib.getMonomerSymbolsByType(polymerType);
+    monomerSymbols.forEach((monomerSymbol) => {
       let isBroken = false;
-      const monomer: Monomer = monomerLib.getMonomer(type, symbol);
+      const monomer: Monomer = monomerLib.getMonomer(polymerType, monomerSymbol);
       const webEditorMonomer: WebEditorMonomer = {
-        id: symbol,
+        id: monomerSymbol,
         m: monomer.molfile,
         n: monomer.name,
         na: monomer.naturalAnalog,
@@ -64,13 +64,13 @@ function rewriteLibraries() {
       if (monomer.rgroups.length > 0) {
         webEditorMonomer.rs = monomer.rgroups.length;
         const at = {};
-        monomer.rgroups.forEach(it => {
+        monomer.rgroups.forEach((it) => {
           at[it[RGROUP_LABEL]] = it[RGROUP_CAP_GROUP_NAME];
         });
         webEditorMonomer.at = at;
-      } else if (monomer.data[SMILES] != null) {
-        webEditorMonomer.rs = Object.keys(getRS(monomer.data[SMILES].toString())).length;
-        webEditorMonomer.at = getRS(monomer.data[SMILES].toString());
+      } else if (monomer[SMILES] != null) {
+        webEditorMonomer.rs = Object.keys(getRS(monomer[SMILES].toString())).length;
+        webEditorMonomer.at = getRS(monomer[SMILES].toString());
       } else {
         isBroken = true;
       }
@@ -81,7 +81,7 @@ function rewriteLibraries() {
   });
 
   // Obsolete
-  let grid: DG.Grid = grok.shell.tv.grid;
+  const grid: DG.Grid = grok.shell.tv.grid;
   if (grid) grid.invalidate();
 }
 
@@ -97,16 +97,17 @@ export function helmCellRenderer(): HelmCellRenderer {
 function checkMonomersAndOpenWebEditor(cell?: DG.Cell, value?: string, units?: string) {
   const cellValue = typeof units === 'undefined' ? cell.value : value;
   const monomers = findMonomers(cellValue);
-  if (monomers.size == 0) 
+  if (monomers.size == 0) {
     webEditor(cell, value, units);
-  else
+  } else {
     grok.shell.warning(`Monomers ${Array.from(monomers).join(', ')} are absent! <br/>` +
     `Please, upload the monomer library! <br/>` +
     `<a href="https://datagrok.ai/help/domains/bio/macromolecules" target="_blank">Learn more</a>`);
+  }
 }
 
 //tags: cellEditor
-//description: Macromolecule  
+//description: Macromolecule
 //input: grid_cell cell
 //meta.columnTags: quality=Macromolecule, units=helm
 export function editMoleculeCell(cell: DG.GridCell): void {
@@ -118,13 +119,13 @@ export function editMoleculeCell(cell: DG.GridCell): void {
 //meta.action: Open Helm Web Editor
 //input: string mol { semType: Macromolecule }
 export function openEditor(mol: string): void {
-  let df = grok.shell.tv.grid.dataFrame;
-  let col = df.columns.bySemType('Macromolecule');
+  const df = grok.shell.tv.grid.dataFrame;
+  const col = df.columns.bySemType('Macromolecule');
   const colUnits = col.getTag(DG.TAGS.UNITS);
-  if (colUnits === NOTATION.HELM) 
+  if (colUnits === NOTATION.HELM)
     checkMonomersAndOpenWebEditor(df.currentCell, undefined, undefined);
-  let converter = new NotationConverter(col);
-  const resStr = converter.convertStringToHelm(mol, '/');   
+  const converter = new NotationConverter(col);
+  const resStr = converter.convertStringToHelm(mol, '/');
   checkMonomersAndOpenWebEditor(df.currentCell, resStr, col.getTag(DG.TAGS.UNITS));
 }
 
@@ -133,17 +134,17 @@ export function openEditor(mol: string): void {
 //input: string helmString {semType: Macromolecule}
 //output: widget result
 export async function propertiesPanel(helmString: string) {
-  let grid = grok.shell.tv.grid;
-  let parent = grid.root.parentElement;
+  const grid = grok.shell.tv.grid;
+  const parent = grid.root.parentElement;
   const host = ui.div([]);
   parent.appendChild(host);
-  let editor = new JSDraw2.Editor(host, {viewonly: true});
+  const editor = new JSDraw2.Editor(host, {viewonly: true});
   host.style.width = '0px';
   host.style.height = '0px';
   editor.setHelm(helmString);
-  let formula = editor.getFormula(true);
-  let molWeight = Math.round(editor.getMolWeight() * 100) / 100;
-  let coef = Math.round(editor.getExtinctionCoefficient(true) * 100) / 100;
+  const formula = editor.getFormula(true);
+  const molWeight = Math.round(editor.getMolWeight() * 100) / 100;
+  const coef = Math.round(editor.getExtinctionCoefficient(true) * 100) / 100;
   parent.lastChild.remove();
   return new DG.Widget(
     ui.tableFromMap({
@@ -155,11 +156,11 @@ export async function propertiesPanel(helmString: string) {
 }
 
 function webEditor(cell?: DG.Cell, value?: string, units?: string) {
-  let view = ui.div();
-  let df = grok.shell.tv.grid.dataFrame;
-  let converter = new NotationConverter(df.columns.bySemType('Macromolecule'));
+  const view = ui.div();
+  const df = grok.shell.tv.grid.dataFrame;
+  const converter = new NotationConverter(df.columns.bySemType('Macromolecule'));
   org.helm.webeditor.MolViewer.molscale = 0.8;
-  let app = new scil.helm.App(view, {
+  const app = new scil.helm.App(view, {
     showabout: false,
     mexfontsize: '90%',
     mexrnapinontab: true,
@@ -169,9 +170,9 @@ function webEditor(cell?: DG.Cell, value?: string, units?: string) {
     mexfavoritefirst: true,
     mexfilter: true
   });
-  var sizes = app.calculateSizes();
+  const sizes = app.calculateSizes();
   app.canvas.resize(sizes.rightwidth - 100, sizes.topheight - 210);
-  var s = {width: sizes.rightwidth - 100 + 'px', height: sizes.bottomheight + 'px'};
+  let s = {width: sizes.rightwidth - 100 + 'px', height: sizes.bottomheight + 'px'};
   //@ts-ignore
   scil.apply(app.sequence.style, s);
   //@ts-ignore
@@ -181,22 +182,22 @@ function webEditor(cell?: DG.Cell, value?: string, units?: string) {
   scil.apply(app.properties.parent.style, s);
   app.structureview.resize(sizes.rightwidth, sizes.bottomheight + app.toolbarheight);
   app.mex.resize(sizes.topheight - 80);
-  setTimeout(function() {
-    if (typeof units === 'undefined') {
+  setTimeout(() => {
+    if (typeof units === 'undefined')
       app.canvas.helm.setSequence(cell.value, 'HELM');
-    } else {
+    else
       app.canvas.helm.setSequence(value, 'HELM');
-    }
   }, 200);
   //@ts-ignore
   ui.dialog({showHeader: false, showFooter: true})
     .add(view)
     .onOK(() => {
-      let helmValue = app.canvas.getHelm(true).replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
+      const helmValue = app.canvas.getHelm(true).replace(/<\/span>/g, '')
+        .replace(/<span style='background:#bbf;'>/g, '');
       if (typeof units === 'undefined') {
         cell.value = helmValue;
       } else {
-        let convertedRes = converter.convertHelmToFastaSeparator(helmValue, units);
+        const convertedRes = converter.convertHelmToFastaSeparator(helmValue, units);
         cell.value = convertedRes;
       }
     }).show({modal: true, fullScreen: true});
@@ -226,19 +227,19 @@ function getRS(smiles: string) {
 
 //name: getMolfiles
 //input: column col {semType: Macromolecule}
-//output: column res 
+//output: column res
 export function getMolfiles(col: DG.Column): DG.Column {
-  let grid = grok.shell.tv.grid;
-  let parent = grid.root.parentElement;
-  let res = DG.Column.string('mols', col.length);
+  const grid = grok.shell.tv.grid;
+  const parent = grid.root.parentElement;
+  const res = DG.Column.string('mols', col.length);
   const host = ui.div([]);
   parent.appendChild(host);
-  let editor = new JSDraw2.Editor(host, {viewonly: true});
+  const editor = new JSDraw2.Editor(host, {viewonly: true});
   host.style.width = '0px';
   host.style.height = '0px';
   res.init((i) => {
     editor.setHelm(col.get(i));
-    let mol = editor.getMolfile();
+    const mol = editor.getMolfile();
     return mol;
   });
   parent.lastChild.remove();