@datagrok/sequence-translator 1.3.10 → 1.3.12

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.3.10",
+  "version": "1.3.12",
   "author": {
     "name": "Alexey Choposky",
     "email": "achopovsky@datagrok.ai"
@@ -22,9 +22,9 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "5.42.5",
+    "@datagrok-libraries/bio": "5.42.9",
     "@datagrok-libraries/chem-meta": "^1.2.5",
-    "@datagrok-libraries/tutorials": "^1.3.12",
+    "@datagrok-libraries/tutorials": "^1.3.13",
     "@datagrok-libraries/utils": "^4.2.13",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
@@ -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": "^1.1.8",
+    "@datagrok-libraries/js-draw-lite": "^0.0.6",
+    "@datagrok/bio": "^2.14.2",
+    "@datagrok/helm": "^2.4.1",
+    "@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/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} 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();
+export const _package: OligoToolkitPackage = new OligoToolkitPackage(/*{debug: true}/**/);
 
 //name: Oligo Toolkit
 //meta.icon: img/icons/toolkit.png
@@ -169,15 +169,15 @@ export async function polyToolConvert(): Promise<void> {
 //name: polyToolEnumerateHelm
 //description: Perform cyclization of polymers
 export async function polyToolEnumerateHelm(): Promise<void> {
-  polyToolEnumerateHelmUI();
+  await 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> {
+  await 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/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 +3,14 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
+import $ from 'cash-dom';
 import wu from 'wu';
+import {Unsubscribable} from 'rxjs';
 
 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 {HelmAtom, HelmMol} from '@datagrok-libraries/bio/src/helm/types';
+// import {FormsViewer} from '@datagrok-libraries/utils/src/viewers/forms-viewer';
 
 import {RuleInputs, RULES_PATH, RULES_STORAGE_NAME} from './pt-rules';
 import {addTransformedColumn} from './pt-conversion';
@@ -15,20 +18,87 @@ 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 {getPtEnumeratorHelm, PT_HELM_EXAMPLE} from './pt-enumeration-helm';
 import {getEnumerationChem, PT_CHEM_EXAMPLE} from './pt-enumeration-chem';
+import {
+  PolyToolEnumeratorParams, PolyToolEnumeratorType, PolyToolEnumeratorTypes, PolyToolPlaceholders
+} from './types';
+
+import {_package} from '../package';
+import {PolyToolPlaceholdersInput} from './pt-placeholders-input';
+import {InputBase} from 'datagrok-api/dg';
+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';
+import {PolyToolEnumerateDialog} from './pt-enumeration-helm-dialog';
+
+export async function polyToolEnumerateHelmUI(cell?: DG.Cell): Promise<void> {
+  const maxWidth = window.innerWidth;
+  const maxHeight = window.innerHeight;
+
+  try {
+    const resizeInputs = () => {
+      const contentHeight = $(dialog.root).find('div.d4-dialog-contents').get(0)!.clientHeight;
+
+      const fitInputs: { [idx: number]: number } = {1: 1 /*, 3: 0.5*/};
+      const fitInputsSumHeight = Object.values(fitInputs).reduce((sum, h) => sum + h, 0);
+
+      const otherInputsHeight: number = dialog.inputs.filter((input, idx) => !(idx in fitInputs))
+        .map((input) => input.root.offsetHeight).reduce((sum, h) => sum + h, 0);
+      const remainFitHeight = contentHeight - otherInputsHeight - 38;
+      dialog.inputs.forEach((input, idx) => {
+        if (idx in fitInputs) {
+          const inputFitHeight = remainFitHeight * fitInputs[idx] / fitInputsSumHeight;
+          input.root.style.height = `${inputFitHeight}px`;
+        }
+      });
+    };
+    const [dialog, inputs] = await PolyToolEnumerateDialog.create2(cell, resizeInputs);
+
+    let isFirstShow = true;
+    ui.onSizeChanged(dialog.root).subscribe(() => {
+      if (isFirstShow) {
+        const dialogInputList = dialog.inputs;
+        const dialogRootCash = $(dialog.root);
+        const contentMaxHeight = maxHeight
+          - dialogRootCash.find('div.d4-dialog-header').get(0)!.offsetHeight
+          - dialogRootCash.find('div.d4-dialog-footer').get(0)!.offsetHeight;
+
+        // dialog.inputs2.macromolecule.root.style.backgroundColor = '#CCFFCC';
+
+        const dialogWidth = maxWidth * 0.7;
+        const dialogHeight = maxHeight * 0.7;
+
+        // Centered, but resizable dialog
+        dialog.root.style.width = `${Math.min(maxWidth, dialogWidth)}px`;
+        dialog.root.style.height = `${Math.min(maxHeight, dialogHeight)}px`;
+        dialog.root.style.left = `${Math.floor((maxWidth - dialog.root.offsetWidth) / 2)}px`;
+        dialog.root.style.top = `${Math.floor((maxHeight - dialog.root.offsetHeight) / 2)}px`;
+
+        isFirstShow = false;
+      }
+
+      resizeInputs();
+    });
 
-const PT_ERROR_DATAFRAME = 'No dataframe with macromolecule columns open';
-const PT_WARNING_COLUMN = 'No marcomolecule column chosen!';
+    _package.logger.debug('PolyToolEnumerateHelmUI: dialog before show');
+    const res = dialog.show({width: Math.max(350, maxWidth * 0.7), /* center: true,*/ resizable: true});
+    _package.logger.debug('PolyToolEnumerateHelmUI: dialog after show');
+    const k = 42;
+  } catch (_err: any) {
+    grok.shell.warning('To run PolyTool Enumeration, sketch the macromolecule and select monomers to vary');
+  }
+}
 
-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 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(): Promise<DG.Dialog> {
+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 +108,8 @@ 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);
 
@@ -82,62 +154,7 @@ export async function getPolyToolConversionDialog(): Promise<DG.Dialog> {
   return dialog;
 }
 
-export 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;
-}
-
-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 +164,6 @@ 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 +81,24 @@ 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, JSON.stringify({mappedDummiesAreRGroups: true}))
+      let molV3 = molRes.get_v3Kmolblock();
+      enumerations[i] = molV3;
+    } 
+    catch(err:any) {
+      enumerations[i] = '';
+    }
+    finally {
+      molRes?.delete();
+    }
   }
+  
 
   return enumerations;
 }