@datagrok/bio 2.23.2 → 2.25.0

package/src/utils/monomer-lib/library-file-manager/ui.ts

@@ -6,19 +6,21 @@ import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
 import {Subject} from 'rxjs';
-import './style.css';
 
 import {
   getUserLibSettings, setUserLibSettings
 } from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {getMonomerLibHelper, IMonomerLibFileManager} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {findProviderWithLibraryName,
+  getMonomerLibHelper, IMonomerLibHelper,
+  IMonomerLibProvider} from '@datagrok-libraries/bio/src/types/monomer-library';
 
-import {MonomerLibFileEventManager} from './event-manager';
 import {_package} from '../../../package';
 import {MonomerManager} from '../monomer-manager/monomer-manager';
 import {DuplicateMonomerManager} from '../monomer-manager/duplicate-monomer-manager';
 import {MonomerLibManager} from '../lib-manager';
+// @ts-ignore
+import './style.css';
 
 export async function showManageLibrariesDialog(): Promise<void> {
   await DialogWrapper.showDialog();
@@ -38,8 +40,6 @@ export async function getMonomerLibraryManagerLink(): Promise<DG.Widget> {
 }
 
 class MonomerLibraryManagerWidget {
-  private _fileManager: IMonomerLibFileManager;
-
   private _widget: DG.Widget;
   public get widget(): DG.Widget { return this._widget; }
 
@@ -47,12 +47,14 @@ class MonomerLibraryManagerWidget {
 
   private static instancePromise?: Promise<MonomerLibraryManagerWidget>;
 
+  private libHelper: IMonomerLibHelper;
+
   static async getInstance(): Promise<MonomerLibraryManagerWidget> {
-    if (MonomerLibraryManagerWidget.instancePromise === undefined) {
+    if (MonomerLibraryManagerWidget.instancePromise == undefined) {
       MonomerLibraryManagerWidget.instancePromise = (async () => {
         const instance = new MonomerLibraryManagerWidget();
         const libHelper = await getMonomerLibHelper();
-        instance._fileManager = await libHelper.getFileManager();
+        instance.libHelper = libHelper;
         instance._widget = await instance.createWidget();
         return instance;
       })();
@@ -69,7 +71,7 @@ class MonomerLibraryManagerWidget {
     const content = await this.getWidgetContent();
     const monomerLibHelper = await getMonomerLibHelper();
     // eslint-disable-next-line rxjs/no-ignored-subscription
-    monomerLibHelper.eventManager.addLibraryFileRequested$.subscribe(
+    monomerLibHelper.fileUploadRequested.subscribe(
       () => this.promptToAddLibraryFiles()
     );
     return new DG.Widget(content);
@@ -89,17 +91,38 @@ class MonomerLibraryManagerWidget {
     DG.Utils.openFile({
       accept: '.json',
       open: async (selectedFile) => {
-        const content = await selectedFile.text();
-        const name = selectedFile.name;
-        const progressIndicator = DG.TaskBarProgressIndicator.create(`Adding ${name} as a monomer library`);
-        try {
-          await this._fileManager.addLibraryFile(content, name);
+        const doAdd = async (provider: IMonomerLibProvider) => {
+          const content = await selectedFile.text();
+          const name = selectedFile.name;
+          const progressIndicator = DG.TaskBarProgressIndicator.create(`Adding ${name} as a monomer library`);
+          try {
+            await provider.addOrUpdateLibraryString(name, content);
           // this.eventManager.updateLibrarySelectionStatus(name, true);
-        } catch (e) {
-          grok.shell.error(`File ${name} is not a valid monomer library, verify it is aligned to HELM JSON schema.`);
-        } finally {
-          progressIndicator.close();
+          } catch (e) {
+            grok.shell.error(`File ${name} is not a valid monomer library, verify it is aligned to HELM JSON schema.`);
+          } finally {
+            progressIndicator.close();
+          }
+        };
+        const providers = await this.libHelper.getProviders();
+        if (providers.length === 0) {
+          grok.shell.error('No monomer library providers available to add the library.');
+          return;
         }
+        if (providers.length === 1) {
+          await doAdd(providers[0]);
+          return;
+        }
+        const dialog = ui.dialog('Select storage for new monomer library');
+        const providersInput =
+        ui.input.choice('Storage', {items: providers.map((p) => p.name), value: providers[0].name,
+          nullable: false, tooltipText: 'Storage provider for new monomer library'});
+        dialog
+          .add(providersInput)
+          .onOK(async () => {
+            const provider = providers.find((p) => p.name === providersInput.value)!; // should not be null
+            await doAdd(provider);
+          });
       },
     });
   }
@@ -107,16 +130,11 @@ class MonomerLibraryManagerWidget {
 
 class LibraryControlsManager {
   private constructor(
-    private fileManager: IMonomerLibFileManager,
+    private readonly libHelper: IMonomerLibHelper,
     private readonly userLibSettings: UserLibSettings,
   ) {
-    // eslint-disable-next-line rxjs/no-ignored-subscription
-    this.fileManager.eventManager.updateUIControlsRequested$.subscribe(() => {
-      this.updateControlsForm();
-    });
-    // eslint-disable-next-line rxjs/no-ignored-subscription
-    this.fileManager.eventManager.librarySelectionRequested$.subscribe(([fileName, isSelected]) => {
-      this.updateLibrarySelectionStatus(isSelected, fileName);
+    this.libHelper.providersDataChanged.subscribe(async () => {
+      await this.updateControlsForm();
     });
   }
 
@@ -127,30 +145,28 @@ class LibraryControlsManager {
   static async createControlsForm(): Promise<HTMLElement> {
     const logPrefix = 'LibraryControlsForm.createControlsForm()';
     _package.logger.debug(`${logPrefix}, start`);
-    const [fileManager, userLibSettings] = await Promise.all([
-      getMonomerLibHelper().then((libHelper) => libHelper.getFileManager()),
-      await getUserLibSettings(),
-    ]);
-    const manager = new LibraryControlsManager(fileManager, userLibSettings);
+    const userLibSettings = await getUserLibSettings();
+    const libHelper = await getMonomerLibHelper();
+    const manager = new LibraryControlsManager(libHelper, userLibSettings);
 
     return manager._createControlsForm();
   }
 
-  private _createControlsForm(): HTMLElement {
-    const libraryControls = this.createLibraryControls();
+  private async _createControlsForm(): Promise<HTMLElement> {
+    const libraryControls = await this.createLibraryControls();
     const inputsForm = ui.wideForm(libraryControls, undefined);
     $(inputsForm).addClass('monomer-lib-controls-form');
 
     return inputsForm;
   }
 
-  public updateControlsForm(): void {
-    const updatedForm = this._createControlsForm();
+  public async updateControlsForm(): Promise<void> {
+    const updatedForm = await this._createControlsForm();
     $('.monomer-lib-controls-form').replaceWith(updatedForm);
   }
 
-  private createLibraryControls(): DG.InputBase<boolean | null>[] {
-    const libFileNameList: string[] = this.fileManager.getValidLibraryPaths();
+  private async createLibraryControls(): Promise<DG.InputBase<boolean | null>[]> {
+    const libFileNameList: string[] = await this.libHelper.getAvaliableLibraryNames();
     return libFileNameList.map((libFileName) => this.createLibInput(libFileName));
   }
 
@@ -159,7 +175,7 @@ class LibraryControlsManager {
     _package.logger.debug(`${logPrefix}, libFileName = '${libFileName}', start`);
     const isMonomerLibrarySelected = !this.userLibSettings.exclude.includes(libFileName);
     const libInput = ui.input.bool(libFileName, {value: isMonomerLibrarySelected, onValueChanged: () => {
-      this.fileManager.eventManager.updateLibrarySelectionStatus(libFileName, libInput.value);
+      updateLibrarySelectionStatus(libInput.value, libFileName);
     }});
     ui.tooltip.bind(libInput.root, `Include monomers from ${libFileName}`);
     const deleteIcon = ui.iconFA('trash-alt', () => this.promptForLibraryDeletion(libFileName));
@@ -173,38 +189,19 @@ class LibraryControlsManager {
     return libInput;
   }
 
-  private async updateLibrarySelectionStatus(
-    isMonomerLibrarySelected: boolean,
-    libFileName: string
-  ): Promise<void> {
-    this.updateLibrarySettings(isMonomerLibrarySelected, libFileName);
-    await setUserLibSettings(this.userLibSettings);
-    const monomerLibHelper = await getMonomerLibHelper();
-    await monomerLibHelper.loadMonomerLib(true);
-    grok.shell.info('Monomer library user settings saved');
-  }
-
-  private updateLibrarySettings(
-    isLibrarySelected: boolean | null,
-    libFileName: string,
-  ): void {
-    if (isLibrarySelected) {
-      // Remove selected library from exclusion list
-      this.userLibSettings.exclude = this.userLibSettings.exclude.filter((libName) => libName !== libFileName);
-    } else if (!this.userLibSettings.exclude.includes(libFileName)) {
-      // Add unselected library to exclusion list
-      this.userLibSettings.exclude.push(libFileName);
-    }
-  }
 
   private promptForLibraryDeletion(fileName: string): void {
     const dialog = ui.dialog('Warning');
-    dialog.add(ui.divText(`Delete file ${fileName}?`))
+    dialog.add(ui.divText(`Are you sure you want to delete library "${fileName}"?`))
       .onOK(async () => {
         try {
           const progressIndicator = DG.TaskBarProgressIndicator.create(`Deleting ${fileName} library`);
-          await this.updateLibrarySelectionStatus(false, fileName);
-          await this.fileManager.deleteLibraryFile(fileName);
+          await updateLibrarySelectionStatus(false, fileName);
+          const provider = await findProviderWithLibraryName(await this.libHelper.getProviders(), fileName);
+          if (!provider)
+            throw new Error(`Cannot find provider for library ${fileName}`);
+          await provider.deleteLibrary(fileName);
+          // await this.fileManager.deleteLibraryFile(fileName);
           progressIndicator.close();
         } catch (e) {
           console.error(e);
@@ -215,6 +212,33 @@ class LibraryControlsManager {
   }
 }
 
+async function updateLibrarySelectionStatus(
+  isMonomerLibrarySelected: boolean,
+  libFileName: string
+): Promise<void> {
+  const userLibSettings = await getUserLibSettings();
+  updateLibrarySettings(userLibSettings, isMonomerLibrarySelected, libFileName);
+  await setUserLibSettings(userLibSettings);
+  const monomerLibHelper = await getMonomerLibHelper();
+  await monomerLibHelper.loadMonomerLib(true);
+  grok.shell.info('Monomer library user settings saved');
+  monomerLibHelper.notifyLibrarySelectionChanged();
+}
+
+function updateLibrarySettings(
+  userLibSettings: UserLibSettings,
+  isLibrarySelected: boolean | null,
+  libFileName: string,
+): void {
+  if (isLibrarySelected) {
+    // Remove selected library from exclusion list
+    userLibSettings.exclude = userLibSettings.exclude.filter((libName) => libName !== libFileName);
+  } else if (!userLibSettings.exclude.includes(libFileName)) {
+    // Add unselected library to exclusion list
+    userLibSettings.exclude.push(libFileName);
+  }
+}
+
 class DialogWrapper {
   private constructor() { }
 
@@ -238,8 +262,8 @@ class DialogWrapper {
   }
 
   private async getDialog(): Promise<DG.Dialog> {
-    const eventManager = MonomerLibFileEventManager.getInstance();
     const widget = (await MonomerLibraryManagerWidget.getInstance()).widget;
+    const libHelper = await getMonomerLibHelper();
     const dialog = ui.dialog(
       {
         title: 'Manage monomer libraries',
@@ -250,7 +274,7 @@ class DialogWrapper {
     dialog.clear();
     dialog.addButton(
       'Add',
-      () => eventManager.addLibraryFile(),
+      () => libHelper.requestFileUpload(),
       undefined,
       'Upload new HELM monomer library'
     );
@@ -264,17 +288,17 @@ class DialogWrapper {
 }
 
 class LibManagerView {
-  private constructor() {};
+  private constructor(
+  ) {};
   private static _instance: LibManagerView;
   static viewName = 'Manage Monomer Libraries';
   private _view: DG.View;
   private _duplicateManager: DuplicateMonomerManager;
   private libManager: MonomerLibManager;
   private async getView(addView = true) {
-    const eventManager = MonomerLibFileEventManager.getInstance();
     const widget = (await MonomerLibraryManagerWidget.getInstance()).widget;
     const addButton = ui.bigButton('Add',
-      () => eventManager.addLibraryFile(), 'Upload new HELM monomer library');
+      () => this.libManager.requestFileUpload(), 'Upload new HELM monomer library');
     const mergeButton =
       ui.bigButton('Merge', () => { this.mergeSelectedLibs(); }, 'Merge selected libraries into one');
 
@@ -349,7 +373,6 @@ class LibManagerView {
     const libraryExistsError = 'Library with this name already exists';
     const libManager = await MonomerLibManager.getInstance();
     await libManager.awaitLoaded();
-    await libManager.loadLibrariesPromise;
     if (!libManager.duplicatesHandled) {
       grok.shell.warning(`Selected libraries contain repeating symbols with different monomers.
         Please choose the correct monomer for each symbol using duplicate monomomer manager.`);
@@ -366,37 +389,53 @@ class LibManagerView {
         dialog.getButton('Save')?.classList?.toggle('d4-disabled', !!res);
       }
     });
-    const validLibPaths = (await this.libManager.getFileManager()).getValidLibraryPaths();
+    const validLibPaths = await this.libManager.getAvaliableLibraryNames();
     newFileNameInput.addValidator(validateInput);
-    function getFileNameInputValue() {
-      let fileName = newFileNameInput.value;
-      if (!fileName.endsWith('.json'))
-        fileName += '.json';
-      return fileName;
-    };
 
     function validateInput(v: string) {
       if (!v || !v.trim()) return 'Library name cannot be empty';
-      if ((v.endsWith('.json') && validLibPaths.includes(v)) || validLibPaths.includes(v + '.json'))
+      if (validLibPaths.includes(v) || validLibPaths.includes(v + '.json'))
         return libraryExistsError;
       return null;
     }
+    const providers = await this.libManager.getProviders();
+    if (providers.length === 0) {
+      grok.shell.error('No monomer library providers available to save the merged library.');
+      return; // I mean, this should not happen, but ....
+    }
+    const providersInput = ui.input.choice('Storage', {items: providers.map((p) => p.name), value: providers[0].name,
+      nullable: false, tooltipText: 'Storage provider for saving new monomer library'});
+
+    const getFileNameInputValue = () => {
+      let fileName = newFileNameInput.value.trim();
+      if (!fileName)
+        fileName = 'New';
+      if (!fileName.toLowerCase().endsWith('.json'))
+        fileName += '.json';
+      return fileName;
+    };
     dialog
+      .add(providersInput)
       .add(newFileNameInput)
       .add(ui.divText(`Total monomers: ${libJSON.length}`))
       .addButton('Download', () => { DG.Utils.download(getFileNameInputValue(), JSON.stringify(libJSON)); })
       .addButton('Save', async () => {
+        if (!newFileNameInput.value || !newFileNameInput.value.trim() || !providersInput.value) {
+          providersInput.validate();
+          newFileNameInput.validate(); // this will force showing validation error
+          return;
+        }
         dialog.close();
-        const fileName = getFileNameInputValue();
+        const fileName = newFileNameInput.value!;
         const content = JSON.stringify(libJSON);
-        const fileManager = await this.libManager.getFileManager();
         this._view && ui.setUpdateIndicator(this._view.root, true);
         try {
-          await fileManager.addLibraryFile(content, fileName, false); // we will reload after updating settings
+          const provider = providers.find((p) => p.name === providersInput.value)!; // should not be null
+          await provider.addOrUpdateLibraryString(fileName, content); // we will reload after updating settings
           const settings = await getUserLibSettings();
           settings.exclude = validLibPaths; // exclude all previous libraries
           await setUserLibSettings(settings);
-          await this.libManager.loadLibraries(true);
+          await this.libManager.loadMonomerLib(true);
           await MonomerLibraryManagerWidget.reloadWidget();
         } catch (e) {
           grok.shell.error(`Failed to save library ${fileName}. see console for details.`);

package/src/utils/monomer-lib/monomer-colors.ts

@@ -1,6 +1,4 @@
 import {HelmTypes} from '@datagrok-libraries/bio/src/helm/consts';
-import {Helm} from '../helm-to-molfile/converter/helm';
-import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
 
 /**
  * MonomerColors class from HelmWebEditor for natural monomers
@@ -8,64 +6,64 @@ import {HelmType} from '@datagrok-libraries/bio/src/helm/types';
 export const naturalMonomerColors = {
   [HelmTypes.BASE]: {
     // Chromatogram palette  // HELMWebEditor monomerColors
-    A: "#20E040",            // "#A0A0FF",
-    G: "#040404",            // "#FF7070",
-    T: "#FF8080",            // "#A0FFA0",
-    C: "#2060FF",            // "#FF8C4B",
-    U: "#FF8080",            // "#FF8080"
+    A: '#20E040', // "#A0A0FF",
+    G: '#040404', // "#FF7070",
+    T: '#FF8080', // "#A0FFA0",
+    C: '#2060FF', // "#FF8C4B",
+    U: '#FF8080', // "#FF8080"
   },
 
   [HelmTypes.NUCLEOTIDE]: {
     // Chromatogram palette  // HELMWebEditor monomerColors
-    A: "#20E040",            // "#A0A0FF",
-    G: "#040404",            // "#FF7070",
-    T: "#FF8080",            // "#A0FFA0",
-    C: "#2060FF",            // "#FF8C4B",
-    U: "#FF8080",            // "#FF8080"
+    A: '#20E040', // "#A0A0FF",
+    G: '#040404', // "#FF7070",
+    T: '#FF8080', // "#A0FFA0",
+    C: '#2060FF', // "#FF8C4B",
+    U: '#FF8080', // "#FF8080"
   },
 
   [HelmTypes.LINKER]: {
-    P: "#9aa5e1",
-    p: "#9aa5e1"
+    P: '#9aa5e1',
+    p: '#9aa5e1'
   },
 
   [HelmTypes.SUGAR]: {
-    R: "#7a85c1",
-    r: "#7a85c1",
+    R: '#7a85c1',
+    r: '#7a85c1',
     // TODO: deoxyribose
   },
 
   [HelmTypes.AA]: {
     // GrokGroups palette    // HELMWebEditor monomerColors
-    A: "rgb(44,160,44)",     // "#C8C8C8",
-    R: "rgb(23,190,207)",    // "#145AFF",
-    N: "rgb(235,137,70)",    // "#00DCDC",
-    D: "rgb(31,119,180)",    // "#E60A0A",
-    C: "rgb(188,189,34)",    // "#E6E600",
-    E: "rgb(31, 120, 150)",  // "#00DCDC",
-    Q: "rgb(205, 111, 71)",  // "#E60A0A",
-    G: "rgb(214,39,40)",     // "#EBEBEB",
-    H: "rgb(158,218,229)",   // "#8282D2",
-    I: "rgb(23,103,57)",     // "#0F820F",
-    L: "rgb(30,110,96)",     // "#0F820F",
-    K: "rgb(108, 218, 229)", //"#145AFF",
-    M: "rgb(60,131,95)",     // "#E6E600",
-    F: "rgb(24,110,79)",     // "#3232AA",
-    P: "rgb(255,152,150)",   // "#DC9682",
-    S: "rgb(255,187,120)",   // "#FA9600",
-    T: "rgb(245,167,100)",   // "#FA9600",
-    W: "rgb(182, 223, 138)", // "#B45AB4",
-    Y: "rgb(152,223,138)",   // "#3232AA",
-    V: "rgb(74,160,74)",     // "#0F820F",
+    A: 'rgb(44,160,44)', // "#C8C8C8",
+    R: 'rgb(23,190,207)', // "#145AFF",
+    N: 'rgb(235,137,70)', // "#00DCDC",
+    D: 'rgb(31,119,180)', // "#E60A0A",
+    C: 'rgb(188,189,34)', // "#E6E600",
+    E: 'rgb(31, 120, 150)', // "#00DCDC",
+    Q: 'rgb(205, 111, 71)', // "#E60A0A",
+    G: 'rgb(214,39,40)', // "#EBEBEB",
+    H: 'rgb(158,218,229)', // "#8282D2",
+    I: 'rgb(23,103,57)', // "#0F820F",
+    L: 'rgb(30,110,96)', // "#0F820F",
+    K: 'rgb(108, 218, 229)', //"#145AFF",
+    M: 'rgb(60,131,95)', // "#E6E600",
+    F: 'rgb(24,110,79)', // "#3232AA",
+    P: 'rgb(255,152,150)', // "#DC9682",
+    S: 'rgb(255,187,120)', // "#FA9600",
+    T: 'rgb(245,167,100)', // "#FA9600",
+    W: 'rgb(182, 223, 138)', // "#B45AB4",
+    Y: 'rgb(152,223,138)', // "#3232AA",
+    V: 'rgb(74,160,74)', // "#0F820F",
   },
 
   [HelmTypes.CHEM]: {
-    R: "#eeeeee",
+    R: '#eeeeee',
   },
 
   [HelmTypes.BLOB]: {
-    B: "#999999",
-    G: "#e2e2e2"
+    B: '#999999',
+    G: '#e2e2e2'
   }
 };
 

package/src/utils/monomer-lib/monomer-lib-base.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 /* eslint-disable max-lines */
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
@@ -6,7 +7,7 @@ import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import {Observable, Subject} from 'rxjs';
 
-import {IMonomerLibBase, Monomer, RGroup} from '@datagrok-libraries/bio/src/types/index';
+import {IMonomerLibBase, Monomer, RGroup} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {HelmAtom, HelmType, IMonomerColors,
   IWebEditorMonomer, MonomerType, PolymerType} from '@datagrok-libraries/bio/src/helm/types';
 import {getMonomerHandleArgs} from '@datagrok-libraries/bio/src/helm/helm-helper';
@@ -18,11 +19,14 @@ import {GAP_SYMBOL, GapOriginals, NOTATION} from '@datagrok-libraries/bio/src/ut
 import {Vector} from '@datagrok-libraries/utils/src/type-declarations';
 import {vectorAdd, vectorDotProduct, vectorLength} from '@datagrok-libraries/utils/src/vector-operations';
 
-import {AmbiguousWebEditorMonomer, GapWebEditorMonomer, MissingWebEditorMonomer} from './web-editor-monomer-dummy';
+import {AmbiguousWebEditorMonomer, GapWebEditorMonomer, MissingWebEditorMonomer, SmilesWebEditorMonomer} from './web-editor-monomer-dummy';
 import {LibraryWebEditorMonomer} from './web-editor-monomer-of-library';
 import {naturalMonomerColors} from './monomer-colors';
 
 import {_package} from '../../package';
+import {MonomerLibData} from '@datagrok-libraries/bio/src/types/monomer-library';
+import {smiles2Monomer} from './smiles2Monomer';
+import {polymerTypeToHelmType} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 
 const monomerRe = /[\w()]+/;
 //** Do not mess with monomer symbol with parenthesis enclosed in square brackets */
@@ -34,8 +38,6 @@ const drawMoleculeCall = (s: string) => {
   return canvas;
 };
 
-export type MonomerLibDataType = { [polymerType: string]: { [monomerSymbol: string]: Monomer } };
-
 const whiteColorV = new Vector([255.0, 255.0, 255.0]);
 const blackColorV = new Vector([0.0, 0.0, 0.0]);
 const maxTextColorVLen = vectorLength(whiteColorV) * 0.7;
@@ -50,7 +52,7 @@ export class MonomerLibBase implements IMonomerLibBase {
 
 
   constructor(
-    protected _monomers: MonomerLibDataType,
+    protected _monomers: MonomerLibData,
     public readonly source: string,
   ) {
     this._isEmpty = !this._monomers || Object.keys(this._monomers).length === 0 ||
@@ -62,9 +64,15 @@ export class MonomerLibBase implements IMonomerLibBase {
   }
 
   getMonomerSymbolsByType(polymerType: PolymerType): string[] {
-    return Object.keys(this._monomers[polymerType]);
+    const res = Object.keys(this._monomers[polymerType]);
+    if (this._smilesMonomerCache[polymerType])
+      res.push(...Object.keys(this._smilesMonomerCache[polymerType]));
+    return res;
   }
 
+  // smiles to symbol Mapping cache
+  private _smilesMonomerCache: {[polymerType: string]: {[smiles: string]: string}} = {};
+
   /** Creates missing {@link Monomer} */
   addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer {
     let mSet = this._monomers[polymerType];
@@ -79,6 +87,22 @@ export class MonomerLibBase implements IMonomerLibBase {
     else if (polymerType === PolymerTypes.RNA && monomerSymbol === 'N')
       monomerName = 'Any';
 
+    // test if it is smiles
+    // check if the missing monomer symbol is a valid SMILES string
+    const smilesMonomer = smiles2Monomer(monomerSymbol, polymerType);
+    if (smilesMonomer) {
+      this._smilesMonomerCache[polymerType] = this._smilesMonomerCache[polymerType] ?? {};
+      const smSet = this._smilesMonomerCache[polymerType];
+      const symbol = Object.keys(smSet).length + 1;
+      smSet[monomerSymbol] = `#${polymerType[0]}${symbol}`; // e.g. #P1, #R2, #C3, #B4
+      const m: Monomer = {...smilesMonomer, symbol: smSet[monomerSymbol]};
+      // note, the ID becomes #<index> for smiles based monomers, and as the smiles, original smiles is passed (which is in monomerSymbol), to avoid key duplication
+      const wem = new SmilesWebEditorMonomer(polymerTypeToHelmType(polymerType), m.symbol, monomerSymbol, `SMILES Monomer ${m.symbol}`, m.rgroups.map((rg) => rg[RGP.LABEL]));
+      m.wem = wem;
+      mSet[m.symbol] = m;
+      return m;
+    }
+
     const m = mSet[monomerSymbol] = {
       [REQ.SYMBOL]: monomerSymbol,
       [REQ.NAME]: monomerName,
@@ -125,8 +149,11 @@ export class MonomerLibBase implements IMonomerLibBase {
         if (res) break;
       }
     } else {
+      // Check smiles cache, modify with mapped symbol
+      if (this._smilesMonomerCache[polymerType]?.[monomerSymbol])
+        monomerSymbol = this._smilesMonomerCache[polymerType][monomerSymbol];
       const dict = this._monomers[polymerType];
-      res = dict ? dict[monomerSymbol] : null;
+      res = dict?.[monomerSymbol] ?? null;
     }
     return res;
   }

package/src/utils/monomer-lib/monomer-lib.ts

@@ -12,16 +12,17 @@ import {
   MonomerSetType, PolymerType,
 } from '@datagrok-libraries/bio/src/helm/types';
 import {IMonomerLibBase, IMonomerLib, Monomer,
-  MonomerLibData, MonomerLibSummaryType} from '@datagrok-libraries/bio/src/types';
+  MonomerLibData, MonomerLibSummaryType} from '@datagrok-libraries/bio/src/types/monomer-library';
 import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';
 import {helmTypeToPolymerType} from '@datagrok-libraries/bio/src/monomer-works/monomer-works';
 import {getUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
 
-import {MonomerLibBase, MonomerLibDataType} from './monomer-lib-base';
+import {MonomerLibBase} from './monomer-lib-base';
 
 import {_package} from '../../package';
 
+//@ts-ignore
 import '../../../css/cell-renderer.css';
 
 /** Wrapper for monomers obtained from different sources. For managing monomere
@@ -38,7 +39,7 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
   private duplicatesNotified: boolean = false;
 
   constructor(
-    monomers: MonomerLibDataType,
+    monomers: MonomerLibData,
     source: string,
     public readonly error: string | undefined = undefined,
   ) {
@@ -54,32 +55,6 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
     return resJSON;
   }
 
-  getMonomer(polymerType: PolymerType | null, argMonomerSymbol: string): Monomer | null {
-    const logPrefix = `Bio: MonomerLib.getMonomer()`;
-    // Adjust RNA's 'R' for ribose to 'r' and 'P' for phosphate to 'p' for case-sensitive monomer names.
-    // There are uppercase 'R' and 'P' at RNA samples in test data 'helm2.csv' but lowercase in HELMCoreLibrary.json
-    let monomerSymbol = argMonomerSymbol;
-    if (polymerType == 'RNA' && monomerSymbol == 'R')
-      monomerSymbol = 'r';
-    if (polymerType == 'RNA' && monomerSymbol == 'P')
-      monomerSymbol = 'p';
-
-    let res: Monomer | null = null;
-
-    if (!polymerType) {
-      _package.logger.warning(`${logPrefix} symbol '${argMonomerSymbol}', polymerType not specified.`);
-      // Assume any polymer type
-      for (const [_polymerType, dict] of Object.entries(this._monomers)) {
-        res = dict[monomerSymbol];
-        if (res) break;
-      }
-    } else {
-      const dict = this._monomers[polymerType];
-      res = dict?.[monomerSymbol] ?? null;
-    }
-    return res;
-  }
-
   private _monomerSets: { [biotype: string /*HelmType*/]: MonomerSetType } | null = null;
 
   getMonomerSet(biotype: HelmType): MonomerSetType | null {
@@ -158,7 +133,7 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
     this._isEmpty = this.isEmpty && lib.isEmpty;
   }
 
-  public updateLibs(libList: IMonomerLib[], reload: boolean = false): void {
+  public async updateLibs(libList: IMonomerLib[], reload: boolean = false): Promise<void> {
     if (reload) {
       this._monomers = {};
       this._isEmpty = true;
@@ -167,9 +142,8 @@ export class MonomerLib extends MonomerLibBase implements IMonomerLib {
     for (const lib of libList)
       if (!lib.error) this._updateLibInt(lib);
     if (Object.entries(this.duplicateMonomers).length > 0) {
-      getUserLibSettings().then((settings) => {
-        this.assignDuplicatePreferences(settings);
-      });
+      const settings = await getUserLibSettings();
+      this.assignDuplicatePreferences(settings);
     } else
       this._duplicatesHandled = true;