@datagrok/sequence-translator 1.3.11 → 1.3.13

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.3.11",
+  "version": "1.3.13",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"
@@ -22,10 +22,10 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "5.42.5",
+    "@datagrok-libraries/bio": "^5.42.11",
     "@datagrok-libraries/chem-meta": "^1.2.5",
-    "@datagrok-libraries/tutorials": "^1.3.12",
-    "@datagrok-libraries/utils": "^4.2.13",
+    "@datagrok-libraries/tutorials": "^1.3.13",
+    "@datagrok-libraries/utils": "^4.2.29",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
     "datagrok-api": "^1.20.0",
@@ -39,10 +39,11 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.6",
-    "@datagrok-libraries/js-draw-lite": "^0.0.4",
-    "@datagrok/bio": "^2.13.3",
-    "@datagrok/chem": "1.9.2",
+    "@datagrok-libraries/helm-web-editor": "^1.1.10",
+    "@datagrok-libraries/js-draw-lite": "^0.0.8",
+    "@datagrok/bio": "^2.14.2",
+    "@datagrok/helm": "^2.4.4",
+    "@datagrok/chem": "^1.11.3",
     "@types/jquery": "^3.5.14",
     "@types/js-yaml": "^4.0.5",
     "@types/lodash": "^4.14.202",

package/src/apps/common/model/oligo-toolkit-package.ts

@@ -4,6 +4,7 @@ import * as DG from 'datagrok-api/dg';
 
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
+import {LoggerWrapper} from '@datagrok-libraries/bio/src/utils/logger';
 
 import {APP_NAME} from '../view/const';
 import {DEFAULT_LIB_FILENAME, FALLBACK_LIB_PATH} from './data-loader/const';
@@ -12,7 +13,6 @@ import {ITranslationHelper} from '../../../types';
 import {SequenceValidator} from './parsing-validation/sequence-validator';
 import {JsonData, loadJsonData} from './data-loader/json-loader';
 import {MonomerLibWrapper} from './monomer-lib/lib-wrapper';
-import {_package} from '../../../package';
 import {FormatConverter} from '../../translator/model/format-converter';
 import {FormatDetector} from './parsing-validation/format-detector';
 import {highlightInvalidSubsequence} from '../view/components/colored-input/input-painters';
@@ -39,8 +39,10 @@ export class OligoToolkitPackage extends DG.Package implements ITranslationHelpe
     return this._monomerLibWrapper;
   }
 
-  constructor() {
+  constructor(opts: { debug: boolean } = {debug: false}) {
     super();
+    // @ts-ignore
+    super._logger = new LoggerWrapper(super.logger, opts.debug);
   }
 
   private initPromise?: Promise<void>;
@@ -51,7 +53,7 @@ export class OligoToolkitPackage extends DG.Package implements ITranslationHelpe
         const packageSettings = await this.getSettings();
         let monomersPath: string = packageSettings['MonomersPath'];
         if (!monomersPath || !(await grok.dapi.files.exists(monomersPath))) {
-          _package.logger.warning(`Monomers path '${monomersPath}' not found. ` +
+          this.logger.warning(`Monomers path '${monomersPath}' not found. ` +
             `Fallback to monomers sample path '${FALLBACK_LIB_PATH}'.`);
           monomersPath = FALLBACK_LIB_PATH;
         }

package/src/apps/common/view/components/colored-input/style.css

@@ -25,4 +25,5 @@
   color: transparent;
   white-space: pre-wrap;
   word-wrap: break-word;
+  padding-left: 35px;
 }

package/src/apps/structure/view/style.css

@@ -4,25 +4,6 @@
   padding-right: 20px;
 }
 
-.st-structure-input-form {
-  text-align: right;
-  vertical-align: top;
-  min-width: 95px;
-}
-
-.st-structure-direction-choice label {
-  min-width: 100px;
-  float: right;
-}
-
-.st-structure-direction-choice div {
-  justify-content: right;
-}
-
-.st-structure-text-input-td { /* Style for td containing textarea */
-  width: 100%;
-}
-
 .st-structure-mol-img {
   margin-right: 30px;
   float: right;
@@ -37,3 +18,17 @@
   flex-direction: row-reverse;
   padding-top: 20px;
 }
+
+.st-structure-clear-buttons {
+  justify-content: space-between;
+  padding: 13px 10px 13px 10px;
+}
+
+.st-direction-inputs {
+  align-items: end;
+}
+
+.st-structure-inputs {
+  flex-grow: 2;
+  padding-left: 10px;
+}

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

@@ -33,7 +33,7 @@ class StructureAppLayout {
     this.onInvalidInput = new rxjs.Subject<string>();
     this.inputBase = Object.fromEntries(
       STRANDS.map(
-        (key) => [key, ui.input.textArea('', {value: '', onValueChanged: () => { this.onInput.next(); }})]
+        (key) => [key, ui.input.textArea(key.toUpperCase(), {value: '', onValueChanged: () => { this.onInput.next(); }})]
       )
     );
     this.useChiralInput = ui.input.bool('Use chiral', {value: true});
@@ -91,7 +91,7 @@ class StructureAppLayout {
     return boolInputsAndButton;
   }
 
-  private getTableInput(th: ITranslationHelper): HTMLTableElement {
+  private getTableInput(th: ITranslationHelper): HTMLElement {
     const coloredInput = Object.fromEntries(
       STRANDS.map(
         (key) => [key, new ColoredTextInput(this.inputBase[key], th.highlightInvalidSubsequence)]
@@ -140,32 +140,16 @@ class StructureAppLayout {
         }
       ));
 
-    const tableRows = STRANDS.map((strand) => {
-      return {
-        label: label[strand],
-        textInput: coloredInput[strand].root,
-        clear: clearBlock[strand],
-        choiceInput: directionChoiceInput[strand].root,
-      };
-    });
-    const tableLayout = ui.table(
-      tableRows, (item) => [item.label, item.textInput, item.clear, item.choiceInput]);
-    $(tableLayout).css('margin-top', '10px');
+    const sequenseInputs = ui.form([], 'st-structure-inputs');
+    const clearButtons = ui.divV([], 'st-structure-clear-buttons');
+    const directionInputs = ui.form([], 'st-direction-inputs'); 
 
     for (const strand of STRANDS) {
-      let element = label[strand].parentElement!;
-      element.classList.add('st-structure-input-form');
-      // the following line is necessary because otherwise overridden by
-      // d4-item-table class
-      $(element).css('padding-top', '3px');
-
-      element = directionChoiceInput[strand].root.parentElement!;
-      element.classList.add('st-structure-input-form', 'st-structure-direction-choice');
-
-      element = this.inputBase[strand].root.parentElement!;
-      element.classList.add('st-structure-text-input-td');
+      sequenseInputs.append(this.inputBase[strand].root);
+      clearButtons.append(clearBlock[strand]);
+      directionInputs.append(directionChoiceInput[strand].root);
     }
-    return tableLayout;
+    return ui.divH([sequenseInputs, clearButtons, directionInputs]);
   }
 
   private getStrandData() {

package/src/package-test.ts

@@ -8,6 +8,7 @@ import './tests/formats-to-helm';
 import './tests/helm-to-nucleotides';
 import './tests/formats-support';
 import './tests/files-tests';
+import './tests/polytool-enumerate-tests';
 
 import {OligoToolkitTestPackage} from './tests/utils';
 

package/src/package.ts

@@ -16,14 +16,14 @@ import {demoOligoPatternUI, demoOligoStructureUI, demoOligoTranslatorUI} from '.
 import {getExternalAppViewFactories} from './plugins/mermade';
 
 //polytool specific
-import {getPolyToolConversionDialog, polyToolEnumerateHelmUI, polyToolEnumerateChemUI} from './polytool/pt-dialog';
+import {getPolyToolConversionDialog, polyToolEnumerateChemUI} from './polytool/pt-dialog';
+import {polyToolEnumerateHelmUI} from './polytool/pt-enumeration-helm-dialog';
 import {_setPeptideColumn} from './polytool/utils';
 import {PolyToolCsvLibHandler} from './polytool/csv-to-json-monomer-lib-converter';
 import {ITranslationHelper} from './types';
 import {addContextMenuUI} from './utils/context-menu';
-import { NOTATION } from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 
-export const _package: OligoToolkitPackage = new OligoToolkitPackage();
+export const _package: OligoToolkitPackage = new OligoToolkitPackage(/*{debug: true}/**/);
 
 //name: Oligo Toolkit
 //meta.icon: img/icons/toolkit.png
@@ -152,7 +152,7 @@ async function getSpecifiedAppView(appName: string): Promise<DG.ViewBase> {
   return view;
 }
 
-//top-menu: Bio | Convert | PolyTool-Convert
+//top-menu: Bio | PolyTool | Convert...
 //name: polyToolConvert
 //description: Perform cyclization of polymers
 export async function polyToolConvert(): Promise<void> {
@@ -165,14 +165,14 @@ export async function polyToolConvert(): Promise<void> {
   }
 }
 
-//top-menu: Bio | Convert | PolyTool-Enumerate HELM
+//top-menu: Bio | PolyTool | Enumerate HELM...
 //name: polyToolEnumerateHelm
 //description: Perform cyclization of polymers
 export async function polyToolEnumerateHelm(): Promise<void> {
-  polyToolEnumerateHelmUI();
+  await polyToolEnumerateHelmUI(grok.shell.tv?.dataFrame.currentCell);
 }
 
-//top-menu: Bio | Convert | PolyTool-Enumerate Chem
+//top-menu: Bio | PolyTool | Enumerate Chem...
 //name: polyToolEnumerateChem
 //description: Perform cyclization of polymers
 export async function polyToolEnumerateChem(): Promise<void> {
@@ -213,7 +213,7 @@ export function addContextMenu(event: DG.EventData): void {
 // export async function ptConverterApp(): Promise<void> {
 //   const view = grok.shell.v as DG.TableView;
 //   const table = view.dataFrame;
-//   const colNames = table.columns.names(); 
+//   const colNames = table.columns.names();
 //   let covertableName = '';
 
 //   for (let i = 0; i < colNames.length; i++) {
@@ -229,7 +229,7 @@ export function addContextMenu(event: DG.EventData): void {
 //   else {
 //     const dialog = await getPolyToolConversionDialog();
 //     dialog.show();
-//   }  
+//   }
 // }
 
 //name: PolyTool Enumerator Helm
@@ -237,7 +237,7 @@ export function addContextMenu(event: DG.EventData): void {
 //meta.browsePath: PolyTool
 //tags: app
 export async function ptEnumeratorHelmApp(): Promise<void> {
-  polyToolEnumerateHelmUI();
+  await polyToolEnumerateHelmUI();
 }
 
 //name: PolyTool Enumerator Chem
@@ -246,4 +246,4 @@ export async function ptEnumeratorHelmApp(): Promise<void> {
 //tags: app
 export async function ptEnumeratorChemApp(): Promise<void> {
   polyToolEnumerateChemUI();
-}
+}

package/src/polytool/const.ts

@@ -26,3 +26,13 @@ export const R_GROUP_BLOCK_DUMMY = [
     'label': 'R3'
   }
 ];
+
+export const PT_ERROR_DATAFRAME = 'No dataframe with macromolecule columns open';
+export const PT_WARNING_COLUMN = 'No marcomolecule column chosen!';
+
+export const PT_UI_GET_HELM = 'Get HELM';
+export const PT_UI_ADD_HELM = 'Add HELM column';
+export const PT_UI_USE_CHIRALITY = 'Chirality engine';
+export const PT_UI_DIALOG_CONVERSION = 'Poly Tool Conversion';
+export const PT_UI_DIALOG_ENUMERATION = 'Poly Tool Enumeration';
+export const PT_UI_RULES_USED = 'Rules used';

package/src/polytool/pt-conversion.ts

@@ -297,6 +297,7 @@ export async function addTransformedColumn(
     df.columns.add(targetHelmCol);
   }
 
+  // toAtomicLevel
   const molCol = await grok.functions.call('Bio:getMolFromHelm', {
     'df': df,
     'helmCol': targetHelmCol,

package/src/polytool/pt-dialog.ts

@@ -3,11 +3,9 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import wu from 'wu';
+import $ from 'cash-dom';
 
-import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {HelmAtom} from '@datagrok-libraries/bio/src/helm/types';
 
 import {RuleInputs, RULES_PATH, RULES_STORAGE_NAME} from './pt-rules';
 import {addTransformedColumn} from './pt-conversion';
@@ -15,28 +13,13 @@ import {addTransformedColumn} from './pt-conversion';
 import {handleError} from './utils';
 import {defaultErrorHandler} from '../utils/err-info';
 import {getLibrariesList} from './utils';
-import {getEnumerationHelm, PT_HELM_EXAMPLE} from './pt-enumeration-helm';
 import {getEnumerationChem, PT_CHEM_EXAMPLE} from './pt-enumeration-chem';
+import {
+  PT_ERROR_DATAFRAME, PT_UI_ADD_HELM, PT_UI_DIALOG_CONVERSION, PT_UI_DIALOG_ENUMERATION,
+  PT_UI_GET_HELM, PT_UI_RULES_USED, PT_UI_USE_CHIRALITY, PT_WARNING_COLUMN
+} from './const';
 
-const PT_ERROR_DATAFRAME = 'No dataframe with macromolecule columns open';
-const PT_WARNING_COLUMN = 'No marcomolecule column chosen!';
-
-const PT_UI_GET_HELM = 'Get HELM';
-const PT_UI_ADD_HELM = 'Add HELM column';
-const PT_UI_USE_CHIRALITY = 'Chirality engine';
-const PT_UI_DIALOG_CONVERSION = 'Poly Tool Conversion';
-const PT_UI_DIALOG_ENUMERATION = 'Poly Tool Enumeration';
-const PT_UI_RULES_USED = 'Rules used';
-
-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');
-    });
-}
+import {_package} from '../package';
 
 export function polyToolEnumerateChemUI(cell?: DG.Cell): void {
   getPolyToolEnumerationChemDialog(cell)
@@ -104,61 +87,6 @@ export async function getPolyToolConversionDialog(targetCol?: DG.Column): Promis
   return dialog;
 }
 
-async function getPolyToolEnumerationHelmDialog(cell?: DG.Cell): Promise<DG.Dialog> {
-  const [libList, helmHelper] = await Promise.all([
-    getLibrariesList(), getHelmHelper()]);
-
-  const helmValue = cell ? cell.value : PT_HELM_EXAMPLE;
-
-  const helmInput = helmHelper.createHelmInput('Macromolecule', {value: helmValue});
-  const screenLibrary = ui.input.choice('Library to use', {value: null, items: libList});
-
-  helmInput.input.setAttribute('style', `min-width:250px!important;`);
-  screenLibrary.input.setAttribute('style', `min-width:250px!important;`);
-
-  const div = ui.div([
-    helmInput.root,
-    screenLibrary.root
-  ]);
-
-  // Displays the molecule from a current cell (monitors changes)
-  const cccSubs = grok.events.onCurrentCellChanged.subscribe(() => {
-    const cell = grok.shell.tv.dataFrame.currentCell;
-
-    if (cell.column.semType === DG.SEMTYPE.MACROMOLECULE && cell.column.meta.units === NOTATION.HELM)
-      helmInput.stringValue = cell.value;
-  });
-
-  const dialog = ui.dialog(PT_UI_DIALOG_ENUMERATION)
-    .add(div)
-    .onOK(async () => {
-      try {
-        const helmString = helmInput.stringValue;
-        const helmSelections: number[] = wu.enumerate<HelmAtom>(helmInput.value.atoms)
-          .filter(([a, aI]) => a.highlighted)
-          .map(([a, aI]) => aI).toArray();
-        if (helmString === undefined || helmString === '') {
-          grok.shell.warning('PolyTool: no molecule was provided');
-        } else if (helmSelections === undefined || helmSelections.length < 1) {
-          grok.shell.warning('PolyTool: no selection was provided');
-        } else {
-          const molecules = await getEnumerationHelm(helmString, helmSelections, screenLibrary.value!);
-          const molCol = DG.Column.fromStrings('Enumerated', molecules);
-          const df = DG.DataFrame.fromColumns([molCol]);
-          grok.shell.addTableView(df);
-        }
-      } catch (err: any) {
-        defaultErrorHandler(err);
-      } finally {
-        cccSubs.unsubscribe();
-      }
-    }).onCancel(() => {
-      cccSubs.unsubscribe();
-    });
-
-  return dialog;
-}
-
 async function getPolyToolEnumerationChemDialog(cell?: DG.Cell): Promise<DG.Dialog> {
   const [libList, helmHelper] = await Promise.all([
     getLibrariesList(), getHelmHelper()]);

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

@@ -87,23 +87,8 @@ export async function getEnumerationChem(molString: string, screenLibrary: strin
       //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);
+      molRes = rdkitModule.get_mol(smiRes, JSON.stringify({mappedDummiesAreRGroups: true}))
       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) {