@datagrok/bio 2.16.3 → 2.16.5

package/files/tests/placer_MSA.csv

@@ -0,0 +1,5 @@
+MSA,Activity
+meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca//Phe_4Me,5.307510973968128
+meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca//Phe_4Me,5.723876853431544
+Lys_Boc/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca//Phe_4Me,5.185811246022437
+meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2///Phe_4Me,6.223502390804369

package/package.json

@@ -5,7 +5,7 @@
     "name": "Aleksandr Tanas",
     "email": "atanas@datagrok.ai"
   },
-  "version": "2.16.3",
+  "version": "2.16.5",
   "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",
@@ -37,9 +37,9 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.45.2",
+    "@datagrok-libraries/bio": "^5.45.3",
     "@datagrok-libraries/chem-meta": "^1.2.7",
-    "@datagrok-libraries/math": "^1.2.1",
+    "@datagrok-libraries/math": "^1.2.2",
     "@datagrok-libraries/ml": "^6.7.4",
     "@datagrok-libraries/tutorials": "^1.4.3",
     "@datagrok-libraries/utils": "^4.3.6",

package/src/global.d.ts

@@ -0,0 +1,13 @@
+import * as grokNamespace from 'datagrok-api/grok';
+import * as uiNamespace from 'datagrok-api/ui';
+import * as DGNamespace from 'datagrok-api/dg';
+import * as rxjsNamespace from 'rxjs';
+import $Namespace from 'cash-dom';
+
+declare global {
+    const grok: typeof grokNamespace;
+    const ui: typeof uiNamespace;
+    const DG: typeof DGNamespace;
+    const rjxs: typeof rxjsNamespace;
+    const $: typeof $Namespace;
+}

package/src/package.ts

@@ -26,6 +26,7 @@ import {getUserLibSettings, setUserLibSettings} from '@datagrok-libraries/bio/sr
 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 {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 
 import {getMacromoleculeColumns} from './utils/ui-utils';
 import {MacromoleculeDifferenceCellRenderer, MacromoleculeSequenceCellRenderer,} from './utils/cell-renderer';
@@ -69,7 +70,6 @@ import {getMolColumnFromHelm} from './utils/helm-to-molfile/utils';
 import {MonomerManager} from './utils/monomer-lib/monomer-manager/monomer-manager';
 import {calculateScoresWithEmptyValues} from './utils/calculate-scores';
 import {SeqHelper} from './utils/seq-helper/seq-helper';
-import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';
 
 export const _package = new BioPackage(/*{debug: true}/**/);
 

package/src/tests/helm-tests.ts

@@ -12,58 +12,75 @@ category('helm', () => {
     'single-linear': {
       src: {helm: 'PEPTIDE1{R.F.Y.[GGaz].T.[meI]}$$$$'},
       tgt: {
-        simplePolymers: [6],
+        simplePolymers: [6], connections: [],
         bondedRGroups: [1, 2, 2, 2, 2, 1],
       }
     },
     'single-cyclized-C-2-2': {
-      src: {helm: 'PEPTIDE1{R.F.C.Y.G.H.[GGaz].C.T.[meI]}$PEPTIDE1,PEPTIDE1,3:R3-8,R3$$$'},
+      src: {helm: 'PEPTIDE1{R.F.C.Y.G.H.[GGaz].C.T.[meI]}$PEPTIDE1,PEPTIDE1,3:R3-8:R3$$$'},
       tgt: {
-        simplePolymers: [10],
+        simplePolymers: [10], connections: [[['PEPTIDE1', 3, 'R3'], ['PEPTIDE1', 8, 'R3']]],
         bondedRGroups: [1, 2, 3, 2, 2, 2, 2, 3, 2, 1],
       }
     },
     'single-cyclized-C-1-1': {
-      src: {helm: 'PEPTIDE1{F.C.Y.G.H.[GGaz].C.[meI]}$PEPTIDE1,PEPTIDE1,2:R3-7,R3$$$'},
+      src: {helm: 'PEPTIDE1{F.C.Y.G.H.[GGaz].C.[meI]}$PEPTIDE1,PEPTIDE1,2:R3-7:R3$$$'},
       tgt: {
-        simplePolymers: [8],
+        simplePolymers: [8], connections: [[['PEPTIDE1', 2, 'R3'], ['PEPTIDE1', 7, 'R3']]],
         bondedRGroups: [1, 3, 2, 2, 2, 1, 3, 1],
       }
     },
     'single-cyclized-C-0-0': {
-      src: {helm: 'PEPTIDE1{C.Y.G.H.[GGaz].C}$PEPTIDE1,PEPTIDE1,2:R3-7,R3$$$'},
+      src: {helm: 'PEPTIDE1{C.Y.G.H.[GGaz].C}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$'},
       tgt: {
-        simplePolymers: [6],
+        simplePolymers: [6], connections: [[['PEPTIDE1', 1, 'R3'], ['PEPTIDE1', 6, 'R3']]],
         bondedRGroups: [2, 2, 2, 2, 2, 2],
       }
     },
-    'two-separated-1': {
+    'two-separated-5-1': {
       src: {helm: 'PEPTIDE1{R.F.Y.[GGaz].T}|PEPTIDE2{[meI]}$$$$'},
       tgt: {
-        simplePolymers: [5, 1],
-        bondedRGroups: [1, 2, 2, 2, 1, 1],
+        simplePolymers: [5, 1], connections: [],
+        bondedRGroups: [1, 2, 2, 2, 1, 0],
       }
     },
-    'two-separated-2': {
+    'two-separated-1-5': {
+      src: {helm: 'PEPTIDE1{[meI]}|PEPTIDE2{R.F.Y.[GGaz].T}$$$$'},
+      tgt: {
+        simplePolymers: [1, 5], connections: [],
+        bondedRGroups: [0, 1, 2, 2, 2, 1],
+      }
+    },
+    'two-separated-4-2': {
       src: {helm: 'PEPTIDE1{R.F.Y.[GGaz]}|PEPTIDE2{T.[meI]}$$$$'},
       tgt: {
-        simplePolymers: [4, 2],
+        simplePolymers: [4, 2], connections: [],
         bondedRGroups: [1, 2, 2, 1, 1, 1],
       }
     },
     'two-connected-1': {
-      src: {helm: 'PEPTIDE1{R.F.Y.[GGaz].T}|PEPTIDE2{[meI]}$PEPTIDE1,PEPTIDE2,5:R2-1,R1$$$'},
+      src: {helm: 'PEPTIDE1{R.F.Y.[GGaz].T}|PEPTIDE2{[meI]}$PEPTIDE1,PEPTIDE2,5:R2-1:R1$$$'},
       tgt: {
-        simplePolymers: [5, 1],
+        simplePolymers: [5, 1], connections: [[['PEPTIDE1', 5, 'R2'], ['PEPTIDE2', 1, 'R1']]],
         bondedRGroups: [1, 2, 2, 2, 2, 1],
       }
     },
     'two-connected-2': {
-      src: {helm: 'PEPTIDE1{R.F.Y.[GGaz]}|PEPTIDE2{T.[meI]}$PEPTIDE1,PEPTIDE2,4:R2-1,R1$$$'},
+      src: {helm: 'PEPTIDE1{R.F.Y.[GGaz]}|PEPTIDE2{T.[meI]}$PEPTIDE1,PEPTIDE2,4:R2-1:R1$$$'},
       tgt: {
-        simplePolymers: [4, 2],
+        simplePolymers: [4, 2], connections: [[['PEPTIDE1', 4, 'R2'], ['PEPTIDE2', 1, 'R1']]],
         bondedRGroups: [1, 2, 2, 2, 2, 1],
       }
+    },
+    'two-cyclized-1-9': {
+      src: {helm: 'PEPTIDE1{[meI]}|PEPTIDE2{R.F.[GGaz].T.G.H.F.Y.P}$PEPTIDE2,PEPTIDE2,3:R3-9:R2|PEPTIDE2,PEPTIDE1,3:R4-1:R1$$$V2.0'},
+      tgt: {
+        simplePolymers: [1, 9],
+        connections: [
+          [['PEPTIDE2', 3, 'R3'], ['PEPTIDE2', 9, 'R2']],
+          [['PEPTIDE2', 3, 'R4'], ['PEPTIDE1', 1, 'R1']]],
+        bondedRGroups: [1, 1, 2, 4, 2, 2, 2, 2, 2, 1],
+      }
     }
   };
 
@@ -74,12 +91,21 @@ category('helm', () => {
       const simplePolymers = resHelm.simplePolymers
         .map((sp) => sp.monomers.length);
       const totalMonomerCount = simplePolymers.reduce((a, b) => a + b, 0);
-      expect(simplePolymers, tgt.simplePolymers);
+      expectArray(simplePolymers, tgt.simplePolymers);
+
+      const connections = resHelm.connectionList.getConnectionData()
+        .map((cdi) => {
+          return [
+            [cdi[0].polymerId, cdi[0].bond.monomerIdx + 1, `R${cdi[0].bond.rGroupId}`],
+            [cdi[1].polymerId, cdi[1].bond.monomerIdx + 1, `R${cdi[1].bond.rGroupId}`]];
+        });
+
+      expectArray(connections, tgt.connections);
 
-      const bondedRGroups = wu.count(0).take(resHelm.bondedRGroupsMap.size)
-        .map((i) => resHelm.bondedRGroupsMap.get(i)!.length).toArray();
+      const bondedRGroups = wu.count(0).take(resHelm.bondedRGroupsMap.length)
+        .map((i) => resHelm.bondedRGroupsMap[i].length).toArray();
       expect(totalMonomerCount, bondedRGroups.length);
       // expectArray(bondedRGroups, tgt.bondedRGroups);
-    }, {skipReason: 'new tests'});
+    });
   }
 });

package/src/tests/renderers-monomer-placer-tests.ts

@@ -4,10 +4,9 @@ import * as ui from 'datagrok-api/ui';
 
 import wu from 'wu';
 
-import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
 import {MonomerPlacer, hitBounds} from '@datagrok-libraries/bio/src/utils/cell-renderer-monomer-placer';
 import {monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {getSeqHelper, ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {
   getUserLibSettings, setUserLibSettings
@@ -164,4 +163,60 @@ id3,QHIRE--LT
       expect(res, testData.tgt);
     });
   }
+
+  const lengthsTests = {
+    mono1: {
+      src: {
+        csv: 'seq' + '\n' +
+          'm1/m2/m3/m4/m5/m6/m7/m8/m9' + '\n' +
+          'n1/m2/n3/m4/n5/m6/n7/m8/n9' + '\n' +
+          'm1/n2/m3/n4/m5/n6/m7/n8/m9' + '\n',
+      },
+      tgt: {
+        lengths: [5, 31, 57, 83, 109, 135, 161, 187, 213, 239],
+      }
+    },
+    monoWithGaps: {
+      src: {
+        csv: 'seq' + '\n' +
+          'm1/m2/m3/m4/m5/m6//m8/m9' + '\n' +
+          'n1/m2/n3/m4/n5/m6//m8/n9' + '\n' +
+          'm1/n2/m3/n4/m5/n6/m7/n8/m9' + '\n',
+      },
+      tgt: {
+        lengths: [5, 31, 57, 83, 109, 135, 161, 187, 213, 239],
+      }
+    },
+    monoWithGapColumn: {
+      src: {
+        csv: 'seq' + '\n' +
+          'm1/m2/m3/m4/m5/m6//m8/m9' + '\n' +
+          'n1/m2/n3/m4/n5/m6//m8/n9' + '\n' +
+          'm1/n2/m3/n4/m5///n8/m9' + '\n',
+      },
+      tgt: {lengths: [5, 31, 57, 83, 109, 135, 161, 180, 206, 232],}
+    },
+  };
+
+  for (const [testName, testData] of Object.entries(lengthsTests)) {
+    test(`getCellMonomerLengths-${testName}`, async () => {
+      const df: DG.DataFrame = DG.DataFrame.fromCsv(testData.src.csv);
+      await grok.data.detectSemanticTypes(df);
+      const seqCol = df.getCol('seq');
+
+      const monLengthLimit: number = 3;
+      const charWidth: number = 7;
+      const sepWidth: number = 12;
+      const colTemp = new MonomerPlacer(null, seqCol, _package.logger, monLengthLimit, () => {
+        return {
+          monomerCharWidth: charWidth,
+          separatorWidth: sepWidth,
+          monomerToShort: monomerToShort,
+        };
+      });
+      await colTemp.init();
+      const resLengths = colTemp.getCellMonomerLengths(0, 1000)[1];
+      expectArray(resLengths, testData.tgt.lengths);
+    });
+  }
 });

package/src/utils/helm-to-molfile/converter/connection-list.ts

@@ -4,12 +4,12 @@ import {Bond} from './types';
 
 export class ConnectionList {
   constructor(connectionList: string) {
-    const splitted = connectionList.split(HELM_ITEM_SEPARATOR);
+    const splitted = connectionList.split(HELM_ITEM_SEPARATOR).filter((ci) => ci);
     splitted.forEach((connectionItem: string) => this.validateConnectionItem(connectionItem));
     this.connectionItems = splitted;
   }
 
-  private connectionItems: string[];
+  public connectionItems: string[];
 
   private validateConnectionItem(connectionItem: string): void {
     const allowedType = `(${HELM_POLYMER_TYPE.PEPTIDE}|${HELM_POLYMER_TYPE.RNA})`;
@@ -18,10 +18,10 @@ export class ConnectionList {
       throw new Error(`Cannot parse connection item from ${connectionItem}`);
   }
 
-  getConnectionData(): {polymerId: string, bond: Bond}[][] {
-    const result: {polymerId: string, bond: Bond}[][] = [];
+  getConnectionData(): { polymerId: string, bond: Bond }[][] {
+    const result: { polymerId: string, bond: Bond }[][] = [];
     this.connectionItems.forEach((connectionItem: string) => {
-      const pair: {polymerId: string, bond: Bond}[] = [];
+      const pair: { polymerId: string, bond: Bond }[] = [];
       const splitted = connectionItem.split(',');
       splitted[2].split('-').forEach((item, idx) => {
         const polymerId = splitted[idx];

package/src/utils/helm-to-molfile/converter/helm.ts

@@ -10,8 +10,7 @@ export class Helm {
     const simplePolymers = helmSections[0].split(HELM_ITEM_SEPARATOR);
     this.simplePolymers = simplePolymers
       .map((item) => new SimplePolymer(item));
-    if (helmSections[1] !== '')
-      this.connectionList = new ConnectionList(helmSections[1]);
+    this.connectionList = new ConnectionList(helmSections[1]);
     this.bondData = this.getBondData();
 
     this.bondedRGroupsMap = this.getBondedRGroupsMap();
@@ -22,25 +21,25 @@ export class Helm {
   readonly bondData: Bond[][];
 
   public readonly simplePolymers: SimplePolymer[];
-  public readonly connectionList?: ConnectionList;
+  public readonly connectionList: ConnectionList;
 
   /** Maps global monomer index to r-group ids (starting from 1) participating
    * in connection */
-  readonly bondedRGroupsMap: Map<number, number[]>;
+  readonly bondedRGroupsMap: number[][];
 
-  private getBondedRGroupsMap(): Map<number, number[]> {
-    const bondedRGroupsMap = new Map<number, number[]>();
+  private getBondedRGroupsMap(): number[][] {
+    const monomerCount = this.simplePolymers.map((sp) => sp.monomers.length)
+      .reduce((a, b) => a + b, 0);
+    const bondedRGroupsList: number[][] = Array.from({length: monomerCount}, () => []);
     this.bondData.forEach((bond) => {
       bond.forEach((bondPart) => {
         const monomerIdx = bondPart.monomerIdx;
         const rGroupId = bondPart.rGroupId;
-        if (!bondedRGroupsMap.get(monomerIdx))
-          bondedRGroupsMap.set(monomerIdx, []);
-        bondedRGroupsMap.get(monomerIdx)!.push(rGroupId);
+        bondedRGroupsList[monomerIdx].push(rGroupId);
       });
     });
 
-    return bondedRGroupsMap;
+    return bondedRGroupsList;
   }
 
   toString() {
@@ -93,19 +92,17 @@ export class Helm {
       this.shiftBondMonomerIds(shift, bondData);
       result.push(...bondData);
     });
-    if (this.connectionList) {
-      const connectionData = this.connectionList.getConnectionData();
-      connectionData.forEach((connection) => {
-        const data: Bond[] = [];
-        connection.forEach((connectionItem) => {
-          const shift = shifts[connectionItem.polymerId];
-          const bond = connectionItem.bond;
-          bond.monomerIdx += shift;
-          data.push(bond);
-        });
-        result.push(data);
+    const connectionData = this.connectionList.getConnectionData();
+    connectionData.forEach((connection) => {
+      const data: Bond[] = [];
+      connection.forEach((connectionItem) => {
+        const shift = shifts[connectionItem.polymerId];
+        const bond = connectionItem.bond;
+        bond.monomerIdx += shift;
+        data.push(bond);
       });
-    }
+      result.push(data);
+    });
     return result;
   }
 }

package/src/utils/helm-to-molfile/converter/monomer-wrapper.ts

@@ -28,8 +28,7 @@ export class MonomerWrapper {
     this.molfileWrapper = MolfileWrapperFactory.getInstance(molfile, monomerSymbol);
     this.capGroupElements = this.getCapGroupElements(libraryMonomerObject);
 
-    if (helm.bondedRGroupsMap.has(monomerIdx))
-      this.removeRGroups(helm.bondedRGroupsMap.get(monomerIdx)!);
+    this.removeRGroups(helm.bondedRGroupsMap[monomerIdx]!);
     this.capRemainingRGroups();
 
     this.shiftCoordinates(shift);

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

@@ -161,12 +161,12 @@ export class MonomerLibBase implements IMonomerLibBase {
   getTooltip(biotype: HelmType, monomerSymbol: string): HTMLElement {
     const polymerType = helmTypeToPolymerType(biotype);
     const res = ui.div([], {classes: 'ui-form ui-tooltip'});
+    const wem = this.getWebEditorMonomer(biotype, monomerSymbol)!;
     const monomer = this.getMonomer(polymerType, monomerSymbol);
     if (monomer) {
       // Symbol & Name
       const symbol = monomer[REQ.SYMBOL];
       const _name = monomer[REQ.NAME];
-      const wem = this.getWebEditorMonomer(biotype, monomerSymbol)!;
 
       const htmlColor = wem.backgroundcolor;
       res.append(ui.divH([

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

@@ -16,7 +16,7 @@ import {MonomerLibManager} from '../lib-manager';
 import {LIB_PATH} from '../consts';
 
 import '../../../../css/monomer-manager.css';
-import { MONOMER_RENDERER_TAGS } from '@datagrok-libraries/bio/src/utils/cell-renderer';
+import {MONOMER_RENDERER_TAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 
 // columns of monomers dataframe, note that rgroups is hidden and will be displayed as separate columns
 export enum MONOMER_DF_COLUMN_NAMES {
@@ -51,7 +51,6 @@ export const MONOMER_DF_COLUMNS = {
 
 
 export class MonomerManager implements IMonomerManager {
-
   private adjustColWidths() {
     setTimeout(() => {
       if (this.tv?.grid) {
@@ -87,7 +86,6 @@ export class MonomerManager implements IMonomerManager {
           }, 500);
         }
       }
-      
     }, () => this.tv?.dataFrame);
   }
 
@@ -203,6 +201,7 @@ export class MonomerManager implements IMonomerManager {
         }
       })
     );
+    this.tv.grid && (this.tv.grid.props.allowEdit = false); // disable editing
     return this.tv;
   }
 
@@ -239,6 +238,10 @@ export class MonomerManager implements IMonomerManager {
     });
     ribbons = ribbons.filter((r) => r.length > 0);
 
+    const newMonomerButton = ui.icons.add(() => {
+      this._newMonomerForm.setEmptyMonomer();
+    }, 'Add New Monomer');
+
     const editButton = ui.icons.edit(() => {
       if ((this.tv?.dataFrame?.currentRowIdx ?? -1) < 0) return;
       this.cloneMonomer(this.tv!.dataFrame.rows.get(this.tv!.dataFrame.currentRowIdx));
@@ -277,19 +280,19 @@ export class MonomerManager implements IMonomerManager {
       DG.Utils.download(libName!, lib!, 'text/plain');
     }, 'Download Monomer Library');
 
-    ribbons.push([editButton, deleteButton, downloadButton]);
+    ribbons.push([newMonomerButton, editButton, deleteButton, downloadButton]);
     this.tv.setRibbonPanels(ribbons);
 
 
     this.tv.name = MonomerManager.VIEW_NAME;
     this.libInput = ui.input.choice('Monomer Library', {value: libName, items: availableMonLibs, nullable: false, onValueChanged: async () => {
-        try {
-          const df = await this.getMonomersDf(this.libInput.value!);
+      try {
+        const df = await this.getMonomersDf(this.libInput.value!);
           this.tv!.dataFrame = df;
           this.adjustColWidths();
-        } catch (e) {
-          console.error(e);
-        }
+      } catch (e) {
+        console.error(e);
+      }
     }});
     this.libInput.addOptions(ui.icons.add(() => { this.createNewLibDialog(); }, 'Create new monomer library...'));
     const monForm = this._newMonomerForm.form;
@@ -370,6 +373,7 @@ export class MonomerManager implements IMonomerManager {
         df.col(rgName)!.semType = DG.SEMTYPE.MOLECULE;
       });
       df.currentRowIdx = -1;
+      // eslint-disable-next-line rxjs/no-ignored-subscription
       df.onCurrentRowChanged.subscribe((_) => {
         try {
           if (df.currentRowIdx === -1 || this._newMonomerForm.molChanged)
@@ -541,6 +545,7 @@ class MonomerForm implements INewMonomerForm {
       await this.saveMonomer();
     });
     // this.saveButton.style.pointerEvents = 'revert';
+    // eslint-disable-next-line rxjs/no-async-subscribe
     this.molSketcher.subs.push(this.molSketcher.onChanged.subscribe(async () => {
       if (!this.triggerMolChange) {
         this.triggerMolChange = true;
@@ -551,6 +556,9 @@ class MonomerForm implements INewMonomerForm {
         let smiles = this.molSketcher.getSmiles();
         if (!smiles) {
           this.rgroupsGrid.items = [];
+          this.rgroupsGrid.render();
+          this.saveValidationResult = 'Monomer molecule is required';
+          this.invalidateSaveButton();
           return;
         }
         smiles = getCorrectedSmiles([], smiles);
@@ -559,6 +567,8 @@ class MonomerForm implements INewMonomerForm {
         if (rGroupMatches.length === 0) {
           this.rgroupsGrid.items = [];
           this.rgroupsGrid.render();
+          this.saveValidationResult = 'At least one R-group is required';
+          this.invalidateSaveButton();
           return;
         }
         const rGroupNums = rGroupMatches.map((match) => Number.parseInt(match[0].match(/[1-9]/g)![0]));
@@ -606,6 +616,7 @@ class MonomerForm implements INewMonomerForm {
         [HELM_RGROUP_FIELDS.LABEL]: 'Label',
       },
     });
+    // eslint-disable-next-line rxjs/no-ignored-subscription
     this.rgroupsGrid.onItemChanged.subscribe(() => this.onMonomerInputChanged());
 
     this.rgroupsGridRoot = ui.divV([this.rgroupsGrid.root]);
@@ -633,17 +644,19 @@ class MonomerForm implements INewMonomerForm {
       'Meta': ui.divV([this.metaGrid.root]),
       'Colors': this.colorsEditor.form,
     }, false);
+  }
 
+  invalidateSaveButton() {
+    if (this.saveValidationResult)
+      this.saveButton.classList.add('d4-disabled');
+    else
+      this.saveButton.classList.remove('d4-disabled');
   }
 
   onMonomerInputChanged() {
     setTimeout(() => {
       this.saveValidationResult = this.validateInputs();
-      if (this.saveValidationResult)
-        this.saveButton.classList.add('d4-disabled');
-      else
-        this.saveButton.classList.remove('d4-disabled');
-
+      this.invalidateSaveButton();
       const monomerExists = this.polymerTypeInput.value && this.polymerTypeInput.value &&
         !!this.getMonomerLib()?.getMonomer(this.polymerTypeInput.value as PolymerType, this.monomerSymbolInput.value);
 
@@ -651,6 +664,27 @@ class MonomerForm implements INewMonomerForm {
     }, 200);
   }
 
+  setEmptyMonomer() {
+    this.triggerMolChange = false;
+    this.molSketcher.setSmiles('');
+    // leave polymer and monomer type as is
+    this.monomerSymbolInput.value = '';
+    this.monomerNameInput.value = '';
+    this.monomerIdInput.value = null;
+    this.monomerNaturalAnalogInput.value = null;
+    this.rgroupsGrid.items = [];
+    this.metaGrid.items = [];
+    this.rgroupsGrid.render();
+    this.metaGrid.render();
+    this.rgroupsGridRoot.style.display = 'none';
+    this.onMonomerInputChanged();
+    this.colorsEditor.colors = {
+      line: '#000000',
+      background: '#000000',
+      text: '#000000',
+    };
+  }
+
   setMonomer(monomer: Monomer) {
     this.triggerMolChange = false;
     this.molSketcher.setSmiles(monomer.smiles);
@@ -661,7 +695,7 @@ class MonomerForm implements INewMonomerForm {
     this.monomerIdInput.value = monomer.id;
     this.monomerNaturalAnalogInput.value = monomer.naturalAnalog ?? null;
     this.rgroupsGrid.items = resolveRGroupInfo(monomer.rgroups);
-    this.metaGrid.items = Object.entries(monomer.meta ?? {}).filter(([k, v]) => k?.toLowerCase() !== 'colors').map(([k, v]) => {
+    this.metaGrid.items = Object.entries(monomer.meta ?? {}).filter(([k, _v]) => k?.toLowerCase() !== 'colors').map(([k, v]) => {
       return {Property: k, Value: v};
     });
     this.rgroupsGrid.render();
@@ -681,7 +715,7 @@ class MonomerForm implements INewMonomerForm {
     } catch (e) {
       console.error(e);
     }
-    
+
     this.colorsEditor.colors = {
       line: colorsObj.line ?? '#000000',
       background: colorsObj.background ?? '#000000',
@@ -693,7 +727,7 @@ class MonomerForm implements INewMonomerForm {
     const rGroupsPane = this.inputsTabControl.panes.find((p) => p.name?.toLowerCase() === 'r-groups');
     rGroupsPane && (rGroupsPane.header.style.removeProperty('background-color'));
     if (!this.molSketcher.getSmiles()) return 'Monomer Molecule field is required';
-    for (const i of [this.polymerTypeInput, this.monomerTypeInput, this.monomerSymbolInput, this.monomerNameInput, this.monomerIdInput]) {
+    for (const i of [this.polymerTypeInput, this.monomerTypeInput, this.monomerSymbolInput, this.monomerNameInput]) {
       if (i.value == null || i.value === '')
         return `${i.caption} field is required`;
     }
@@ -703,17 +737,18 @@ class MonomerForm implements INewMonomerForm {
     if (!rgroupError) {
       outerFor:
       for (const item of this.rgroupsGrid.items) {
-        for (const [k, v] of Object.entries(item))
-          if (!v){
+        for (const [k, v] of Object.entries(item)) {
+          if (!v) {
             rgroupError = `R-group ${k} field is required for ${item[HELM_RGROUP_FIELDS.LABEL]}`;
             break outerFor;
-          } 
+          }
+        }
       }
     }
 
-    if (!rgroupError && this.rgroupsGrid.hasErrors()){ 
+    if (!rgroupError && this.rgroupsGrid.hasErrors())
       rgroupError = 'R-group fields contain errors';
-    }
+
     if (rgroupError) {
       rGroupsPane && (rGroupsPane.header.style.setProperty('background-color', '#ff000030'));
       return rgroupError;
@@ -730,7 +765,6 @@ class MonomerForm implements INewMonomerForm {
   }
 
   get form() {
-    
     this.inputsTabControl.root.classList.add('monomer-manager-form-tab-control');
     this.inputsTabControl.header.style.marginBottom = '10px';
     const saveB = ui.buttonsInput([this.saveButton]);
@@ -826,11 +860,11 @@ class MonomerForm implements INewMonomerForm {
       try {
         // first remove the existing monomer with that symbol
         const monomerIdx = libJSON.findIndex((m) => m.symbol === monomer.symbol && m.polymerType === monomer.polymerType);
-        if (monomerIdx >= 0) {
+        if (monomerIdx >= 0)
           libJSON[monomerIdx] = {...monomer, lib: undefined, wem: undefined};
-        } else {
+        else
           libJSON.push({...monomer, lib: undefined, wem: undefined});
-        }
+
         await grok.dapi.files.writeAsText(LIB_PATH + libName, JSON.stringify(libJSON));
         await (await MonomerLibManager.getInstance()).loadLibraries(true);
         await this.refreshTable(monomer.symbol);
@@ -839,6 +873,7 @@ class MonomerForm implements INewMonomerForm {
         grok.shell.error('Error saving monomer');
         console.error(e);
       }
+      this.onMonomerInputChanged();
     };
     let infoTable: HTMLDivElement | null = null;
     let promptMessage = '';
@@ -882,9 +917,9 @@ class MonomerForm implements INewMonomerForm {
       meta[item['Property']] = item['Value'];
     });
     const addingItem = this.metaGrid.addingItem;
-    if (addingItem && addingItem['Property'] && addingItem['Value']) {
+    if (addingItem && addingItem['Property'] && addingItem['Value'])
       meta[addingItem['Property']] = addingItem['Value'];
-    }
+
     //console.log(this.metaGrid.addingItem);
     if (this.colorsEditor.colors.line !== '#000000' || this.colorsEditor.colors.background !== '#000000' || this.colorsEditor.colors.text !== '#000000')
       meta.colors = {default: this.colorsEditor.colors};
@@ -975,7 +1010,7 @@ function getCorrectedMolBlock(molBlock: string) {
 
   if (rgpLineIdx === -1) {
     // number of r groups has 3 empty slots before it, atom numbers have 4 empty slots before them
-    let rgpLine = `M  RGP${rgroupLineNums.length.toString().padStart(3,' ')}${Object.entries(rgroupLineNumbers).map(([atomLine, rGroupNum]) => `${atomLine.toString().padStart(4, ' ')}${rGroupNum.toString().padStart(4, ' ')}`).join('')}`;
+    const rgpLine = `M  RGP${rgroupLineNums.length.toString().padStart(3, ' ')}${Object.entries(rgroupLineNumbers).map(([atomLine, rGroupNum]) => `${atomLine.toString().padStart(4, ' ')}${rGroupNum.toString().padStart(4, ' ')}`).join('')}`;
     const mEndIdx = lines.findIndex((line) => line.startsWith('M') && line.includes('END'));
     lines.splice(mEndIdx, 0, rgpLine);
   }
@@ -1042,9 +1077,8 @@ class ColorsEditor {
     };
 
     this._colors = colsHex;
-    for (const key in this._colorInputs) {
+    for (const key in this._colorInputs)
       this._colorInputs[key as keyof ColorsEditor['_colors']].value = colsHex[key as keyof ColorsEditor['_colors']];
-    }
   }
 
   get colorsMetaFormat() {
@@ -1054,4 +1088,4 @@ class ColorsEditor {
   get form() {
     return ui.form(Object.values(this._colorInputs));
   }
-}
+}