@datagrok/bio 1.7.3 → 1.7.6

package/files/samples/sample_SEPARATOR_PT.csv

@@ -0,0 +1,101 @@
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package/files/tests/testCereal.csv

@@ -0,0 +1,78 @@
+cereal_name,Calories,Carbohydrates,Fat,Fiber,Potassium,Protein,Sodium,Sugar,Vitamins/Minerals
+Mueslix_Crispy_Blend,160,17,2,3,160,3,150,13,25
+"Muesli_Raisins,_Dates,_&_Almonds",150,16,3,3,170,4,95,11,25
+"Muesli_Raisins,_Peaches,_&_Pecans",150,16,3,3,170,4,150,11,25
+Just_Right_Fruit_&_Nut,140,20,1,2,95,3,170,9,100
+Nutri-Grain_Almond-Raisin,140,21,2,3,130,3,220,7,25
+Total_Raisin_Bran,140,15,1,4,230,3,190,14,100
+Basic_4,130,18,2,2,100,3,210,8,25
+Oatmeal_Raisin_Crisp,130,null,2,null,120,3,170,10,25
+100%_Natural_Bran,120,8,5,2,135,3,15,8,0
+Cap'n'Crunch,120,12,2,0,35,1,220,12,25
+Cinnamon_Toast_Crunch,120,13,3,0,45,1,210,9,25
+"Fruit_&_Fibre_Dates,_Walnuts,_and_Oats",120,12,2,5,200,3,160,10,25
+Fruitful_Bran,120,14,0,5,190,3,240,12,25
+Great_Grains_Pecan,120,13,3,3,100,3,75,4,25
+Honey_Graham_Ohs,120,12,2,1,45,1,220,11,25
+Nut&Honey_Crunch,120,15,1,0,40,2,190,9,25
+Post_Nat._Raisin_Bran,120,11,1,6,260,3,200,14,25
+Raisin_Bran,120,14,1,5,240,3,210,12,25
+Almond_Delight,110,14,2,1,-1,2,200,8,25
+Apple_Cinnamon_Cheerios,110,null,2,null,70,2,180,10,25
+Apple_Jacks,110,11,0,1,30,2,125,14,25
+Cheerios,110,17,2,2,105,6,290,1,25
+Clusters,110,13,2,2,105,3,140,7,25
+Cocoa_Puffs,110,12,1,0,55,1,180,13,25
+Corn_Chex,110,22,0,0,25,2,280,3,25
+Corn_Pops,110,13,0,1,20,1,90,12,25
+Count_Chocula,110,12,1,0,65,1,180,13,25
+Cracklin'_Oat_Bran,110,10,3,4,160,3,140,7,25
+Crispix,110,21,0,1,30,2,220,3,25
+Froot_Loops,110,11,1,1,30,2,125,13,25
+Frosted_Flakes,110,14,0,1,25,1,200,11,25
+Fruity_Pebbles,110,13,1,0,25,1,135,12,25
+Golden_Grahams,110,15,1,0,45,1,280,9,25
+Grape-Nuts,110,17,0,3,90,3,170,3,25
+Honey-comb,110,14,0,0,35,1,180,11,25
+Honey_Nut_Cheerios,110,null,1,null,90,3,250,10,25
+Just_Right_Crunchy__Nuggets,110,17,1,1,60,2,170,6,100
+Kix,110,21,1,0,40,2,260,3,25
+Lucky_Charms,110,12,1,0,55,2,180,12,25
+Rice_Chex,110,23,0,0,30,1,240,2,25
+Rice_Krispies,110,22,0,0,35,2,290,3,25
+Smacks,110,9,1,1,40,2,70,15,25
+Special_K,110,16,0,1,55,6,230,3,25
+Total_Corn_Flakes,110,21,1,0,35,2,200,3,100
+Triples,110,21,1,0,60,2,250,3,25
+Trix,110,13,1,0,25,1,140,12,25
+Wheaties_Honey_Gold,110,16,1,1,60,2,200,8,25
+Corn_Flakes,100,21,0,1,35,2,290,2,25
+Cream_of_Wheat_(Quick),100,21,0,1,-1,3,80,0,0
+Crispy_Wheat_&_Raisins,100,11,1,2,120,2,140,10,25
+Double_Chex,100,18,0,1,80,2,190,5,25
+Frosted_Mini-Wheats,100,14,0,3,100,3,0,7,25
+Golden_Crisp,100,11,0,0,40,2,45,15,25
+Grape_Nuts_Flakes,100,15,1,3,85,3,140,5,25
+Life,100,12,2,2,95,4,150,6,25
+Maypo,100,16,1,0,95,4,0,3,25
+Multi-Grain_Cheerios,100,15,1,2,90,2,220,6,25
+Product_19,100,20,0,1,45,3,320,3,100
+Quaker_Oat_Squares,100,14,1,2,110,4,135,6,25
+Quaker_Oatmeal,100,-1,2,null,110,5,0,-1,0
+Raisin_Nut_Bran,100,null,2,null,140,3,140,8,25
+Total_Whole_Grain,100,16,1,3,110,3,200,3,100
+Wheat_Chex,100,17,1,3,115,3,230,3,25
+Wheaties,100,17,1,3,110,3,200,3,25
+Bran_Chex,90,15,1,4,125,2,200,6,25
+Bran_Flakes,90,13,0,5,190,3,210,5,25
+Nutri-grain_Wheat,90,18,0,3,90,3,170,2,25
+Raisin_Squares,90,15,0,2,110,2,0,6,25
+Shredded_Wheat_'n'Bran,90,19,0,4,140,3,0,0,0
+Shredded_Wheat_spoon_size,90,20,0,3,120,3,0,0,0
+Strawberry_Fruit_Wheats,90,15,0,3,90,2,15,5,25
+Shredded_Wheat,80,16,0,3,95,2,0,0,0
+100%_Bran,70,5,1,10,280,4,130,6,25
+All-Bran,70,7,1,9,320,4,260,5,25
+All-Bran_with_Extra_Fiber,50,8,0,14,330,4,140,0,25
+Puffed_Rice,50,13,0,0,15,1,0,0,0
+Puffed_Wheat,50,10,0,1,50,2,0,0,0

package/package.json

@@ -2,7 +2,7 @@
   "name": "@datagrok/bio",
   "beta": false,
   "friendlyName": "Bio",
-  "version": "1.7.3",
+  "version": "1.7.6",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -11,12 +11,13 @@
   },
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "2.8.1",
+    "@datagrok-libraries/bio": "2.8.3",
     "@datagrok-libraries/utils": "^1.0.0",
     "@datagrok-libraries/ml": "^2.0.10",
     "cash-dom": "latest",
     "datagrok-api": "^1.4.12",
     "dayjs": "latest",
+    "rxjs": "^6.5.5",
     "ts-loader": "^9.2.5",
     "typescript": "^4.4.2",
     "openchemlib": "6.0.1"
@@ -60,7 +61,10 @@
   ],
   "sources": [
     "css/helm.css",
-    "https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js"
+    "https://ajax.googleapis.com/ajax/libs/dojo/1.10.4/dojo/dojo.js",
+    "helm/JSDraw/Scilligence.JSDraw2.Lite.js",
+    "helm/JSDraw/Scilligence.JSDraw2.Resources.js",
+    "helm/JSDraw/Pistoia.HELM-uncompressed.js"
   ],
   "category": "Bioinformatics"
 }

package/src/__jest__/remote.test.ts

@@ -16,15 +16,30 @@ beforeAll(async () => {
 }, P_START_TIMEOUT);
 
 afterAll(async () => {
-  await browser.close();
+  await browser?.close();
+});
+
+expect.extend({
+  checkOutput(received, expected, context) {
+    if (received === expected) {
+      return {
+        message: () => context,
+        pass: true
+      };
+    } else {
+      return {
+        message: () => context,
+        pass: false
+      };
+    }
+  }
 });
 
 it('TEST', async () => {
-  const targetPackage: string = process.env.TARGET_PACKAGE ?? 'Bio';
+  const targetPackage:string = process.env.TARGET_PACKAGE ?? 'Bio';
   console.log(`Testing ${targetPackage} package`);
 
-  //console.log(require('root-require')('package.json').version);
-  const r = await page.evaluate((targetPackage): Promise<object> => {
+  const r = await page.evaluate((targetPackage):Promise<object> => {
     return new Promise<object>((resolve, reject) => {
       (<any>window).grok.functions.eval(targetPackage + ':test()').then((df: any) => {
         const cStatus = df.columns.byName('success');
@@ -32,23 +47,22 @@ it('TEST', async () => {
         const cCat = df.columns.byName('category');
         const cName = df.columns.byName('name');
         let failed = false;
-        let report = '';
+        let passReport = '';
+        let failReport = '';
         for (let i = 0; i < df.rowCount; i++) {
-          if (!cStatus.get(i)) {
-            report += `${cCat.get(i)}.${cName.get(i)}: ${cMessage.get(i)}\n`;
+          if (cStatus.get(i)) {
+            passReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+          } else {
             failed = true;
+            failReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
           }
         }
-        resolve({report, failed});
+        resolve({failReport, passReport, failed});
       }).catch((e: any) => reject(e));
     });
   }, targetPackage);
   // @ts-ignore
-  console.log(r.report);
+  console.log(r.passReport);
   // @ts-ignore
-  expect(r.failed).toBe(false);
+  expect(r.failed).checkOutput(false, r.failReport);
 }, 100000);
-
-// it('WebLogo.getAlphabetSimilarity', () => {
-//
-// });

package/src/const.ts

@@ -2,3 +2,24 @@ import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
+export const jsonSdfMonomerLibDict = {
+  'monomerType': null,
+  'smiles': null,
+  'name': 'MonomerName',
+  'author': null,
+  'molfile': 'molecule',
+  'naturalAnalog': 'MonomerNaturalAnalogCode',
+  'rgroups': 'MonomerCaps',
+  'createDate': null,
+  'id': null,
+  'polymerType': 'MonomerType',
+  'symbol': 'MonomerCode'
+};
+
+export const RGROUP_FIELD = 'rgroups';
+export const CAP_GROUP_SMILES = 'capGroupSmiles';
+export const RGROUP_ALTER_ID = 'alternateId';
+export const CAP_GROUP_NAME = 'capGroupName';
+export const RGROUP_LABEL = 'label';
+export const MONOMER_SYMBOL = 'symbol';
+export const SDF_MONOMER_NAME = 'MonomerName';

package/src/package-test.ts

@@ -9,7 +9,7 @@ import './tests/msa-tests';
 import './tests/sequence-space-test';
 import './tests/activity-cliffs-tests';
 import './tests/splitters-test';
-import './tests/renderer-test';
+import './tests/renderers-test';
 import './tests/convert-test';
 
 export const _package = new DG.Package();

package/src/package.ts

@@ -15,10 +15,9 @@ import {getEmbeddingColsNames, sequenceSpace} from './utils/sequence-space';
 import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {sequenceGetSimilarities, drawTooltip} from './utils/sequence-activity-cliffs';
-import {getMolfilesFromSeq, HELM_CORE_LIB_FILENAME} from './utils/utils';
+import {createJsonMonomerLibFromSdf, getMolfilesFromSeq, HELM_CORE_LIB_FILENAME} from './utils/utils';
 import {getMacroMol} from './utils/atomic-works';
 import {MacromoleculeSequenceCellRenderer} from './utils/cell-renderer';
-import {delay} from '@datagrok-libraries/utils/src/test';
 import {convert} from './utils/convert';
 
 //tags: init
@@ -245,7 +244,15 @@ export async function compositionAnalysis(): Promise<void> {
     return;
   }
 
-  tv.addViewer('WebLogo', {sequenceColumnName: col.name});
+  const wlViewer = tv.addViewer('WebLogo', {sequenceColumnName: col.name});
+  grok.shell.tv.dockManager.dock(wlViewer, DG.DOCK_TYPE.DOWN, null, 'Composition analysis', 0.25);
+}
+
+//top-menu: Bio | Sdf to Json lib...
+//name: sdfToJsonLib
+//input: dataframe table
+export async function sdfToJsonLib(table: DG.DataFrame) {
+  const jsonMonomerLibrary = createJsonMonomerLibFromSdf(table);
 }
 
 // helper function for importFasta
@@ -325,7 +332,7 @@ export function importFasta(fileContent: string): DG.DataFrame [] {
   ])];
 }
 
-//name: Bio | Convert
+//name: Bio | Convert ...
 //friendly-name: Bio | Convert
 //tags: panel, bio
 //input: column col {semType: Macromolecule}

package/src/tests/convert-test.ts

@@ -83,7 +83,7 @@ MKP---SEYV
 
     separatorGaps: `seq
 F/W//P/H//E/Y
-//Y/N/R/Q/W/Y/V//
+/Y/N/R/Q/W/Y/V/
 M/K/P////S/E/Y/V
 `,
 
@@ -133,6 +133,7 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   }
 
   // FASTA tests
+  // fasta -> separator
   test('testFastaPtToSeparator', async () => {
     await _testConvert(Samples.fastaPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
   });
@@ -142,7 +143,11 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testFastaRnaToSeparator', async () => {
     await _testConvert(Samples.fastaRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
   });
+  test('testFastaGapsToSeparator', async () => {
+    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
+  });
 
+  // fasta -> helm
   test('testFastaPtToHelm', async () => {
     await _testConvert(Samples.fastaPt, converter(NOTATION.HELM), Samples.helmPt);
   });
@@ -152,16 +157,13 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testFastaRnaToHelm', async () => {
     await _testConvert(Samples.fastaRna, converter(NOTATION.HELM), Samples.helmRna);
   });
-
-  test('testFastaGapsToSeparator', async () => {
-    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR, '/'), Samples.separatorGaps);
-  });
   test('testFastaGapsToHelm', async () => {
-    await _testConvert(Samples.fastaGaps, converter(NOTATION.SEPARATOR), Samples.helmGaps);
+    await _testConvert(Samples.fastaGaps, converter(NOTATION.HELM), Samples.helmGaps);
   });
 
 
   // SEPARATOR tests
+  // separator -> fasta
   test('testSeparatorPtToFasta', async () => {
     await _testConvert(Samples.separatorPt, converter(NOTATION.FASTA), Samples.fastaPt);
   });
@@ -171,7 +173,11 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testSeparatorRnaToFasta', async () => {
     await _testConvert(Samples.separatorRna, converter(NOTATION.FASTA), Samples.fastaRna);
   });
+  test('testSeparatorGapsToFasta', async () => {
+    await _testConvert(Samples.separatorGaps, converter(NOTATION.FASTA), Samples.fastaGaps);
+  });
 
+  // separator -> helm
   test('testSeparatorPtToHelm', async () => {
     await _testConvert(Samples.separatorPt, converter(NOTATION.HELM), Samples.helmPt);
   });
@@ -181,13 +187,31 @@ PEPTIDE1{M.K.P.*.*.*.S.E.Y.V}$$$
   test('testSeparatorRnaToHelm', async () => {
     await _testConvert(Samples.separatorRna, converter(NOTATION.HELM), Samples.helmRna);
   });
-  test('testSeparatorGapsToFasta', async () => {
-    await _testConvert(Samples.separatorGaps, converter(NOTATION.FASTA), Samples.fastaGaps);
-  });
   test('testSeparatorGapsToHelm', async () => {
     await _testConvert(Samples.separatorGaps, converter(NOTATION.HELM), Samples.helmGaps);
   });
 
 
-  // HELM tests: TODO
+  // HELM tests
+  // helm -> fasta
+  test('HelmDnaToFasta', async () => {
+    await _testConvert(Samples.helmDna, converter(NOTATION.FASTA), Samples.fastaDna);
+  });
+  test('HelmRnaToFasta', async () => {
+    await _testConvert(Samples.helmRna, converter(NOTATION.FASTA), Samples.fastaRna);
+  });
+  test('HelmPtToFasta', async () => {
+    await _testConvert(Samples.helmPt, converter(NOTATION.FASTA), Samples.fastaPt);
+  });
+
+  // helm -> separator
+  test('HelmDnaToSeparator', async () => {
+    await _testConvert(Samples.helmDna, converter(NOTATION.SEPARATOR), Samples.separatorDna);
+  });
+  test('HelmRnaToSeparator', async () => {
+    await _testConvert(Samples.helmRna, converter(NOTATION.SEPARATOR, '*'), Samples.separatorRna);
+  });
+  test('HelmPtToSeparator', async () => {
+    await _testConvert(Samples.helmPt, converter(NOTATION.SEPARATOR, '-'), Samples.separatorPt);
+  });
 });

package/src/tests/detectors-test.ts

@@ -113,6 +113,7 @@ MWRSWY-CKHP
     testIdCsv = 'testIdCsv',
     testSmilesCsv = 'testSmilesCsv',
     testSmiles2Csv = 'testSmiles2Csv',
+    testCerealCsv = 'testCerealCsv',
   }
 
   const samples: { [key: string]: string } = {
@@ -128,6 +129,7 @@ MWRSWY-CKHP
     'testIdCsv': 'System:AppData/Bio/tests/testId.csv',
     'testSmilesCsv': 'System:AppData/Bio/tests/testSmiles.csv',
     'testSmiles2Csv': 'System:AppData/Bio/tests/testSmiles2.csv',
+    'testCerealCsv': 'System:AppData/Bio/tests/testCereal.csv',
   };
 
   const _samplesDfs: { [key: string]: Promise<DG.DataFrame> } = {};
@@ -306,6 +308,10 @@ MWRSWY-CKHP
   test('samplesFastaPtPosSequence', async () => {
     await (_testPos(readSamples(Samples.fastaPtCsv), 'sequence', 'fasta:SEQ:PT'));
   });
+
+  test('samplesTestCerealNegativeCerealName', async () => {
+    await (_testNeg(readSamples(Samples.testCerealCsv), 'cereal_name'));
+  });
 });
 
 export async function _testNeg(readDf: DfReaderFunc, colName: string) {

package/src/tests/{renderer-test.ts → renderers-test.ts}

@@ -1,9 +1,11 @@
-import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
+import {after, before, category, expect, test} from '@datagrok-libraries/utils/src/test';
 
 import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {importFasta, multipleSequenceAlignmentAny} from '../package';
+import {readDataframe} from './utils';
+import {convertDo} from '../utils/convert';
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/notation-converter';
 
 category('renderers', () => {
   let tvList: DG.TableView[];
@@ -23,42 +25,49 @@ category('renderers', () => {
     await _testAfterMsa();
   });
 
+  test('afterConvert', async () => {
+    await _testAfterConvert();
+  });
+
   async function _testAfterMsa() {
     const fastaTxt: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/sample_FASTA.fasta');
     const df: DG.DataFrame = importFasta(fastaTxt)[0];
-    // await grok.data.detectSemanticTypes(df);
-
-    const srcSeqCol: DG.Column | null = df.col('sequence');
-    expect(srcSeqCol !== null, true);
-    console.log('Bio: tests/renderers/afterMsa, src data loaded');
-
     const tv: DG.TableView = grok.shell.addTableView(df);
+    await grok.data.detectSemanticTypes(df);
     console.log('Bio: tests/renderers/afterMsa, table view');
 
-    // await grok.data.detectSemanticTypes(df);
-    console.log('Bio: tests/renderers/afterMsa, detectSemanticTypes');
+    const srcSeqCol: DG.Column | null = df.col('sequence');
+    expect(srcSeqCol !== null, true);
 
     console.log('Bio: tests/renderers/afterMsa, src before test ' +
       `semType="${srcSeqCol!.semType}", units="${srcSeqCol!.getTag(DG.TAGS.UNITS)}", ` +
       `cell.renderer="${srcSeqCol!.getTag('cell.renderer')}"`);
     expect(srcSeqCol!.semType, DG.SEMTYPE.MACROMOLECULE);
     expect(srcSeqCol!.getTag(DG.TAGS.UNITS), 'fasta:SEQ:PT');
-    // TODO: Find the way to check renderer for columns
     expect(srcSeqCol!.getTag('cell.renderer'), 'Macromolecule');
-    console.log('Bio: tests/renderers/afterMsa, src semType tested');
 
     const msaSeqCol: DG.Column | null = await multipleSequenceAlignmentAny(df, srcSeqCol!);
-    console.log('Bio: tests/renderers/afterMsa, msaSeqCol created');
-
     tv.grid.invalidate();
-    console.log('Bio: tests/renderers/afterMsa, tv.grid invalidated');
 
     expect(msaSeqCol!.semType, DG.SEMTYPE.MACROMOLECULE);
     expect(msaSeqCol!.getTag(DG.TAGS.UNITS), 'fasta:SEQ.MSA:PT');
     expect(msaSeqCol!.getTag('cell.renderer'), 'Macromolecule');
-    console.log('Bio: tests/renderers/afterMsa, msa semType tested');
 
     dfList.push(df);
     tvList.push(tv);
   }
+
+  async function _testAfterConvert() {
+    const csv: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/sample_FASTA_PT.csv');
+    const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
+    const tv: DG.TableView = grok.shell.addTableView(df);
+    await grok.data.detectSemanticTypes(df);
+
+    const srcCol: DG.Column = df.col('sequence')!;
+    const tgtCol: DG.Column = await convertDo(srcCol, NOTATION.SEPARATOR, '/');
+    expect(tgtCol.getTag('cell.renderer'), 'Macromolecule');
+
+    tvList.push(tv);
+    dfList.push(df);
+  };
 });

package/src/utils/cell-renderer.ts

@@ -9,6 +9,7 @@ import * as ui from 'datagrok-api/ui';
 
 const lru = new DG.LruCache<any, any>();
 const undefinedColor = 'rgb(100,100,100)';
+const grayColor = '#808080'
 
 function getPalleteByType(paletteType: string): SeqPalette {
   switch (paletteType) {
@@ -81,7 +82,7 @@ function printLeftOrCentered(
     g.fillStyle = color;
     g.globalAlpha = transparencyRate;
     g.fillText(colorPart, x + dx1, y + dy);
-    g.fillStyle = '#808080';
+    g.fillStyle = grayColor;
     g.fillText(grayPart, x + dx2, y + dy);
   }
 
@@ -96,6 +97,22 @@ function printLeftOrCentered(
   }
 }
 
+function findMonomers(helmString: string) {
+  //@ts-ignore
+  const types = Object.keys(org.helm.webeditor.monomerTypeList());
+  const monomers: any = [];
+  const monomer_names: any = [];
+  for (var i = 0; i < types.length; i++) {
+    //@ts-ignore
+    monomers.push(new scil.helm.Monomers.getMonomerSet(types[i]));
+    Object.keys(monomers[i]).forEach(k => {
+      monomer_names.push(monomers[i][k].id);
+    });
+  }
+  const split_string = WebLogo.splitterAsHelm(helmString);
+  return new Set(split_string.filter(val => !monomer_names.includes(val)));
+}
+
 export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   get name(): string { return 'macromoleculeSequence'; }
 
@@ -125,22 +142,47 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const cell = gridCell.cell;
     const tag = gridCell.cell.column.getTag(DG.TAGS.UNITS);
     if (tag === 'HELM') {
-      const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
-      host.setAttribute('dataformat', 'helm');
-      host.setAttribute('data', gridCell.cell.value);
-      gridCell.element = host;
-      //@ts-ignore
-      const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
-      const formula = canvas.getFormula(true);
-      if (!formula) {
-        gridCell.element = ui.divText(gridCell.cell.value, {style: {color: 'red'}});
-      } else {
+      console.log(findMonomers(cell.value));
+      const monomers = findMonomers(cell.value);
+      if (monomers.size == 0) {
+        const host = ui.div([], {style: {width: `${w}px`, height: `${h}px`}});
+        host.setAttribute('dataformat', 'helm');
+        host.setAttribute('data', gridCell.cell.value);
         gridCell.element = host;
-        const molWeight = Math.round(canvas.getMolWeight() * 100) / 100;
-        const coef = Math.round(canvas.getExtinctionCoefficient(true) * 100) / 100;
-        const molfile = canvas.getMolfile();
-        const result = formula + ', ' + molWeight + ', ' + coef + ', ' + molfile;
-        lru.set(gridCell.cell.value, result);
+        //@ts-ignore
+        const canvas = new JSDraw2.Editor(host, {width: w, height: h, skin: 'w8', viewonly: true});
+        const formula = canvas.getFormula(true);
+        if (!formula) {
+          gridCell.element = ui.divText(gridCell.cell.value, {style: {color: 'red'}});
+        }
+        return;
+      }
+      if (monomers.size > 0) {
+        w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
+        g.save();
+        g.beginPath();
+        g.rect(x, y, w, h);
+        g.clip();
+        g.font = '12px monospace';
+        g.textBaseline = 'top';
+        let x1 = x;
+        const s: string = cell.value ?? '';
+        let subParts: string[] = WebLogo.splitterAsHelm(s);
+        let color = undefinedColor;
+        subParts.forEach((amino, index) => {
+          if (monomers.has(amino)) {
+            color = 'red';
+          } else {
+            color = grayColor;
+          }
+          g.fillStyle = undefinedColor;
+          let last = false;
+          if (index === subParts.length - 1)
+            last = true;
+          x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0, '/', last);
+        });
+        g.restore();
+        return;
       }
     } else {
       const [type, subtype, paletteType] = gridCell.cell.column.getTag(DG.TAGS.UNITS).split(':');
@@ -176,6 +218,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       });
 
       g.restore();
+      return;
     }
   }
 }