@datagrok/sequence-translator 1.3.10 → 1.3.11

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.3.10",
+  "version": "1.3.11",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"

package/src/package.ts

@@ -16,12 +16,12 @@ import {demoOligoPatternUI, demoOligoStructureUI, demoOligoTranslatorUI} from '.
 import {getExternalAppViewFactories} from './plugins/mermade';
 
 //polytool specific
-import {getPolyToolConversionDialog} from './polytool/pt-dialog';
+import {getPolyToolConversionDialog, polyToolEnumerateHelmUI, polyToolEnumerateChemUI} from './polytool/pt-dialog';
 import {_setPeptideColumn} from './polytool/utils';
 import {PolyToolCsvLibHandler} from './polytool/csv-to-json-monomer-lib-converter';
 import {ITranslationHelper} from './types';
-import {polyToolEnumerateHelmUI, polyToolEnumerateChemUI} from './polytool/pt-ui';
 import {addContextMenuUI} from './utils/context-menu';
+import { NOTATION } from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 
 export const _package: OligoToolkitPackage = new OligoToolkitPackage();
 
@@ -172,12 +172,12 @@ export async function polyToolEnumerateHelm(): Promise<void> {
   polyToolEnumerateHelmUI();
 }
 
-// //top-menu: Bio | Convert | PolyTool-Enumerate Chem
-// //name: polyToolEnumerateChem
-// //description: Perform cyclization of polymers
-// export async function polyToolEnumerateChem(): Promise<void> {
-//   polyToolEnumerateChemUI();
-// }
+//top-menu: Bio | Convert | PolyTool-Enumerate Chem
+//name: polyToolEnumerateChem
+//description: Perform cyclization of polymers
+export async function polyToolEnumerateChem(): Promise<void> {
+  polyToolEnumerateChemUI();
+}
 
 //name: polyToolColumnChoice
 //input: dataframe df [Input data table]
@@ -210,28 +210,40 @@ export function addContextMenu(event: DG.EventData): void {
 // //meta.icon: img/icons/structure.png
 // //meta.browsePath: PolyTool
 // //tags: app
-// //output: view v
-// export async function ptConverterApp(): Promise<DG.ViewBase> {
-//   const view = await getSpecifiedAppView(APP_NAME.STRUCTURE);
-//   return view;
+// export async function ptConverterApp(): Promise<void> {
+//   const view = grok.shell.v as DG.TableView;
+//   const table = view.dataFrame;
+//   const colNames = table.columns.names(); 
+//   let covertableName = '';
+
+//   for (let i = 0; i < colNames.length; i++) {
+//     const col = table.columns.byName(colNames[i]);
+//     if (col.semType === DG.SEMTYPE.MACROMOLECULE && col.meta.units === NOTATION.SEPARATOR) {
+//       covertableName = colNames[i];
+//       break;
+//     }
+//   }
+
+//   if (covertableName === '')
+//     grok.shell.error('To run the app open a view with convertable separator notation for macromolecules');
+//   else {
+//     const dialog = await getPolyToolConversionDialog();
+//     dialog.show();
+//   }  
 // }
 
-// //name: PolyTool Enumerator Helm
-// //meta.icon: img/icons/structure.png
-// //meta.browsePath: PolyTool
-// //tags: app
-// //output: view v
-// export async function ptEnumeratorHelmApp(): Promise<DG.ViewBase> {
-//   const view = await getSpecifiedAppView(APP_NAME.STRUCTURE);
-//   return view;
-// }
+//name: PolyTool Enumerator Helm
+//meta.icon: img/icons/structure.png
+//meta.browsePath: PolyTool
+//tags: app
+export async function ptEnumeratorHelmApp(): Promise<void> {
+  polyToolEnumerateHelmUI();
+}
 
-// //name: PolyTool Enumerator Chem
-// //meta.icon: img/icons/structure.png
-// //meta.browsePath: PolyTool
-// //tags: app
-// //output: view v
-// export async function ptEnumeratorChemApp(): Promise<DG.ViewBase> {
-//   const view = await getSpecifiedAppView(APP_NAME.STRUCTURE);
-//   return view;
-// }
+//name: PolyTool Enumerator Chem
+//meta.icon: img/icons/structure.png
+//meta.browsePath: PolyTool
+//tags: app
+export async function ptEnumeratorChemApp(): Promise<void> {
+  polyToolEnumerateChemUI();
+}

package/src/polytool/pt-dialog.ts

@@ -28,7 +28,27 @@ const PT_UI_DIALOG_CONVERSION = 'Poly Tool Conversion';
 const PT_UI_DIALOG_ENUMERATION = 'Poly Tool Enumeration';
 const PT_UI_RULES_USED = 'Rules used';
 
-export async function getPolyToolConversionDialog(): Promise<DG.Dialog> {
+export function polyToolEnumerateHelmUI(cell?: DG.Cell): void {
+  getPolyToolEnumerationHelmDialog(cell)
+    .then((dialog) => {
+      dialog.show({resizable: true});
+    })
+    .catch((_err: any) => {
+      grok.shell.warning('To run PolyTool Enumeration, sketch the macromolecule and select monomers to vary');
+    });
+}
+
+export function polyToolEnumerateChemUI(cell?: DG.Cell): void {
+  getPolyToolEnumerationChemDialog(cell)
+    .then((dialog) => {
+      dialog.show({resizable: true});
+    })
+    .catch((_err: any) => {
+      grok.shell.warning('To run PolyTool Enumeration, sketch the molecule and specify the R group to vary');
+    });
+}
+
+export async function getPolyToolConversionDialog(targetCol?: DG.Column): Promise<DG.Dialog> {
   const targetColumns = grok.shell.t.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
   if (!targetColumns)
     throw new Error(PT_ERROR_DATAFRAME);
@@ -38,6 +58,8 @@ export async function getPolyToolConversionDialog(): Promise<DG.Dialog> {
     filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE
   });
 
+  targetColumnInput.value = targetCol ? targetCol : targetColumnInput.value;
+
   const generateHelmChoiceInput = ui.input.bool(PT_UI_GET_HELM, {value: true});
   ui.tooltip.bind(generateHelmChoiceInput.root, PT_UI_ADD_HELM);
 
@@ -82,7 +104,7 @@ export async function getPolyToolConversionDialog(): Promise<DG.Dialog> {
   return dialog;
 }
 
-export async function getPolyToolEnumerationHelmDialog(cell?: DG.Cell): Promise<DG.Dialog> {
+async function getPolyToolEnumerationHelmDialog(cell?: DG.Cell): Promise<DG.Dialog> {
   const [libList, helmHelper] = await Promise.all([
     getLibrariesList(), getHelmHelper()]);
 
@@ -137,7 +159,7 @@ export async function getPolyToolEnumerationHelmDialog(cell?: DG.Cell): Promise<
   return dialog;
 }
 
-export async function getPolyToolEnumerationChemDialog(cell?: DG.Cell): Promise<DG.Dialog> {
+async function getPolyToolEnumerationChemDialog(cell?: DG.Cell): Promise<DG.Dialog> {
   const [libList, helmHelper] = await Promise.all([
     getLibrariesList(), getHelmHelper()]);
 
@@ -147,9 +169,6 @@ export async function getPolyToolEnumerationChemDialog(cell?: DG.Cell): Promise<
   // sketcher.setMolFile(col.tags[ALIGN_BY_SCAFFOLD_TAG]);
   molInput.onChanged.subscribe((_: any) => {
     molValue = molInput.getMolFile();
-    // col.tags[ALIGN_BY_SCAFFOLD_TAG] = molFile;
-    // col.temp[ALIGN_BY_SCAFFOLD_TAG] = molFile;
-    // col.dataFrame?.fireValuesChanged();
   });
   molInput.root.classList.add('ui-input-editor');
   molInput.root.style.marginTop = '3px';

package/src/polytool/pt-enumeration-chem.ts

@@ -29,7 +29,7 @@ export const PT_CHEM_EXAMPLE = `
     2.4544    0.4877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    -1.8175   -1.9896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    -3.2453    0.4877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    3.1670    1.7285    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
+    3.1670    1.7285    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
     1.7149    2.5513    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
   2  1  2  0  0  0  0
   3  1  1  0  0  0  0
@@ -55,18 +55,15 @@ export const PT_CHEM_EXAMPLE = `
  14 10  1  0  0  0  0
  15 21  1  0  0  0  0
  12 22  1  0  0  0  0
-M  RGP  2  21   1  22   2
+M  RGP  1  22   1
 M  END`;
 
 export async function getEnumerationChem(molString: string, screenLibrary: string):
   Promise<string[]> {
+
   const variableMonomers = await getAvailableMonomers(screenLibrary);
   const variableMols = await getAvailableMonomerMols(screenLibrary);
-
-	const idx = molString.indexOf('M  RGP');
-	const rCount = parseInt(molString.slice(idx + 6, idx + 9)); //extracting from molfile positions
-  const size = 1 * variableMonomers.length;
-  const enumerations = new Array<string>(size);
+  const enumerations = new Array<string>(variableMonomers.length);
 
 	const rdkitModule: RDModule = await grok.functions.call('Chem:getRdKitModule');
   const molScaffold: RDMol = rdkitModule.get_mol(molString);
@@ -84,22 +81,39 @@ export async function getEnumerationChem(molString: string, screenLibrary: strin
     molSubst.delete();
   }
 
-	//TODO: get for all R groups
-  for (let i = 0; i < 1; i++) {
-    for (let j = 0; j < variableMonomers.length; j++) {
-      try {
-        const smiResRaw = `${smiScaffold}.${smilesSubsts[j]}`.replaceAll('[1*]C', 'C([1*])').replaceAll('[1*]c', 'c([1*])').replaceAll('[1*]O', 'O([1*])').replaceAll('[1*]N', 'N([1*])');
-        const smiRes = `${smiResRaw}`.replaceAll('([1*])', '9').replaceAll('[1*]', '9');
-        const molRes: RDMol = rdkitModule.get_mol(smiRes);
-
-        enumerations[i * variableMonomers.length + j] = molRes.get_v3Kmolblock();
-        molRes.delete();
-      } 
-      catch(err:any) {
-        enumerations[i * variableMonomers.length + j] = '';
+  for (let i = 0; i < variableMonomers.length; i++) {
+    let molRes: RDMol | null = null;
+    try {
+      //TODO: use RDKit linking function when exposed
+      const smiResRaw = `${smiScaffold}.${smilesSubsts[i]}`.replaceAll('[1*]C', 'C([1*])').replaceAll('[1*]c', 'c([1*])').replaceAll('[1*]O', 'O([1*])').replaceAll('[1*]N', 'N([1*])');
+      const smiRes = `${smiResRaw}`.replaceAll('([1*])', '9').replaceAll('[1*]', '9');
+      molRes = rdkitModule.get_mol(smiRes);
+      let molV3 = molRes.get_v3Kmolblock();
+
+
+      //TODO: use RDKit when MASS problem is solved
+      while(molV3.includes('MASS')) {
+
+        //MASS=2 VAL=1
+        //RGROUPS=(1 2)
+        const idx = molV3.indexOf('MASS');
+        const rNum = parseInt(molV3.slice(idx + 5, idx + 6));
+        const replace = `RGROUPS=(1 ${rNum})`;
+        molV3 = molV3.substring(0, idx) + replace + molV3.substring(idx + 12);
       }
-		}
+
+      molV3 = molV3.replaceAll('R ', 'R# ')
+
+      enumerations[i] = molV3;
+    } 
+    catch(err:any) {
+      enumerations[i] = '';
+    }
+    finally {
+      molRes?.delete();
+    }
   }
+  
 
   return enumerations;
 }

package/src/utils/context-menu.ts

@@ -6,7 +6,7 @@ import {defaultErrorHandler} from './err-info';
 import {_package, addContextMenu} from '../package';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {polyToolEnumerateHelmUI} from '../polytool/pt-ui';
+import {polyToolEnumerateHelmUI} from '../polytool/pt-dialog';
 
 export type SequenceTranslatorWindowType = Window & {
   $sequenceTranslator?: {

package/src/polytool/pt-ui.ts

@@ -1,25 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as DG from 'datagrok-api/dg';
-import * as ui from 'datagrok-api/ui';
-
-import {getPolyToolEnumerationHelmDialog, getPolyToolEnumerationChemDialog} from './pt-dialog';
-
-export function polyToolEnumerateHelmUI(cell?: DG.Cell): void {
-  getPolyToolEnumerationHelmDialog(cell)
-    .then((dialog) => {
-      dialog.show({resizable: true});
-    })
-    .catch((_err: any) => {
-      grok.shell.warning('To run PolyTool Enumeration, sketch the macromolecule and select monomers to vary');
-    });
-}
-
-export function polyToolEnumerateChemUI(cell?: DG.Cell): void {
-  getPolyToolEnumerationChemDialog(cell)
-    .then((dialog) => {
-      dialog.show({resizable: true});
-    })
-    .catch((_err: any) => {
-      grok.shell.warning('To run PolyTool Enumeration, sketch the molecule and specify the R group to vary');
-    });
-}