@datagrok/bio 2.14.2 → 2.15.0

package/files/monomer-libraries/polytool-lib.json

@@ -0,0 +1,48 @@
+[
+  {
+    "monomerType": "Backbone",
+    "smiles": "[H:2]N[H:1]",
+    "name": "NH2",
+    "author": "Datagrok",
+    "molfile": "\n  MJ201900                      \n\n  3  2  0  0  0  0  0  0  0  0999 V2000\n   -1.0496   -1.2500    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.3572   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    0.3572   -1.2375    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n  2  3  1  0  0  0  0\n  1  2  1  0  0  0  0\nM  RGP  2   1   2   3   1\nM  END\n",
+    "naturalAnalog": "",
+    "rgroups": [
+      {
+        "capGroupSMILES": "[*:1][H]",
+        "alternateId": "R1-H",
+        "capGroupName": "H",
+        "label": "R1"
+      },
+      {
+        "capGroupSMILES": "[*:2][H]",
+        "alternateId": "R2-H",
+        "capGroupName": "H",
+        "label": "R2"
+      }
+    ],
+    "createDate": null,
+    "id": 0,
+    "polymerType": "PEPTIDE",
+    "symbol": "NH2"
+  },
+  {
+    "monomerType": "Backbone",
+    "smiles": "[H:1]C(=O)O",
+    "name": "COOH",
+    "author": "Datagrok",
+    "molfile": "\n     RDKit          2D\n\n  4  3  0  0  0  0  0  0  0  0999 V2000\n   -1.2990   -0.7500    0.0000 R#   0  0  0  0  0  1  0  0  0  0  0  0\n    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0000    1.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2990   -0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  2  0\n  2  4  1  0\nM  RGP  1   1   1\nM  END\n",
+    "naturalAnalog": "",
+    "rgroups": [
+      {
+        "capGroupSMILES": "[*:1][H]",
+        "alternateId": "R1-H",
+        "capGroupName": "H",
+        "label": "R1"
+      }
+    ],
+    "createDate": null,
+    "id": 0,
+    "polymerType": "PEPTIDE",
+    "symbol": "COOH"
+  }
+]

package/files/monomer-libraries/sample-lib-Aca-colored.json

@@ -1,10 +1,10 @@
 [
     {
         "monomerType": "Backbone",
-        "smiles": "CCCCCCCC[C@H](N[H:1])C([OH:2])=O",
+        "smiles": "",
         "name": "2-Aminocapric acid",
         "author": "Pistoia Alliance HELM project",
-        "molfile": "HELM Core Monomer library\n     RDKit          2D\n\n 14 13  0  0  1  0  0  0  0  0999 V2000\n    0.6430   -4.4293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.2375   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0301   -4.7725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.6246   -5.3445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.4172   -5.1157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.0117   -5.6877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    4.8044   -5.4589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.3988   -6.0310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.1915   -5.8021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.7859   -6.3742    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    7.5786   -6.1454    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    6.3896   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.7951   -4.4293    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0\n    7.1823   -4.7725    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0\n  2  3  1  0\n  3  4  1  0\n  4  5  1  0\n  5  6  1  0\n  6  7  1  0\n  7  8  1  0\n  9  8  1  0\n  9 10  1  1\n 10 11  1  0\n  9 12  1  0\n 12 13  1  0\n 12 14  2  0\nM  RGP  2  11   1  13   2\nM  END\n",
+        "molfile": "\n     RDKit          2D\n\n 13 13  0  0  0  0  0  0  0  0999 V2000\n    2.6980   -1.9038    0.0000 R#   0  0  0  0  0  1  0  0  0  0  0  0\n    1.3990   -1.1538    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    1.3990    0.3462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0999    1.0962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1991    0.3462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -1.1991   -1.1538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.4982   -1.9038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.7972   -1.1538    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.7972    0.3462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.4982    1.0962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.6980    1.0962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.6980    2.5962    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    3.9970    0.3462    0.0000 R#   0  0  0  0  0  1  0  0  0  0  0  0\n  1  2  1  0\n  2  3  1  0\n  3  4  1  1\n  4  5  1  0\n  5  6  2  0\n  6  7  1  0\n  7  8  2  0\n  8  9  1  0\n  9 10  2  0\n  3 11  1  0\n 11 12  2  0\n 11 13  1  0\n 10  5  1  0\nM  RGP  2   1   1  13   2\nM  END\n",
         "naturalAnalog": "X",
         "rgroups": [
             {

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.14.2",
+  "version": "2.15.0",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -37,18 +37,18 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.42.9",
+    "@datagrok-libraries/bio": "^5.42.14",
     "@datagrok-libraries/chem-meta": "^1.2.5",
-    "@datagrok-libraries/math": "^1.1.12",
-    "@datagrok-libraries/ml": "^6.6.19",
-    "@datagrok-libraries/tutorials": "^1.3.13",
-    "@datagrok-libraries/utils": "^4.2.22",
+    "@datagrok-libraries/math": "^1.2.0",
+    "@datagrok-libraries/ml": "^6.7.0",
+    "@datagrok-libraries/tutorials": "^1.4.0",
+    "@datagrok-libraries/utils": "^4.3.0",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",
     "cash-dom": "^8.0.0",
     "css-loader": "^6.7.3",
-    "datagrok-api": "^1.20.0",
+    "datagrok-api": "^1.21.1",
     "dayjs": "^1.11.4",
     "fastest-levenshtein": "^1.0.16",
     "openchemlib": "^7.2.3",
@@ -58,11 +58,11 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.8",
-    "@datagrok-libraries/js-draw-lite": "^0.0.6",
-    "@datagrok/chem": "^1.9.2",
-    "@datagrok/dendrogram": "^1.2.29",
-    "@datagrok/helm": "^2.2.1",
+    "@datagrok-libraries/helm-web-editor": "^1.1.11",
+    "@datagrok-libraries/js-draw-lite": "^0.0.8",
+    "@datagrok/chem": "^1.12.0",
+    "@datagrok/dendrogram": "^1.2.33",
+    "@datagrok/helm": "latest",
     "@types/node": "^17.0.24",
     "@types/wu": "latest",
     "@typescript-eslint/eslint-plugin": "latest",
@@ -141,6 +141,14 @@
           "Notation...": null,
           "SDF to JSON Library...": null,
           "To Atomic Level...": null
+        },
+        "Manage": {
+          "Monomer Libraries": null
+        },
+        "PolyTool": {
+          "Convert...": null,
+          "Enumerate Chem...": null,
+          "Enumerate HELM...": null
         }
       }
     }

package/src/analysis/sequence-space.ts

@@ -56,7 +56,8 @@ export async function getEncodedSeqSpaceCol(
       monomerHashToMatrixMap[charCodeMap.get(key)!] = value;
     });
     // sets distance function args in place.
-    options = {scoringMatrix: monomerRes.scoringMatrix, alphabetIndexes: monomerHashToMatrixMap};
+    const maxLength = encList.reduce((acc, val) => Math.max(acc, val.length), 0);
+    options = {scoringMatrix: monomerRes.scoringMatrix, alphabetIndexes: monomerHashToMatrixMap, maxLength};
   }
   return {seqList: encList, options};
 }

package/src/demo/bio05-helm-msa-sequence-space.ts

@@ -93,7 +93,7 @@ export async function demoBio05UI(): Promise<void> {
       .step('Build sequence space', async () => {
         const preprocessingFunc = DG.Func.find({package: 'Bio', name: 'macromoleculePreprocessingFunction'})[0];
         ssViewer = (await sequenceSpaceTopMenu(df, msaHelmCol,
-          dimRedMethod, MmDistanceFunctionsNames.LEVENSHTEIN, true, preprocessingFunc)) as DG.ScatterPlotViewer;
+          dimRedMethod, MmDistanceFunctionsNames.LEVENSHTEIN, true, preprocessingFunc, undefined, undefined, true)) as DG.ScatterPlotViewer;
         view.dockManager.dock(ssViewer, DG.DOCK_TYPE.RIGHT, null, 'Sequence Space', 0.35);
       }, {
         description: 'Reduce sequence space dimensionality to display on 2D representation.',

package/src/package-test.ts

@@ -28,8 +28,10 @@ import './tests/pepsea-tests';
 import './tests/viewers';
 import './tests/seq-handler-tests';
 import './tests/seq-handler-splitted-tests';
-import './tests/seq-handler-get-region';
+import './tests/seq-handler-get-region-tests';
+import './tests/seq-handler-get-helm-tests';
 import './tests/to-atomic-level-tests';
+import './tests/to-atomic-level-ui-tests';
 import './tests/mm-distance-tests';
 import './tests/activity-cliffs-tests';
 import './tests/sequence-space-test';

package/src/package-types.ts

@@ -6,6 +6,7 @@ import {Observable, Subject} from 'rxjs';
 
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {LoggerWrapper} from '@datagrok-libraries/bio/src/utils/logger';
+import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 
 /** Names of package properties/settings declared in properties section of {@link './package.json'} */
 export const enum BioPackagePropertiesNames {
@@ -58,6 +59,10 @@ export class BioPackageProperties extends Map<string, any> {
 
 export class BioPackage extends DG.Package {
   private _properties: BioPackageProperties;
+
+  private _rdKitModule: RDModule;
+  public get rdKitModule(): RDModule { return this._rdKitModule;};
+
   /** Package properties/settings declared in properties section of {@link './package.json'} */
   public get properties(): BioPackageProperties { return this._properties; };
 
@@ -73,7 +78,10 @@ export class BioPackage extends DG.Package {
     super._logger = new LoggerWrapper(super.logger, opts.debug);
   }
 
-  public completeInit(): void { this._initialized = true; }
+  public completeInit(rdKitModule: RDModule): void {
+    this._rdKitModule = rdKitModule;
+    this._initialized = true;
+  }
 
   handleErrorUI(err: any) {
     const [errMsg, errStack] = errInfo(err);

package/src/package.ts

@@ -20,6 +20,22 @@ import {
   createJsonMonomerLibFromSdf, IMonomerLibHelper
 } from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
+import {ActivityCliffsEditor} from '@datagrok-libraries/ml/src/functionEditors/activity-cliffs-function-editor';
+import BitArray from '@datagrok-libraries/utils/src/bit-array';
+import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';
+import {
+  getEmbeddingColsNames, multiColReduceDimensionality
+} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/reduce-dimensionality';
+import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
+import {
+  ITSNEOptions, IUMAPOptions
+} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/multi-column-dim-reducer';
+import {generateLongSequence, generateLongSequence2} from '@datagrok-libraries/bio/src/utils/generator';
+import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
+import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
+import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 
 import {getMacromoleculeColumns} from './utils/ui-utils';
 import {
@@ -40,7 +56,8 @@ import {saveAsFastaUI} from './utils/save-as-fasta';
 import {BioSubstructureFilter} from './widgets/bio-substructure-filter';
 import {WebLogoViewer} from './viewers/web-logo-viewer';
 import {MonomerLibManager} from './utils/monomer-lib/lib-manager';
-import {getMonomerLibraryManagerLink, showManageLibrariesDialog} from './utils/monomer-lib/library-file-manager/ui';
+import {getMonomerLibraryManagerLink, showManageLibrariesDialog,
+  showManageLibrariesView} from './utils/monomer-lib/library-file-manager/ui';
 import {demoBio01UI} from './demo/bio01-similarity-diversity';
 import {demoBio01aUI} from './demo/bio01a-hierarchical-clustering-and-sequence-space';
 import {demoBio01bUI} from './demo/bio01b-hierarchical-clustering-and-activity-cliffs';
@@ -62,23 +79,12 @@ import {GetRegionApp} from './apps/get-region-app';
 import {GetRegionFuncEditor} from './utils/get-region-func-editor';
 import {sequenceToMolfile} from './utils/sequence-to-mol';
 import {detectMacromoleculeProbeDo} from './utils/detect-macromolecule-probe';
-import {ActivityCliffsEditor} from '@datagrok-libraries/ml/src/functionEditors/activity-cliffs-function-editor';
-import BitArray from '@datagrok-libraries/utils/src/bit-array';
-import {BYPASS_LARGE_DATA_WARNING} from '@datagrok-libraries/ml/src/functionEditors/consts';
-import {
-  getEmbeddingColsNames, multiColReduceDimensionality
-} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/reduce-dimensionality';
-import {DimReductionMethods} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/types';
-import {
-  ITSNEOptions, IUMAPOptions
-} from '@datagrok-libraries/ml/src/multi-column-dimensionality-reduction/multi-column-dim-reducer';
-import {generateLongSequence, generateLongSequence2} from '@datagrok-libraries/bio/src/utils/generator';
-
 import {CyclizedNotationProvider} from './utils/cyclized';
+import {DimerizedNotationProvider} from './utils/dimerized';
 import {getMolColumnFromHelm} from './utils/helm-to-molfile/utils';
-import {PackageSettingsEditorWidget} from './widgets/package-settings-editor-widget';
-import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {MonomerManager} from './utils/monomer-lib/monomer-manager/monomer-manager';
 import {calculateScoresWithEmptyValues} from './utils/calculate-scores';
+import {SeqHelper} from './utils/seq-helper/seq-helper';
 
 export const _package = new BioPackage(/*{debug: true}/**/);
 
@@ -113,11 +119,12 @@ let monomerSets: IMonomerSet | null = null;
 export async function initBio() {
   const logPrefix = 'Bio: _package.initBio()';
   _package.logger.debug(`${logPrefix}, start`);
-  const module = await grok.functions.call('Chem:getRdKitModule');
+  let rdKitModule!: RDModule;
+  let monomerLibManager: MonomerLibManager;
   const t1: number = window.performance.now();
   await Promise.all([
     (async () => {
-      const monomerLibManager = await MonomerLibManager.getInstance();
+      monomerLibManager = await MonomerLibManager.getInstance();
       // Fix user lib settings for explicit stuck from a terminated test
       const libSettings = await getUserLibSettings();
       if (libSettings.explicit) {
@@ -133,12 +140,14 @@ export async function initBio() {
       const bioPkgProps = new BioPackageProperties(pkgProps);
       _package.properties = bioPkgProps;
     })(),
+    (async () => { rdKitModule = await getRdKitModule(); })(),
   ]).finally(() => {
-    _package.completeInit();
     const t2: number = window.performance.now();
     _package.logger.debug(`${logPrefix}, loading ET: ${t2 - t1} ms`);
   });
 
+  _package.completeInit(rdKitModule);
+
   const monomers: string[] = [];
   const logPs: number[] = [];
 
@@ -146,7 +155,7 @@ export async function initBio() {
   Object.keys(series).forEach((symbol) => {
     monomers.push(symbol);
     const block = series[symbol].replaceAll('#R', 'O ');
-    const mol = module.get_mol(block);
+    const mol = rdKitModule.get_mol(block);
     const logP = JSON.parse(mol.get_descriptors()).CrippenClogP;
     logPs.push(logP);
     mol?.delete();
@@ -259,7 +268,7 @@ export function SplitToMonomersEditor(call: DG.FuncCall): void {
 //input: funccall call
 export function SequenceSpaceEditor(call: DG.FuncCall) {
   const funcEditor = new DimReductionBaseEditor({semtype: DG.SEMTYPE.MACROMOLECULE});
-  ui.dialog({title: 'Sequence Space'})
+  const dialog = ui.dialog({title: 'Sequence Space'})
     .add(funcEditor.getEditor())
     .onOK(async () => {
       const params = funcEditor.getParams();
@@ -273,8 +282,9 @@ export function SequenceSpaceEditor(call: DG.FuncCall) {
         preprocessingFunction: params.preprocessingFunction,
         clusterEmbeddings: params.clusterEmbeddings,
       }).call();
-    })
-    .show();
+    });
+  dialog.history(() => ({editorSettings: funcEditor.getStringInput()}), (x: any) => funcEditor.applyStringInput(x['editorSettings']));
+  dialog.show();
 }
 
 //name: SeqActivityCliffsEditor
@@ -282,7 +292,7 @@ export function SequenceSpaceEditor(call: DG.FuncCall) {
 //input: funccall call
 export function SeqActivityCliffsEditor(call: DG.FuncCall) {
   const funcEditor = new ActivityCliffsEditor({semtype: DG.SEMTYPE.MACROMOLECULE});
-  ui.dialog({title: 'Activity Cliffs'})
+  const dialog = ui.dialog({title: 'Activity Cliffs'})
     .add(funcEditor.getEditor())
     .onOK(async () => {
       const params = funcEditor.getParams();
@@ -296,7 +306,9 @@ export function SeqActivityCliffsEditor(call: DG.FuncCall) {
         preprocessingFunction: params.preprocessingFunction,
         options: params.options,
       }).call();
-    }).show();
+    });
+  dialog.history(() => ({editorSettings: funcEditor.getStringInput()}), (x: any) => funcEditor.applyStringInput(x['editorSettings']));
+  dialog.show();
 }
 
 // -- Package settings editor --
@@ -370,7 +382,7 @@ export function macromoleculeDifferenceCellRenderer(): MacromoleculeDifferenceCe
 //output: object res
 export function sequenceAlignment(alignType: string, alignTable: string, gap: number, seq1: string, seq2: string) {
   const toAlign = new SequenceAlignment(seq1, seq2, gap, alignTable);
-  const res = alignType == 'Local alignment' ? toAlign.smithWaterman() : toAlign.needlemanWunch();
+  const res = alignType == 'Local alignment' ? toAlign.smithWaterman() : toAlign.needlemanWunsch();
   return res;
 }
 
@@ -411,6 +423,14 @@ export function getRegion(
     start ?? null, end ?? null, name ?? null);
 }
 
+//top-menu: Bio | Manage | Monomers
+//name: manageMonomersView
+//description: Edit and create monomers
+export async function manageMonomersView() {
+  const monomerManager = await MonomerManager.getInstance();
+  await monomerManager.getViewRoot();
+}
+
 //top-menu: Bio | Convert | Get Region...
 //name: Get Region Top Menu
 //description: Get sequences for a region specified from a Macromolecule
@@ -568,13 +588,16 @@ export async function helmPreprocessingFunction(
 //input: func preprocessingFunction {optional: true}
 //input: object options {optional: true}
 //input: bool clusterEmbeddings = true { optional: true }
+//input: bool isDemo {optional: true}
 //output: viewer result
 //editor: Bio:SequenceSpaceEditor
 export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Column,
   methodName: DimReductionMethods, similarityMetric: BitArrayMetrics | MmDistanceFunctionsNames,
   plotEmbeddings: boolean, preprocessingFunction?: DG.Func, options?: (IUMAPOptions | ITSNEOptions) & Options,
-  clusterEmbeddings?: boolean
+  clusterEmbeddings?: boolean, isDemo?: boolean
 ): Promise<DG.ScatterPlotViewer | undefined> {
+  const tableView = isDemo ? (grok.shell.view('Browse')! as DG.BrowseView)!.preview! as DG.TableView :
+    grok.shell.tv.dataFrame == table ? grok.shell.tv : undefined;
   if (!checkInputColumnUI(molecules, 'Sequence Space'))
     return;
   if (!preprocessingFunction)
@@ -583,10 +606,12 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
   const res = await multiColReduceDimensionality(table, [molecules], methodName,
     [similarityMetric as KnownMetrics], [1], [preprocessingFunction], 'MANHATTAN',
     plotEmbeddings, clusterEmbeddings ?? false,
-    {...options, preprocessingFuncArgs: [options.preprocessingFuncArgs ?? {}]}, {
+    /* dimRedOptions */ {...options, preprocessingFuncArgs: [options.preprocessingFuncArgs ?? {}]},
+    /* uiOptions */{
       fastRowCount: 10000,
       scatterPlotName: 'Sequence space',
       bypassLargeDataWarning: options?.[BYPASS_LARGE_DATA_WARNING],
+      tableView: tableView,
     });
   return res;
 }
@@ -595,8 +620,9 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
 //name: To Atomic Level
 //description: Converts sequences to molblocks
 //input: dataframe table [Input data table]
-//input: column macroMolecule {caption: Sequence; semType: Macromolecule}
-//input: bool nonlinear =false {description: Slower mode for cycling/branching HELM structures}
+//input: column seqCol {caption: Sequence; semType: Macromolecule}
+//input: bool nonlinear =false {caption: Non linear; description: Slower mode for cycling/branching HELM structures}
+//output:
 export async function toAtomicLevel(table: DG.DataFrame, seqCol: DG.Column, nonlinear: boolean): Promise<void> {
   const pi = DG.TaskBarProgressIndicator.create('Converting to atomic level ...');
   try {
@@ -893,13 +919,18 @@ export async function sequenceSimilarityScoring(
 }
 
 
-//top-menu: Bio | Manage | Monomer Libraries
 //name: Manage Monomer Libraries
 //description: Manage HELM monomer libraries
 export async function manageMonomerLibraries(): Promise<void> {
   showManageLibrariesDialog();
 }
 
+//top-menu: Bio | Manage | Monomer Libraries
+//name: Manage Monomer Libraries View
+export async function manageLibrariesView(): Promise<void> {
+  await showManageLibrariesView();
+}
+
 //name: saveAsFasta
 //description: As FASTA...
 //tags: fileExporter
@@ -1076,13 +1107,19 @@ export async function detectMacromoleculeProbe(file: DG.FileInfo, colName: strin
   await detectMacromoleculeProbeDo(csv, colName, probeCount);
 }
 
+//name: getSeqHelper
+//output: object result
+export async function getSeqHelper(): Promise<ISeqHelper> {
+  return SeqHelper.getInstance();
+}
+
 //name: getMolFromHelm
 //input: dataframe df
 //input: column helmCol
-//input: bool chiralityEngine
+//input: bool chiralityEngine = true
 //output: column result
-export async function getMolFromHelm(
-  df: DG.DataFrame, helmCol: DG.Column<string>, chiralityEngine?: boolean
+export function getMolFromHelm(
+  df: DG.DataFrame, helmCol: DG.Column<string>, chiralityEngine: boolean
 ): Promise<DG.Column<string>> {
   return getMolColumnFromHelm(df, helmCol, chiralityEngine);
 }
@@ -1095,3 +1132,10 @@ export async function getMolFromHelm(
 export function applyNotationProviderForCyclized(col: DG.Column<string>, separator: string) {
   col.temp[SeqTemps.notationProvider] = new CyclizedNotationProvider(separator);
 }
+
+//name: applyNotationProviderForDimerized
+//input: column col
+//input: string separator
+export function applyNotationProviderForDimerized(col: DG.Column<string>, separator: string) {
+  col.temp[SeqTemps.notationProvider] = new DimerizedNotationProvider(separator);
+}

package/src/seq_align.ts

@@ -449,7 +449,7 @@ export class SequenceAlignment {
   }
 
 
-  public needlemanWunch():Aligned {
+  public needlemanWunsch():Aligned {
     this.dpGrid=[];
     for (let i:number = 0; i<this.len1+1; i++) {
       const row : Cell[] =[];

package/src/substructure-search/substructure-search.ts

@@ -63,8 +63,8 @@ export class SubstructureSearchDialog {
 
   createUI(): void {
     const dataframe = grok.shell.tv.dataFrame;
-    this.columnsInput = ui.input.column('Column', {table: dataframe, value: this.col, onValueChanged: (input) => {
-      this.col = input.value;
+    this.columnsInput = ui.input.column('Column', {table: dataframe, value: this.col, onValueChanged: (value) => {
+      this.col = value;
       this.updateNotationDiv();
       this.updateInputs();
     }, filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE});

package/src/tests/WebLogo-project-tests.ts

@@ -51,13 +51,12 @@ export async function uploadProject(projectName: string, tableInfo: DG.TableInfo
   const project = DG.Project.create();
   const viewLayout = view.saveLayout();
 
-  await grok.dapi.layouts.save(view.saveLayout());
-  await grok.dapi.tables.uploadDataFrame(df);
-  await grok.dapi.tables.save(tableInfo);
-
   project.name = projectName;
   project.addChild(tableInfo);
   project.addChild(viewLayout); // cause error
 
+  await grok.dapi.layouts.save(view.saveLayout());
+  await grok.dapi.tables.uploadDataFrame(df);
+  await grok.dapi.tables.save(tableInfo);
   await grok.dapi.projects.save(project);
 }

package/src/tests/activity-cliffs-tests.ts

@@ -20,9 +20,6 @@ import {_package} from '../package-test';
 
 
 category('activityCliffs', async () => {
-  let viewList: DG.ViewBase[] = [];
-  let dfList: DG.DataFrame[] = [];
-
   let helmHelper: IHelmHelper;
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
@@ -37,38 +34,28 @@ category('activityCliffs', async () => {
     // Test 'helm' requires default monomer library loaded
     await setUserLibSettingsForTests();
     await monomerLibHelper.loadMonomerLib(true); // load default libraries
-
-    viewList = [];
-    dfList = [];
   });
 
   after(async () => {
-    // for (const df of dfList) grok.shell.closeTable(df);
-    // for (const view of viewList) view.close();
-
     // UserDataStorage.put() replaces existing data
     await setUserLibSettings(userLibSettings);
     await monomerLibHelper.loadMonomerLib(true); // load user settings libraries
   });
 
   test('activityCliffsOpens', async () => {
-    const actCliffsDf = await readDataframe(
-      DG.Test.isInBenchmark ? 'test/peptides_motif-with-random_10000.csv' : 'tests/100_3_clustests.csv',
-    );
-    dfList.push(actCliffsDf);
+    const testData = !DG.Test.isInBenchmark ?
+      {fileName: 'tests/100_3_clustests.csv', tgt: {cliffCount: 3}} :
+      {fileName: 'tests/peptides_motif-with-random_10000.csv', tgt: {cliffCount: 53}};
+    const actCliffsDf = await readDataframe(testData.fileName);
     const actCliffsTableView = grok.shell.addTableView(actCliffsDf);
-    viewList.push(actCliffsTableView);
-    const cliffsNum = DG.Test.isInBenchmark ? 6 : 3;
 
     await _testActivityCliffsOpen(actCliffsDf, DimReductionMethods.UMAP,
-      'sequence', 'Activity', 90, cliffsNum, MmDistanceFunctionsNames.LEVENSHTEIN, seqEncodingFunc);
+      'sequence', 'Activity', 90, testData.tgt.cliffCount, MmDistanceFunctionsNames.LEVENSHTEIN, seqEncodingFunc);
   }, {benchmark: true});
 
   test('activityCliffsWithEmptyRows', async () => {
     const actCliffsDfWithEmptyRows = await readDataframe('tests/100_3_clustests_empty_vals.csv');
-    dfList.push(actCliffsDfWithEmptyRows);
     const actCliffsTableViewWithEmptyRows = grok.shell.addTableView(actCliffsDfWithEmptyRows);
-    viewList.push(actCliffsTableViewWithEmptyRows);
 
     await _testActivityCliffsOpen(actCliffsDfWithEmptyRows, DimReductionMethods.UMAP,
       'sequence', 'Activity', 90, 3, MmDistanceFunctionsNames.LEVENSHTEIN, seqEncodingFunc);

package/src/tests/detectors-benchmark-tests.ts

@@ -6,6 +6,8 @@ import {before, category, test, expect} from '@datagrok-libraries/utils/src/test
 import {ALPHABET, getAlphabet, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
+import {_package} from '../package-test';
+
 category('detectorsBenchmark', () => {
   let detectFunc: DG.Func;
 
@@ -139,17 +141,30 @@ async function benchmark<TData, TRes>(
 ): Promise<number> {
   const data: TData = await prepare();
 
-  const t1: number = Date.now();
-  // console.profile();
-  const res: TRes = await test(data);
-  //console.profileEnd();
-  const t2: number = Date.now();
+  const tryCount = 60;
+  const maxOutCount = 3; // 95%
+  let outCount: number = 0;
+  let outResET: number = 0;
+  const resEtList: number[] = new Array<number>(tryCount);
+  let resET: number = 0;
+  for (let tryI = 0; tryI < 20; ++tryI) {
+    const t1: number = Date.now();
+    // console.profile();
+    const res: TRes = await test(data);
+    //console.profileEnd();
+    const t2: number = Date.now();
+
+    resET = resEtList[tryI] = t2 - t1;
+    if (resET > maxET) {
+      outCount++;
+      outResET = Math.max(outResET, resET);
+    }
 
-  check(res);
+    check(res);
+  }
 
-  const resET: number = t2 - t1;
-  if (resET > maxET) {
-    const errMsg = `ET ${resET} ms is more than max allowed ${maxET} ms.`;
+  if (outCount > maxOutCount) {
+    const errMsg = `ET ${outResET} ms is more than max allowed ${maxET} ms. ET: ${JSON.stringify(resEtList)}`;
     console.error(errMsg);
     throw new Error(errMsg);
   } else

package/src/tests/mm-distance-tests.ts

@@ -118,9 +118,10 @@ ATCGAATCGA`;
       {scoringMatrix, alphabetIndexes, gapOpen: 1, gapExtend: 1},
     );
     if (DG.Test.isInBenchmark) {
-      const seq1 = Array(10000).fill('FWRY').join('');
-      const seq2 = Array(10000).fill('FYWRRY').join('');
-      _testDistance(seq1, seq2, df, 0.667);
+      // max length 10000 for Needleman-Wunsch
+      const seq1 = /* length 3000 */ Array(1000).fill(prot5).join('');
+      const seq2 = /* length 7000 */Array(1000).fill(prot6).join('');
+      _testDistance(seq1, seq2, df, 1.333);
     } else
       _testDistance(prot5, prot6, df, 1.333);
   }, {benchmark: true});

package/src/tests/monomer-libraries-tests.ts

@@ -26,8 +26,8 @@ category('monomerLibraries', () => {
 
   test('default', async () => {
     // Clear settings to test default
-    await setUserLibSettings({exclude: [], explicit: []});
-    await monomerLibHelper.loadMonomerLib(true); // test defaultLib
+    await setUserLibSettings({exclude: [], explicit: [], duplicateMonomerPreferences: {}});
+    await monomerLibHelper.loadLibraries(true); // test defaultLib
 
     // Currently default monomer lib set is of all files at LIB_PATH (at least HELMCoreLibrary.json)
     const currentMonomerLib = monomerLibHelper.getMonomerLib();
@@ -42,7 +42,7 @@ category('monomerLibraries', () => {
     const currentMonomerLib = monomerLibHelper.getMonomerLib();
     // HELMCoreLibrary.json checks
     expect(currentMonomerLib.getPolymerTypes().length, 2);
-    expect(currentMonomerLib.getMonomerSymbolsByType('PEPTIDE').length, 322);
+    expect(currentMonomerLib.getMonomerSymbolsByType('PEPTIDE').length, 324);
     expect(currentMonomerLib.getMonomerSymbolsByType('RNA').length, 383);
   });