@datagrok/sequence-translator 1.9.9 → 1.9.11

package/files/polytool-rules/rules_example.json

@@ -4,13 +4,13 @@
   "linkRules": [
     {
       "firstMonomers": [
-        "NH2"
+        "D"
       ],
       "secondMonomers": [
-        "D"
+        "NH2"
       ],
-      "firstLinkingGroup": "2",
-      "secondLinkingGroup": "3",
+      "firstLinkingGroup": "3",
+      "secondLinkingGroup": "2",
       "code": "2"
     },
     {

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.9.9",
+  "version": "1.9.11",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -22,10 +22,10 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.54.6",
+    "@datagrok-libraries/bio": "^5.54.8",
     "@datagrok-libraries/chem-meta": "^1.2.8",
     "@datagrok-libraries/tutorials": "^1.6.1",
-    "@datagrok-libraries/utils": "^4.5.7",
+    "@datagrok-libraries/utils": "^4.6.3",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
     "datagrok-api": "^1.25.0",
@@ -54,7 +54,7 @@
     "@typescript-eslint/eslint-plugin": "^7.2.0",
     "@typescript-eslint/parser": "^7.2.0",
     "css-loader": "^6.7.3",
-    "datagrok-tools": "^4.14.20",
+    "datagrok-tools": "^4.14.48",
     "eslint": "^8.57.0",
     "eslint-config-google": "^0.14.0",
     "style-loader": "^3.3.1",

package/src/demo/demo-st-ui.ts

@@ -3,19 +3,19 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {delay} from '@datagrok-libraries/utils/src/test';
-import {oligoTranslatorApp, oligoPatternApp, oligoStructureApp} from '../package';
+import {PackageFunctions} from '../package';
 import {tryCatch} from '../apps/common/model/helpers';
 
 export async function demoOligoTranslatorUI() {
   await tryCatch(async () => {
-    const view = await oligoTranslatorApp();
+    const view = await PackageFunctions.oligoTranslatorApp();
     grok.shell.addView(view);
   });
 }
 
 export async function demoOligoPatternUI() {
   await tryCatch(async () => {
-    const view = await oligoPatternApp();
+    const view = await PackageFunctions.oligoPatternApp();
     grok.shell.addView(view);
   });
 }
@@ -31,7 +31,7 @@ export async function demoOligoStructureUI() {
       textarea.dispatchEvent(event);
     }
 
-    const view = await oligoStructureApp();
+    const view = await PackageFunctions.oligoStructureApp();
     grok.shell.addView(view);
     const inputSequences = ['Afcgacsu', 'Afcgacsu', 'Afcgacsu'];
     inputSequences.forEach(async (sequence, idx) => {

package/src/package-api.ts

@@ -8,14 +8,14 @@ import * as DG from 'datagrok-api/dg';
 
 
 export namespace funcs {
-  export async function init(): Promise<void> {
-    return await grok.functions.call('SequenceTranslator:Init', {});
-  }
-
   export async function oligoToolkitApp(): Promise<DG.View> {
     return await grok.functions.call('SequenceTranslator:OligoToolkitApp', {});
   }
 
+  export async function init(): Promise<void> {
+    return await grok.functions.call('SequenceTranslator:Init', {});
+  }
+
   export async function oligoTranslatorApp(): Promise<DG.View> {
     return await grok.functions.call('SequenceTranslator:OligoTranslatorApp', {});
   }

package/src/package.g.ts

@@ -0,0 +1,195 @@
+import {PackageFunctions} from './package';
+import * as DG from 'datagrok-api/dg';
+
+//name: Oligo Toolkit
+//tags: app
+//output: view result
+//meta.icon: img/icons/toolkit.png
+//meta.browsePath: Peptides | Oligo Toolkit
+export async function oligoToolkitApp() : Promise<any> {
+  return await PackageFunctions.oligoToolkitApp();
+}
+
+//tags: init
+export async function init() : Promise<void> {
+  await PackageFunctions.init();
+}
+
+//name: Oligo Translator
+//tags: app
+//output: view result
+//meta.icon: img/icons/translator.png
+//meta.browsePath: Peptides | Oligo Toolkit
+export async function oligoTranslatorApp() : Promise<any> {
+  return await PackageFunctions.oligoTranslatorApp();
+}
+
+//name: Oligo Pattern
+//tags: app
+//output: view result
+//meta.icon: img/icons/pattern.png
+//meta.browsePath: Peptides | Oligo Toolkit
+export async function oligoPatternApp() : Promise<any> {
+  return await PackageFunctions.oligoPatternApp();
+}
+
+//name: Oligo Structure
+//tags: app
+//output: view result
+//meta.icon: img/icons/structure.png
+//meta.browsePath: Peptides | Oligo Toolkit
+export async function oligoStructureApp() : Promise<any> {
+  return await PackageFunctions.oligoStructureApp();
+}
+
+//output: object result
+export async function getTranslationHelper() : Promise<any> {
+  return await PackageFunctions.getTranslationHelper();
+}
+
+//output: object result
+export function getCodeToWeightsMap() : any {
+  return PackageFunctions.getCodeToWeightsMap();
+}
+
+//input: string sequence 
+//output: bool result
+export function validateSequence(sequence: string) : boolean {
+  return PackageFunctions.validateSequence(sequence);
+}
+
+//name: validateSequence
+//input: string sequence 
+//input: bool invert 
+//output: string result
+export function getMolfileFromGcrsSequence(sequence: string, invert: boolean) : string {
+  return PackageFunctions.getMolfileFromGcrsSequence(sequence, invert);
+}
+
+//input: object strands 
+//output: string result
+export function linkStrands(strands: any) : string {
+  return PackageFunctions.linkStrands(strands);
+}
+
+//name: demoOligoTranslator
+//description: Translate oligonucleotide sequences across various formats accepted by different synthesizers
+//meta.demoPath: Bioinformatics | Oligo Toolkit | Translator
+//meta.path: /apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Translate
+//meta.demoSkip: GROK-14320
+export async function demoTranslateSequence() : Promise<void> {
+  await PackageFunctions.demoTranslateSequence();
+}
+
+//description: Design a modification pattern for an oligonucleotide sequence
+//meta.demoPath: Bioinformatics | Oligo Toolkit | Pattern
+//meta.path: %20/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Visualize%20duplex
+export async function demoOligoPattern() : Promise<void> {
+  await PackageFunctions.demoOligoPattern();
+}
+
+//description: Visualize duplex and save SDF
+//meta.demoPath: Bioinformatics | Oligo Toolkit | Structure
+//meta.path: %20/apps/Tutorials/Demo/Bioinformatics/Oligonucleotide%20Sequence:%20Visualize%20duplex
+export async function demoOligoStructure() : Promise<void> {
+  await PackageFunctions.demoOligoStructure();
+}
+
+//input: string sequence 
+//input: string sourceFormat 
+//input: string targetFormat 
+//output: string result
+export async function translateOligonucleotideSequence(sequence: string, sourceFormat: string, targetFormat: string) : Promise<string> {
+  return await PackageFunctions.translateOligonucleotideSequence(sequence, sourceFormat, targetFormat);
+}
+
+//name: polyToolConvert
+//description: Perform cyclization of polymers
+//top-menu: Bio | PolyTool | Convert...
+export async function polyToolConvertTopMenu() : Promise<void> {
+  await PackageFunctions.polyToolConvertTopMenu();
+}
+
+//tags: editor
+//input: funccall call 
+//output: column result
+export async function getPolyToolConvertEditor(call: DG.FuncCall) : Promise<any> {
+  return await PackageFunctions.getPolyToolConvertEditor(call);
+}
+
+//input: dataframe table 
+//input: column seqCol { caption: Sequence }
+//input: bool generateHelm { default: true }
+//input: bool chiralityEngine { default: true }
+//input: object rules 
+//output: column result
+//editor: SequenceTranslator:getPolyToolConvertEditor
+export async function polyToolConvert2(table: DG.DataFrame, seqCol: DG.Column, generateHelm: boolean, chiralityEngine: boolean, rules: string[]) : Promise<any> {
+  return await PackageFunctions.polyToolConvert2(table, seqCol, generateHelm, chiralityEngine, rules);
+}
+
+//name: polyToolEnumerateHelm
+//description: Perform cyclization of polymers
+//top-menu: Bio | PolyTool | Enumerate HELM...
+export async function polyToolEnumerateHelmTopMenu() : Promise<void> {
+  await PackageFunctions.polyToolEnumerateHelmTopMenu();
+}
+
+//name: polyToolEnumerateChem
+//description: Perform cyclization of polymers
+//top-menu: Bio | PolyTool | Enumerate Chem...
+export async function polyToolEnumerateChemTopMenu() : Promise<void> {
+  await PackageFunctions.polyToolEnumerateChemTopMenu();
+}
+
+//input: dataframe df { description: Input data table }
+//input: column macroMolecule 
+export async function polyToolColumnChoice(df: DG.DataFrame, macroMolecule: DG.Column) : Promise<void> {
+  await PackageFunctions.polyToolColumnChoice(df, macroMolecule);
+}
+
+//input: file file 
+export async function createMonomerLibraryForPolyTool(file: DG.FileInfo) : Promise<void> {
+  await PackageFunctions.createMonomerLibraryForPolyTool(file);
+}
+
+//name: HELM Enumerator
+//tags: app
+//meta.icon: img/icons/structure.png
+//meta.browsePath: Peptides | PolyTool
+export async function ptEnumeratorHelmApp() : Promise<void> {
+  await PackageFunctions.ptEnumeratorHelmApp();
+}
+
+//name: Chem Enumerator
+//tags: app
+//meta.icon: img/icons/structure.png
+//meta.browsePath: Peptides | PolyTool
+export async function ptEnumeratorChemApp() : Promise<void> {
+  await PackageFunctions.ptEnumeratorChemApp();
+}
+
+//name: Polytool Helm Enumerator dialog
+//input: object cell { nullable: true }
+export async function getPtHelmEnumeratorDialog(cell?: any) : Promise<void> {
+  await PackageFunctions.getPtHelmEnumeratorDialog(cell);
+}
+
+//name: Polytool Chem Enumerator dialog
+//input: object cell { nullable: true }
+export async function getPtChemEnumeratorDialog(cell?: any) : Promise<void> {
+  await PackageFunctions.getPtChemEnumeratorDialog(cell);
+}
+
+//name: Combine Sequences
+//top-menu: Bio | PolyTool | Combine Sequences...
+export async function getPolyToolCombineDialog() : Promise<void> {
+  await PackageFunctions.getPolyToolCombineDialog();
+}
+
+//name: applyNotationProviderForHarmonizedSequence
+//input: column col 
+//input: string separator 
+export function applyNotationProviderForCyclized(col: DG.Column<any>, separator: string) : void {
+  PackageFunctions.applyNotationProviderForCyclized(col, separator);
+}