@datagrok/helm 0.0.5 → 1.0.0

package/package.json

@@ -1,49 +1,49 @@
 {
-	"name": "@datagrok/helm",
-	"beta": false,
-	"friendlyName": "Helm",
-	"version": "0.0.5",
-	"description": "",
-	"dependencies": {
-		"datagrok-api": "latest",
-		"cash-dom": "latest",
-		"dayjs": "latest",
-		"@datagrok-libraries/utils": "latest"
-	},
-	"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"
-	],
-	"devDependencies": {
-		"webpack": "latest",
-		"webpack-cli": "latest",
-		"ts-loader": "latest",
-		"typescript": "latest"
-	},
-	"scripts": {
-		"link-all": "npm link datagrok-api  @datagrok-libraries/utils",
-		"debug-helm": "webpack && grok publish ",
-		"release-helm": "webpack && grok publish --release",
-		"build-helm": "webpack",
-		"build": "webpack",
-		"debug-helm-dev": "grok publish dev --rebuild",
-		"release-helm-dev": "grok publish dev --rebuild --release",
-		"debug-helm-public": "grok publish public --rebuild",
-		"release-helm-public": "grok publish public --rebuild --release"
-	},
-	"canEdit": [
-		"Developers"
-	],
-	"canView": [
-		"All users"
-	],
-	"repository": {
-		"type": "git",
-		"url": "https://github.com/datagrok-ai/public.git",
-		"directory": "packages/Helm"
-	},
-	"category": "Bioinformatics"
+  "name": "@datagrok/helm",
+  "beta": false,
+  "friendlyName": "Helm",
+  "version": "1.0.0",
+  "description": "",
+  "dependencies": {
+    "datagrok-api": "^1.4.12",
+    "cash-dom": "latest",
+    "dayjs": "latest",
+    "@datagrok-libraries/utils": "latest <1.2.0"
+  },
+  "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"
+  ],
+  "devDependencies": {
+    "webpack": "latest",
+    "webpack-cli": "latest",
+    "ts-loader": "latest",
+    "typescript": "latest"
+  },
+  "scripts": {
+    "link-all": "npm link datagrok-api  @datagrok-libraries/utils",
+    "debug-helm": "webpack && grok publish ",
+    "release-helm": "webpack && grok publish --release",
+    "build-helm": "webpack",
+    "build": "webpack",
+    "debug-helm-dev": "grok publish dev --rebuild",
+    "release-helm-dev": "grok publish dev --rebuild --release",
+    "debug-helm-public": "grok publish public --rebuild",
+    "release-helm-public": "grok publish public --rebuild --release"
+  },
+  "canEdit": [
+    "Developers"
+  ],
+  "canView": [
+    "All users"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/datagrok-ai/public.git",
+    "directory": "packages/Helm"
+  },
+  "category": "Bioinformatics"
 }

package/src/package.ts

@@ -16,16 +16,6 @@ export async function initChem(): Promise<void> {
   });
 }
 
-
-//name: helmCellRenderer
-//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: Macromolecule
 //input: grid_cell cell
@@ -69,14 +59,38 @@ export function detailsPanel(helmString: string){
       'molecular weight': result[1],
       'extinction coefficient': result[2],
       'molfile': result[3],
-      'fasta': ui.wait(async () => ui.divText(await helmToFasta(helmString))),
+      /*'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))),
+      'peptide analogue sequence': ui.wait(async () => ui.divText(await helmToPeptide(helmString))),*/
     })
   )
 }
 
+
+async function loadDialog () {
+  //@ts-ignore
+  let res = await grok.dapi.files.list('System:AppData/Helm', false, '');
+  //@ts-ignore
+  res = res.map((e) => e.path);
+  //@ts-ignore
+  let FilesList = await ui.choiceInput('Monomer Libraries', ' ', res);
+  ui.dialog('Load library from file')
+  .add(FilesList)
+  .onOK(() => monomerManager(FilesList.value)).show();
+};
+
+//name: Library
+//tags: panel, widgets
+//input: string helmString {semType: Macromolecule}
+//output: widget result
+export function libraryPanel(helmString: string) {
+  //@ts-ignore
+  let loadButton = ui.button('Load Library');
+  loadButton.addEventListener('click', loadDialog);
+  return new DG.Widget(ui.divH([loadButton]));
+}
+
 async function accessServer(url: string, key: string) {
   const params: RequestInit = {
     method: 'GET', 
@@ -149,10 +163,8 @@ function getRS(smiles: string) {
   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');
+async function monomerManager(value: string) {
+  const file = await _package.files.readAsText(value.split('/')[1]);
   const df = DG.DataFrame.fromJson(file);
   var m;
   for (var i = 0; i < df.rowCount; i++){
@@ -171,11 +183,26 @@ export async function monomerManager(helmColumn: DG.Column) {
 }
 
 //name: helmColumnToSmiles
-//input: column helmColumn {semType: HELM}
+//input: column helmColumn {semType: Macromolecule}
 export function helmColumnToSmiles(helmColumn: DG.Column) {
   //todo: add column with smiles to col.dataFrame.
 }
 
+//name: findMonomers
+//input: string helmString { semType: Macromolecule }
+export async function findMonomers(helmString: string) {
+  const types = Object.keys(org.helm.webeditor.monomerTypeList());
+  const monomers = [];
+  const monomer_names = [];
+  for (var i = 0; i < types.length; i++) {
+    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 = helmString.match(/[^\s.,\/\\(){}$]+/gim);
+  return new Set(split_string.filter(val => !monomer_names.includes(val)));
+}
 
 class HelmCellRenderer extends DG.GridCellRenderer {
 

package/src/tests/helm-tests.ts

@@ -25,11 +25,19 @@ category('Helm', () => {
     expect(await helmToPeptide('PEPTIDE1{A.R.C.A.A.K.T.C.D.A}$PEPTIDE1,PEPTIDE1,8:R3-3:R3$$$'), 'ARCAAKTCDA');
   });
 
+  test('detectMacromolecule', 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.MACROMOLECULE);
+  });
+
   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);
+    expect(col.tags[DG.TAGS.UNITS], "HELM");
   });
 });