@datagrok/sequence-translator 1.10.13 → 1.10.14

package/files/tests/chem_enum_cores.csv

@@ -0,0 +1,5 @@
+Core
+n1nc([*:3])n([*:2])c1[*:1]
+C1C2CN([*:2])CC2CN1[*:1]
+OC1CN([*:2])CCC1N[*:1]
+CC1(N[*:1])CCN([*:2])C1

package/files/tests/chem_enum_rgroups.csv

@@ -0,0 +1,5 @@
+R1,R2,R3
+CC1CCN([*:1])C1C,O=C(C[*:2])NCC(F)(F)F,Cc1cccc([*:3])n1
+NCCC(=O)[*:1],O=C1NC(C(=O)[*:2])CO1,
+CC(=O)[*:1],O=C(CCCF)[*:2],
+O=C(c1cc[nH]n1)[*:1],c1ccc(C[*:2])nc1,

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.10.13",
+  "version": "1.10.14",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"

package/src/apps/structure/view/ui.ts

@@ -140,7 +140,7 @@ class StructureAppLayout {
     const clearBlock = Object.fromEntries(
       STRANDS.map(
         (key) => {
-          const clearIcon = ui.icons.delete(() => { coloredInput[key].inputBase.value = ''; });
+          const clearIcon = ui.icons.delete(() => { coloredInput[key].inputBase.value = ''; }, 'Delete');
           const clearButton = ui.button(clearIcon, () => {});
           ui.tooltip.bind(clearButton, `Clear ${key.toUpperCase()}`);
           return [key, clearIcon];

package/src/apps/translator/view/ui.ts

@@ -202,7 +202,7 @@ class TranslatorAppLayout {
     const formatChoiceInput = ui.div([this.formatChoiceInput]);
 
     const clearButton = ui.button(
-      ui.icons.delete(() => { sequenceColoredInput.inputBase.value = ''; }),
+      ui.icons.delete(() => { sequenceColoredInput.inputBase.value = ''; }, 'Delete'),
       () => {}
     );
     ui.tooltip.bind(clearButton, 'Clear input');

package/src/package-api.ts

@@ -102,6 +102,13 @@ export namespace funcs {
     return await grok.functions.call('SequenceTranslator:PolyToolEnumerateChemTopMenu', {});
   }
 
+  /**
+  Enumerate cores and R-group lists into a molecule table (Zip or Cartesian)
+  */
+  export async function chemEnumerateReactionsTopMenu(): Promise<void> {
+    return await grok.functions.call('SequenceTranslator:ChemEnumerateReactionsTopMenu', {});
+  }
+
   export async function polyToolColumnChoice(df: DG.DataFrame , macroMolecule: DG.Column ): Promise<void> {
     return await grok.functions.call('SequenceTranslator:PolyToolColumnChoice', { df, macroMolecule });
   }
@@ -114,7 +121,7 @@ export namespace funcs {
     return await grok.functions.call('SequenceTranslator:PtEnumeratorHelmApp', {});
   }
 
-  export async function ptEnumeratorChemApp(): Promise<void> {
+  export async function ptEnumeratorChemApp(): Promise<DG.View> {
     return await grok.functions.call('SequenceTranslator:PtEnumeratorChemApp', {});
   }
 

package/src/package-test.ts

@@ -13,6 +13,7 @@ import './tests/polytool-convert-tests';
 import './tests/polytool-unrule-tests';
 import './tests/polytool-enumerate-tests';
 import './tests/polytool-enumerate-breadth-tests';
+import './tests/polytool-enumerate-chem-tests';
 import './tests/polytool-chain-parse-notation-tests';
 import './tests/polytool-chain-from-notation-tests';
 import './tests/toAtomicLevel-tests';

package/src/package.g.ts

@@ -148,6 +148,13 @@ export async function polyToolEnumerateChemTopMenu() : Promise<void> {
   await PackageFunctions.polyToolEnumerateChemTopMenu();
 }
 
+//name: chemEnumerateReactions
+//description: Enumerate cores and R-group lists into a molecule table (Zip or Cartesian)
+//top-menu: Chem | Transform | Reactions | Enumerate...
+export async function chemEnumerateReactionsTopMenu() : Promise<void> {
+  await PackageFunctions.chemEnumerateReactionsTopMenu();
+}
+
 //input: dataframe df { description: Input data table }
 //input: column macroMolecule 
 export async function polyToolColumnChoice(df: DG.DataFrame, macroMolecule: DG.Column) : Promise<void> {
@@ -170,11 +177,12 @@ export async function ptEnumeratorHelmApp() : Promise<void> {
 
 //name: Chem Enumerator
 //tags: app
+//output: view result
 //meta.icon: img/icons/structure.png
-//meta.browsePath: Peptides | PolyTool
+//meta.browsePath: Chem | PolyTool
 //meta.role: app
-export async function ptEnumeratorChemApp() : Promise<void> {
-  await PackageFunctions.ptEnumeratorChemApp();
+export async function ptEnumeratorChemApp() {
+  return await PackageFunctions.ptEnumeratorChemApp();
 }
 
 //name: Polytool Helm Enumerator dialog

package/src/package.ts

@@ -17,7 +17,7 @@ import {getExternalAppViewFactories} from './plugins/mermade';
 import {defaultErrorHandler} from './utils/err-info';
 
 import {polyToolConvert, polyToolConvertUI} from './polytool/pt-dialog';
-import {polyToolEnumerateChemUI} from './polytool/pt-dialog';
+import {polyToolEnumerateChemApp, polyToolEnumerateChemUI} from './polytool/pt-chem-enum-dialog';
 import {polyToolEnumerateHelmUI, polyToolEnumerateSeq} from './polytool/pt-enumerate-seq-dialog';
 import {_setPeptideColumn} from './polytool/utils';
 import {PolyToolCsvLibHandler} from './polytool/csv-to-json-monomer-lib-converter';
@@ -276,6 +276,16 @@ export class PackageFunctions {
   }
 
 
+  @grok.decorators.func({
+    'top-menu': 'Chem | Transform | Reactions | Enumerate...',
+    'name': 'chemEnumerateReactions',
+    'description': 'Enumerate cores and R-group lists into a molecule table (Zip or Cartesian)'
+  })
+  static async chemEnumerateReactionsTopMenu(): Promise<void> {
+    polyToolEnumerateChemUI();
+  }
+
+
   @grok.decorators.func()
   static async polyToolColumnChoice(
     @grok.decorators.param({options: {description: 'Input data table'}}) df: DG.DataFrame,
@@ -314,14 +324,15 @@ export class PackageFunctions {
   @grok.decorators.func({
     meta: {
       icon: 'img/icons/structure.png',
-      browsePath: 'Peptides | PolyTool',
+      browsePath: 'Chem | PolyTool',
       role: 'app'
     },
     name: 'Chem Enumerator',
-    tags: ['app']
+    tags: ['app'],
+    outputs: [{type: 'view', name: 'result'}]
   })
-  static async ptEnumeratorChemApp(): Promise<void> {
-    polyToolEnumerateChemUI();
+  static async ptEnumeratorChemApp() {
+    return await polyToolEnumerateChemApp();
   }
 
 

package/src/polytool/const.ts

@@ -38,7 +38,7 @@ export const PT_UI_USE_CHIRALITY = 'Chirality engine';
 export const PT_UI_HIGHLIGHT_MONOMERS = 'Highlight monomers';
 export const PT_UI_DIALOG_CONVERSION = 'PolyTool Conversion';
 export const PT_UI_DIALOG_UNRULE = 'PolyTool Unrule';
-export const PT_UI_DIALOG_ENUMERATION = 'PolyTool Enumeration';
+export const PT_HELM_UI_DIALOG_ENUMERATION = 'PolyTool Helm Enumeration';
 export const PT_UI_RULES_USED = 'Rules used';
 
 export const PT_ENUM_TYPE_TOOLTIPS: Record<string, string> = {