@datagrok/helm 0.0.4 → 0.0.5

package/package.json

@@ -2,7 +2,7 @@
 	"name": "@datagrok/helm",
 	"beta": false,
 	"friendlyName": "Helm",
-	"version": "0.0.4",
+	"version": "0.0.5",
 	"description": "",
 	"dependencies": {
 		"datagrok-api": "latest",
@@ -24,7 +24,7 @@
 		"typescript": "latest"
 	},
 	"scripts": {
-		"link-all": "",
+		"link-all": "npm link datagrok-api  @datagrok-libraries/utils",
 		"debug-helm": "webpack && grok publish ",
 		"release-helm": "webpack && grok publish --release",
 		"build-helm": "webpack",
@@ -44,5 +44,6 @@
 		"type": "git",
 		"url": "https://github.com/datagrok-ai/public.git",
 		"directory": "packages/Helm"
-	}
+	},
+	"category": "Bioinformatics"
 }

package/src/package-test.ts

@@ -1,13 +1,18 @@
 import * as DG from "datagrok-api/dg";
 import * as grok from "datagrok-api/grok";
 import {runTests, tests} from '@datagrok-libraries/utils/src/test';
+import './tests/helm-tests.ts'
+
+export const _package = new DG.Package();
+export {tests};
 
-export let _package = new DG.Package();
-export {tests}
 
 //name: test
+//input: string category {optional: true}
+//input: string test {optional: true}
 //output: dataframe result
-export async function test(): Promise<DG.DataFrame> {
-  let data = await runTests();
+//top-menu: Tools | Dev | JS API Tests
+export async function test(category: string, test: string): Promise<DG.DataFrame> {
+  const data = await runTests({category, test});
   return DG.DataFrame.fromObjects(data)!;
-}
+}

package/src/package.ts

@@ -5,6 +5,7 @@ import * as DG from 'datagrok-api/dg';
 
 export const _package = new DG.Package();
 
+const lru = new DG.LruCache<any, any>(); 
 
 //tags: init
 export async function initChem(): Promise<void> {
@@ -17,56 +18,157 @@ export async function initChem(): Promise<void> {
 
 
 //name: helmCellRenderer
-//tags: cellRenderer,cellRenderer-HELM
-//meta.cellType: HELM
-//meta-cell-renderer-sem-type: HELM
+//tags: cellRenderer,cellRenderer-Macromolecule
+//meta.cellType: Macromolecule
+//meta-cell-renderer-sem-type: Macromolecule
 //output: grid_cell_renderer result
 export function helmCellRenderer(): DG.GridCellRenderer {
   return new HelmCellRenderer();
 }
 
 //tags: cellEditor
-//description: HELM
+//description: Macromolecule
 //input: grid_cell cell
 export function editMoleculeCell(cell: DG.GridCell): void {
   let view = ui.div();
-  let app: { canvas: { helm: { setSequence: (arg0: any, arg1: string) => void; }; }; };
-  setTimeout(function () {
-    //@ts-ignore
-    org.helm.webeditor.MolViewer.molscale = 0.8;
-    //@ts-ignore
-    app = new scil.helm.App(view, { showabout: false, mexfontsize: "90%", mexrnapinontab: true, topmargin: 20, mexmonomerstab: true, sequenceviewonly: false, mexfavoritefirst: true, mexfilter: true });
-  });
+  org.helm.webeditor.MolViewer.molscale = 0.8;
+  let app = new scil.helm.App(view, { showabout: false, mexfontsize: "90%", mexrnapinontab: true, topmargin: 20, mexmonomerstab: true, sequenceviewonly: false, mexfavoritefirst: true, mexfilter: true });
+  var sizes = app.calculateSizes();
+  app.canvas.resize(sizes.rightwidth, sizes.topheight - 210);
+  var s = { width: sizes.rightwidth + "px", height: sizes.bottomheight + "px" };
+  //@ts-ignore
+  scil.apply(app.sequence.style, s);
+  //@ts-ignore
+  scil.apply(app.notation.style, s);
+  s = { width: sizes.rightwidth + "px", height: (sizes.bottomheight + app.toolbarheight) + "px" };
+  //@ts-ignore
+  scil.apply(app.properties.parent.style, s);
+  app.structureview.resize(sizes.rightwidth, sizes.bottomheight + app.toolbarheight);
+  app.mex.resize(sizes.topheight - 80);
   setTimeout(function() {
-    //@ts-ignore
     app.canvas.helm.setSequence(cell.cell.value , 'HELM');
   }, 200);
-
-  let dlg = ui.dialog()
+  //@ts-ignore
+  ui.dialog({ showHeader: false, showFooter: true })
   .add(view)
   .onOK(() => {
-    view;
+    cell.cell.value = app.canvas.getHelm(true);
   }).show({ modal: true, fullScreen: true});
-  dlg.root.children[0].remove();
-  dlg.root.children[1].classList.remove('ui-panel'); 
-  dlg.root.children[1].classList.remove('ui-box');
+}
+
+//name: Details
+//tags: panel, widgets
+//input: string helmString {semType: Macromolecule}
+//output: widget result
+export function detailsPanel(helmString: string){
+  //return new DG.Widget(ui.divText(lru.get(helmString)));
+  var result = lru.get(helmString).split(',');
+  return new DG.Widget(
+    ui.tableFromMap({
+      'formula': result[0].replace(/<sub>/g, '').replace(/<\/sub>/g, ''),
+      'molecular weight': result[1],
+      'extinction coefficient': result[2],
+      'molfile': result[3],
+      'fasta': ui.wait(async () => ui.divText(await helmToFasta(helmString))),
+      'rna analogue sequence': ui.wait(async () => ui.divText(await helmToRNA(helmString))),
+      'smiles': ui.wait(async () => ui.divText(await helmToSmiles(helmString))),
+      'peptide analogue sequence': ui.wait(async () => ui.divText(await helmToPeptide(helmString))),
+    })
+  )
+}
+
+async function accessServer(url: string, key: string) {
+  const params: RequestInit = {
+    method: 'GET', 
+    headers: {
+      'Accept': 'application/json',
+    }
+  };
+  const response = await fetch(url, params);
+  const json = await response.json();
+  return json[key];
+}
+
+
+//name: helmToFasta
+//input: string helmString {semType: Macromolecule}
+//output: string res
+export async function helmToFasta(helmString: string) {
+  const url = `http://localhost:8081/WebService/service/Fasta/Produce/${helmString}`
+  return await accessServer(url, 'FastaFile');
+}
+
+//name: helmToRNA
+//description: converts to rna analogue sequence
+//input: string helmString {semType: Macromolecule}
+//output: string res
+export async function helmToRNA(helmString: string) {
+  const url = `http://localhost:8081/WebService/service/Fasta/Convert/RNA/${helmString}`
+  return await accessServer(url, 'Sequence');
+}
+
+
+//name: helmToPeptide
+//description: converts to peptide analogue sequence
+//input: string helmString {semType: Macromolecule}
+//output: string res
+export async function helmToPeptide(helmString: string) {
+  const url = `http://localhost:8081/WebService/service/Fasta/Convert/PEPTIDE/${helmString}`
+  return await accessServer(url, 'Sequence');
 }
 
 //name: helmToSmiles
-//tags: converter
+//description: converts to smiles
+//input: string helmString {semType: Macromolecule}
 //output: string smiles {semType: Molecule}
-export function helmToSmiles(helm: string): string {
-  //todo: call webservice
-  return 'foo';
+export async function helmToSmiles(helmString: string) {
+  const url = `http://localhost:8081/WebService/service/SMILES/${helmString}`
+  return await accessServer(url, 'SMILES');
 }
 
-//name: helmToFasta
-//tags: converter
-//output: string smiles {semType: fasta}
-export function helmToFasta(helm: string): string {
-  return 'foo';
+function getRS(smiles: string) {
+  var new_s = smiles.match(/(?<=\[)[^\][]*(?=])/gm);
+  var res = {};
+  var el = '';
+  var digit;
+  for (var i = 0; i < new_s.length; i++) {
+    if (new_s[i] != null){
+      if (/\d/.test(new_s[i])) {
+        digit = new_s[i][new_s[i].length - 1];
+        new_s[i] = new_s[i].replace(/[0-9]/g, '');
+        for (var j = 0; j < new_s[i].length; j++) {
+            if (new_s[i][j] != ':'){
+                el += new_s[i][j];
+            }
+        }
+        res['R' + digit] = el;
+        el = '';
+      }
+    }
+  }
+  return res;
 }
 
+//name: Monomer Manager
+//input: column helmColumn {semType: Macromolecule}
+export async function monomerManager(helmColumn: DG.Column) {
+  const file = await _package.files.readAsText('HELMCoreLibrary.json');
+  const df = DG.DataFrame.fromJson(file);
+  var m;
+  for (var i = 0; i < df.rowCount; i++){
+    m = {
+      'id': df.get('symbol', i).toString(), 
+      'n': df.get('name', i).toString(),
+      'na': df.get('naturalAnalog', i).toString(),
+      'type': df.get('polymerType', i).toString(),
+      'mt': df.get('monomerType', i).toString(), 
+      'm': df.get('molfile', i).toString(), 
+      rs: Object.keys(getRS(df.get('smiles', i).toString())).length,
+      at: getRS(df.get('smiles', i).toString()),
+    }
+    org.helm.webeditor.Monomers.addOneMonomer(m);
+  }
+}
 
 //name: helmColumnToSmiles
 //input: column helmColumn {semType: HELM}
@@ -74,14 +176,11 @@ export function helmColumnToSmiles(helmColumn: DG.Column) {
   //todo: add column with smiles to col.dataFrame.
 }
 
-// todo: "Details" panel (see Toxicity)
-// smiles, mol weight, mol formula, extinction coefficient, "combined"
-
 
 class HelmCellRenderer extends DG.GridCellRenderer {
 
-  get name() { return 'helm'; }
-  get cellType() { return 'helm'; }
+  get name() { return 'macromolecule'; }
+  get cellType() { return 'macromolecule'; }
   get defaultWidth(): number | null { return 400; }
   get defaultHeight(): number | null { return 100; }
 
@@ -91,7 +190,12 @@ class HelmCellRenderer extends DG.GridCellRenderer {
     host.setAttribute('data', gridCell.cell.value);
 
     gridCell.element = host;
-    // @ts-ignore
-    new JSDraw2.Editor(host, { width: w, height: h, skin: "w8", viewonly: true });
+    var canvas = new JSDraw2.Editor(host, { width: w, height: h, skin: "w8", viewonly: true });
+    var formula = canvas.getFormula(true);
+    var molWeight = Math.round(canvas.getMolWeight() * 100) / 100;
+    var coef = Math.round(canvas.getExtinctionCoefficient(true) * 100) / 100;
+    var molfile = canvas.getMolfile();
+    var result = formula + ', ' + molWeight + ', ' + coef + ', ' + molfile;
+    lru.set(gridCell.cell.value, result);
   }
 }

package/src/tests/helm-tests.ts

@@ -0,0 +1,35 @@
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import { helmToFasta, helmToPeptide, helmToRNA } from '../package';
+import { _package } from '../package-test';
+import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
+
+
+category('Helm', () => {
+
+  test('helmToFasta', async () => {
+    expect(await helmToFasta('RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$'), '>RNA1UTGCA');
+    expect(await helmToFasta('RNA1{P.R(U).P.R(T)}$$$$'), '>RNA1UT');
+    expect(await helmToFasta('PEPTIDE1{A.G}$$$$V2.0'), '>PEPTIDE1AG')
+  });
+
+  test('helmToRNA', async () => {
+    expect(await helmToRNA('RNA1{R(U)P.R(T)P.R(G)P.R(C)P.R(A)}$$$$'), 'UTGCA');
+    expect(await helmToRNA('RNA1{P.R(U).P.R(T)}$$$$'), 'UT');
+    expect(await helmToRNA('RNA1{R(U)P.R(T)P}|RNA2{P.R(A)P.R(A)}$RNA1,RNA2,2:pair-6:pair|RNA1,RNA2,5:pair-3:pair$$$'), 'UT AA');
+  });
+
+  test('helmToPeptide', async () => {
+    expect(await helmToPeptide('PEPTIDE1{A.G}$$$$V2.0'), 'AG');
+    expect(await helmToPeptide('PEPTIDE1{L.V.A}|PEPTIDE2{L.V.A}$$$$'), 'LVA LVA');
+    expect(await helmToPeptide('PEPTIDE1{A.R.C.A.A.K.T.C.D.A}$PEPTIDE1,PEPTIDE1,8:R3-3:R3$$$'), 'ARCAAKTCDA');
+  });
+
+  test('detectHelm', async () => {
+    const file = await _package.files.readAsText('test.csv')
+    const df = DG.DataFrame.fromCsv(file);
+    let col = df.columns.byName('HELM string');
+    await grok.data.detectSemanticTypes(df);
+    expect(col.semType, DG.SEMTYPE.HELM);
+  });
+});

package/tsconfig.json

@@ -7,7 +7,7 @@
     "target": "es6",                                /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
     "module": "es2020",                             /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
     "lib": ["es2020", "dom"],                       /* Specify library files to be included in the compilation. */
-    // "allowJs": true,                             /* Allow javascript files to be compiled. */
+    "allowJs": true,                             /* Allow javascript files to be compiled. */
     // "checkJs": true,                             /* Report errors in .js files. */
     // "jsx": "preserve",                           /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
     // "declaration": true,                         /* Generates corresponding '.d.ts' file. */
@@ -25,7 +25,7 @@
     // "isolatedModules": true,                     /* Transpile each file as a separate module (similar to 'ts.transpileModule'). */
 
     /* Strict Type-Checking Options */
-    "strict": true,                                 /* Enable all strict type-checking options. */
+    "strict": false,                                 /* Enable all strict type-checking options. */
     // "noImplicitAny": true,                       /* Raise error on expressions and declarations with an implied 'any' type. */
     // "strictNullChecks": true,                    /* Enable strict null checks. */
     // "strictFunctionTypes": true,                 /* Enable strict checking of function types. */

package/webpack.config.js

@@ -4,8 +4,12 @@ const packageName = path.parse(require('./package.json').name).name.toLowerCase(
 module.exports = {
   mode: 'development',
   entry: {
-    test: {filename: 'package-test.js', library: {type: 'var', name:`${packageName}_test`}, import: './src/package-test.ts'},
-    package: './src/package.ts'
+    package: './src/package.ts',
+    test: {
+      filename: 'package-test.js',
+      library: {type: 'var', name: `${packageName}_test`},
+      import: './src/package-test.ts',
+    },
   },
   resolve: {
     extensions: ['.wasm', '.mjs', '.js', '.json', '.ts', '.tsx'],