@datagrok/peptides 0.8.8 → 0.8.9

package/src/utils/cell-renderer.ts

@@ -80,7 +80,7 @@ export function measureAAR(s: string): number {
 function printLeftOrCentered(
   x: number, y: number, w: number, h: number,
   g: CanvasRenderingContext2D, s: string, color = ChemPalette.undefinedColor,
-  pivot: number = 0, left = false, hideMod = false, transparencyRate: number = 1.0
+  pivot: number = 0, left = false, hideMod = false, transparencyRate: number = 1.0,
 ) {
   g.textAlign = 'start';
   let colorPart = pivot == -1 ? s.substring(0) : s.substring(0, pivot);
@@ -145,37 +145,57 @@ function printLeftOrCentered(
  * @extends {DG.GridCellRenderer}
  */
 export class AminoAcidsCellRenderer extends DG.GridCellRenderer {
-    chemPalette: ChemPalette | null;
+  chemPalette: ChemPalette | null;
 
-    /**
+  /**
      * Renderer name.
      *
      * @readonly
      * @memberof AminoAcidsCellRenderer
      */
-    get name() {
-      return 'aminoAcidsCR';
-    }
+  get name() {
+    return 'aminoAcidsCR';
+  }
 
-    /**
+  /**
      * Cell type.
      *
      * @readonly
      * @memberof AminoAcidsCellRenderer
      */
-    get cellType() {
-      return 'aminoAcids';
-    }
+  get cellType() {
+    return 'aminoAcids';
+  }
+
+  /**
+     * Cell height.
+     *
+     * @readonly
+     * @memberof AminoAcidsCellRenderer
+     */
+  get defaultHeight() {
+    return 15;
+  }
+
+  /**
+     * Cell width.
+     *
+     * @readonly
+     * @memberof AminoAcidsCellRenderer
+     */
+  get defaultWidth() {
+    return 30;
+  }
 
-    /**
+  /**
      * Constructor.
      */
-    constructor() {
-      super();
-      this.chemPalette = null;
-    }
+  constructor() {
+    super();
+    this.chemPalette = null;
+  }
 
-    /**
+  /**
      * Cell renderer function.
      *
      * @param {CanvasRenderingContext2D} g Canvas rendering context.
@@ -186,22 +206,26 @@ export class AminoAcidsCellRenderer extends DG.GridCellRenderer {
      * @param {DG.GridCell} gridCell Grid cell.
      * @param {DG.GridCellStyle} cellStyle Cell style.
      */
-    render(
-      g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
-      cellStyle: DG.GridCellStyle) {
-      this.chemPalette ??= new ChemPalette('grok', gridCell.tableColumn?.getTag('groups') ? true : false);
-
-      g.save();
-      g.beginPath();
-      g.rect(x, y, w, h);
-      g.clip();
-      g.font = `14px monospace`;
-      g.textBaseline = 'top';
-      const s: string = gridCell.cell.value ? gridCell.cell.value : '-';
-      const [color, pivot] = cp.getColorPivot(s);
-      printLeftOrCentered(x, y, w, h, g, s, color, pivot, false, true);
-      g.restore();
-    }
+  render(
+    g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell,
+    cellStyle: DG.GridCellStyle) {
+    this.chemPalette ??= new ChemPalette('grok', gridCell.tableColumn?.getTag('groups') ? true : false);
+
+    y -= 2;
+    g.save();
+    g.beginPath();
+    g.rect(x, y, w, h);
+    g.clip();
+    g.font = `12px monospace`;
+    g.textBaseline = 'top';
+    const s: string = gridCell.cell.value ? gridCell.cell.value : '-';
+    let [color, outerS, innerS, pivot] = cp.getColorAAPivot(s);
+    if (innerS)
+      outerS = s;
+
+    printLeftOrCentered(x, y, w, h, g, outerS, color, pivot, false, true);
+    g.restore();
+  }
 }
 
 /**
@@ -232,13 +256,23 @@ export class AlignedSequenceCellRenderer extends DG.GridCellRenderer {
     return 'alignedSequence';
   }
 
+  /**
+   * Cell height.
+   *
+   * @readonly
+   * @memberof AlignedSequenceCellRenderer
+   */
+  get defaultHeight() {
+    return 30;
+  }
+
   /**
    * Cell width.
    *
    * @readonly
    * @memberof AlignedSequenceCellRenderer
    */
-   get defaultWidth() {
+  get defaultWidth() {
     return 230;
   }
 
@@ -260,13 +294,12 @@ export class AlignedSequenceCellRenderer extends DG.GridCellRenderer {
   ) {
     const grid = gridCell.dart.grid ? gridCell.grid : gridCell.dart.grid;
     const cell = gridCell.cell;
-
     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 = '14px monospace';
+    g.font = '12px monospace';
     g.textBaseline = 'top';
     const s: string = cell.value ?? '';
 
@@ -277,13 +310,13 @@ export class AlignedSequenceCellRenderer extends DG.GridCellRenderer {
     x = Math.max(x, x + (w - textSize.width) / 2);
 
     subParts.forEach((amino: string, index) => {
-      const [color, pivot] = cp.getColorPivot(amino);
+      let [color, outerAmino,, pivot] = cp.getColorAAPivot(amino);
       g.fillStyle = ChemPalette.undefinedColor;
       if (index + 1 < subParts.length) {
-        const gap = simplified?'':' ';
-        amino += `${amino?'':'-'}${gap}`;
+        const gap = simplified ? '' : ' ';
+        outerAmino += `${outerAmino?'':'-'}${gap}`;
       }
-      x = printLeftOrCentered(x, y, w, h, g, amino, color, pivot, true);
+      x = printLeftOrCentered(x, y, w, h, g, outerAmino, color, pivot, true);
     });
 
     g.restore();
@@ -321,7 +354,7 @@ export function processSequence(subParts: string[]): [string[], boolean] {
  * @class AlignedSequenceDifferenceCellRenderer
  * @extends {DG.GridCellRenderer}
  */
- export class AlignedSequenceDifferenceCellRenderer extends DG.GridCellRenderer {
+export class AlignedSequenceDifferenceCellRenderer extends DG.GridCellRenderer {
   /**
    * Renderer name.
    *
@@ -358,8 +391,8 @@ export function processSequence(subParts: string[]): [string[], boolean] {
    * @readonly
    * @memberof AlignedSequenceDifferenceCellRenderer
    */
-   get defaultWidth() {
-    return 200;
+  get defaultWidth() {
+    return 230;
   }
 
   /**
@@ -382,12 +415,11 @@ export function processSequence(subParts: string[]): [string[], boolean] {
     const cell = gridCell.cell;
 
     w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
-    y += 2;
     g.save();
     g.beginPath();
     g.rect(x, y, w, h);
     g.clip();
-    g.font = '14px monospace';
+    g.font = '12px monospace';
     g.textBaseline = 'top';
     const s: string = cell.value ?? '';
 
@@ -395,33 +427,29 @@ export function processSequence(subParts: string[]): [string[], boolean] {
     const [s1, s2] = s.split('#');
     const subParts1 = s1.split('-');
     const subParts2 = s2.split('-');
-    const [text, simplified] = processSequence(subParts1);
+    const [text] = processSequence(subParts1);
     const textSize = g.measureText(text.join(''));
     x = Math.max(x, x + (w - textSize.width) / 2);
 
     subParts1.forEach((amino1: string, index) => {
-      let color, pivot;
       let amino2 = subParts2[index];
+      const [color1, amino1Outer, amino1Inner, pivot1] = cp.getColorAAPivot(amino1);
+      const [color2, amino2Outer, amino2Inner, pivot2] = cp.getColorAAPivot(amino2);
 
-      if (amino1 != '')
-        [color, pivot] = cp.getColorPivot(amino1);
-      else
-        [color, pivot] = cp.getColorPivot(amino2);
-      
       if (amino1 != amino2) {
         const verticalShift = 7;
 
-        if (amino1 == '') 
-          amino1 = '-';
-        if (amino2 == '') 
-          amino2 = '-';
+        amino1 = amino1Outer + (amino1Inner !== '' ? '(' + amino1Inner + ')' : '');
+        amino2 = amino2Outer + (amino2Inner !== '' ? '(' + amino2Inner + ')' : '');
+        amino1 = amino1 === '' ? '-' : amino1;
+        amino2 = amino2 === '' ? '-' : amino2;
 
-        printLeftOrCentered(x, y - verticalShift, w, h, g, amino1, color, pivot, true);
-        x = printLeftOrCentered(x, y + verticalShift, w, h, g, amino2, color, pivot, true);
-      } else {
-        x = printLeftOrCentered(x, y, w, h, g, amino1, color, pivot, true, false, 0.5);
-      } 
+        const x1 = printLeftOrCentered(x, y - verticalShift, w, h, g, amino1, color1, pivot1, true);
+        x = printLeftOrCentered(x, y + verticalShift, w, h, g, amino2, color2, pivot2, true);
+        x = Math.max(x, x1) + 4;
+      } else
+        x = printLeftOrCentered(x, y, w, h, g, amino1 ? amino1 : '-', color1, pivot1, true, true, 0.5) + 4;
     });
     g.restore();
   }
-}
+}

package/src/utils/chem-palette.ts

@@ -36,26 +36,31 @@ export class ChemPalette {
    * @param {number} y y coordinate of the mouse pointer.
    */
   async showTooltip(cell: DG.GridCell, x: number, y: number) {
-    if(!this.isInit)
+    if (!this.isInit)
       this.monomerLib = new MonomerLibrary(await _package.files.readAsText(`HELMMonomers_June10.sdf`));
 
     const s = cell.cell.value as string;
     let toDisplay = [ui.divText(s)];
-    const [, aar] = this.getColorAAPivot(s);
-    if (this.monomerLib!.monomerNames.includes(aar)) {
-      if (s in ChemPalette.AANames)
-        toDisplay = [ui.divText(ChemPalette.AANames[s])];
+    const [, aarOuter, aarInner] = this.getColorAAPivot(s);
+    for (const aar of [aarOuter, aarInner]) {
+      if (this.monomerLib!.monomerNames.includes(aar)) {
+        if (aar in ChemPalette.AANames)
+          toDisplay = [ui.divText(ChemPalette.AANames[aar])];
 
-      if (s in ChemPalette.AAFullNames)
-        toDisplay = [ui.divText(ChemPalette.AANames[ChemPalette.AAFullNames[s]])];
+        if (aar in ChemPalette.AAFullNames)
+          toDisplay = [ui.divText(ChemPalette.AANames[ChemPalette.AAFullNames[aar]])];
 
-      const options = {
-        autoCrop: true,
-        autoCropMargin: 0,
-        suppressChiralText: true,
-      };
-      const sketch = grok.chem.svgMol(this.monomerLib!.getMonomerMol(aar), undefined, undefined, options);
-      toDisplay.push(sketch);
+        const options = {
+          autoCrop: true,
+          autoCropMargin: 0,
+          suppressChiralText: true,
+        };
+        const sketch = grok.chem.svgMol(this.monomerLib!.getMonomerMol(aar), undefined, undefined, options);
+        if (toDisplay.length == 2)
+          toDisplay.push(ui.divText('Modified'));
+
+        toDisplay.push(sketch);
+      }
     }
     ui.tooltip.show(ui.divV(toDisplay), x, y);
   }
@@ -70,25 +75,54 @@ export class ChemPalette {
     return color;
   }
 
+  /**
+   * Retursn divided amino with its content in the bracket, if the conetent is number, then its omitted
+   *
+   * @param {string} c raw amino
+   * @return {[string, string]} outer and inner content
+   */
+  private getInnerOuter(c: string): [string, string] {
+    let isInner = 0;
+    let inner = '';
+    let outer = '';
+
+    for (let i = 0; i < c.length; ++i) {
+      if (c[i] == '(')
+        isInner++;
+      else if (c[i] == ')')
+        isInner--;
+      else if (isInner)
+        inner += c[i];
+      else
+        outer += c[i];
+    }
+
+    return !isNaN(parseInt(inner)) ? [outer, ''] : [outer, inner];
+  }
+
   /**
    * Get color for the provided amino acid residue pivot
    * @param {string} [c=''] Amino acid residue string.
    * @return {[string, string, number]}
    */
-  getColorAAPivot(c: string = ''): [string, string, number] {
+  getColorAAPivot(c: string = ''): [string, string, string, number] {
+    let [outerC, innerC] = this.getInnerOuter(c);
+    outerC = (outerC.length > 6 ? outerC.slice(0, 3) + '...' : outerC);
+    innerC = (innerC.length > 6 ? innerC.slice(0, 3) + '...' : innerC);
+
     if (c.length == 1 || c[1] == '(') {
       const amino = c[0]?.toUpperCase()!;
       return amino in this.cp?
-        [this.cp[amino], amino, 1]:
-        [ChemPalette.undefinedColor, '', 1];
+        [this.cp[amino], amino, innerC, 1]:
+        [ChemPalette.undefinedColor, outerC, innerC, 1];
     }
 
     if (c[0] == 'd' && c[1]! in this.cp) {
       if (c.length == 2 || c[2] == '(') {
         const amino = c[1]?.toUpperCase()!;
         return amino in this.cp?
-          [this.cp[amino], amino, 2]:
-          [ChemPalette.undefinedColor, '', 2];
+          [this.cp[amino], amino, innerC, 2]:
+          [ChemPalette.undefinedColor, outerC, innerC, 2];
       }
     }
 
@@ -96,8 +130,8 @@ export class ChemPalette {
       if (c.length == 3 || c[3] == '(') {
         const amino = ChemPalette.AAFullNames[c.substr(0, 3)];
         return amino in this.cp?
-          [this.cp[amino], amino, 3]:
-          [ChemPalette.undefinedColor, '', 3];
+          [this.cp[amino], amino, innerC, 3]:
+          [ChemPalette.undefinedColor, outerC, innerC, 3];
       }
     }
 
@@ -106,13 +140,13 @@ export class ChemPalette {
         if (c.length == 4 || c[4] == '(') {
           const amino = ChemPalette.AAFullNames[c.substr(1, 3)];
           return amino in this.cp?
-            [this.cp[amino], amino, 4]:
-            [ChemPalette.undefinedColor, '', 4];
+            [this.cp[amino], amino, innerC, 4]:
+            [ChemPalette.undefinedColor, outerC, innerC, 4];
         }
       }
     }
 
-    return [ChemPalette.undefinedColor, '', 0];
+    return [ChemPalette.undefinedColor, outerC, innerC, 0];
   }
 
   /**
@@ -123,7 +157,7 @@ export class ChemPalette {
    */
   getColorPivot(c = ''): [string, number] {
     //TODO: merge with getColorAAPivot?
-    const [color,, pivot] = this.getColorAAPivot(c);
+    const [color,,, pivot] = this.getColorAAPivot(c);
     return [color, pivot];
   };
 
@@ -155,7 +189,7 @@ export class ChemPalette {
     'gray': ['rgb(127,127,127)', 'rgb(199,199,199)', 'rgb(196,156,148)', 'rgb(222, 222, 180)'],
     'yellow': ['rgb(188,189,34)'],
     'white': ['rgb(230,230,230)'],
-  }
+  };
 
   /**
    * Grok color scheme groups.
@@ -171,7 +205,7 @@ export class ChemPalette {
     'light_blue': ['R', 'H', 'K'],
     'dark_blue': ['D', 'E'],
     'orange': ['S', 'T', 'N', 'Q'],
-  }
+  };
 
   /**
    * Lesk color scheme groups.
@@ -186,7 +220,7 @@ export class ChemPalette {
     'magenta': ['N', 'Q', 'H'],
     'red': ['D', 'E'],
     'all_blue': ['K', 'R'],
-  }
+  };
 
   /**
    * Undefined color.
@@ -245,7 +279,7 @@ export class ChemPalette {
     'I': 'Isoleucine',
     'M': 'Methionine',
     'T': 'Threonine',
-  }
+  };
 
   /**
    * Amino acid residue SMILES.
@@ -275,7 +309,7 @@ export class ChemPalette {
     'I': 'N[C@H]([C@H](C)CC)C(=O)O',
     'M': 'NC(CCSC)C(=O)O',
     'T': 'NC(C(O)C)C(=O)O',
-  }
+  };
 
   /**
    * Amino acid residue truncated SMILES.
@@ -305,7 +339,7 @@ export class ChemPalette {
     'I': 'CC[C@H](C)[C@H](*)*',
     'M': 'CSCCC(*)*',
     'T': 'CC(O)C(*)*',
-  }
+  };
 
   /**
    * Amino acid residue full names.
@@ -335,7 +369,7 @@ export class ChemPalette {
     'Trp': 'W',
     'Tyr': 'Y',
     'Val': 'V',
-  }
+  };
 
   /**
    * Get Datagrok palette.

package/src/utils/peptide-similarity-space.ts

@@ -52,40 +52,30 @@ export function cleanAlignedSequencesColumn(col: DG.Column): Array<string> {
  * @return {Promise<DG.ScatterPlotViewer>} A viewer.
  */
 export async function createPeptideSimilaritySpaceViewer(
-  table: DG.DataFrame,
-  alignedSequencesColumn: DG.Column,
-  method: string,
-  measure: string,
-  cyclesCount: number,
-  view: DG.TableView | null,
-  activityColumnName?: string | null,
-): Promise<DG.ScatterPlotViewer> {
-  const pi = DG.TaskBarProgressIndicator.create('Creating embedding.');
+  table: DG.DataFrame, alignedSequencesColumn: DG.Column, method: string, measure: string, cyclesCount: number,
+  view: DG.TableView | null, activityColumnName?: string | null): Promise<DG.ScatterPlotViewer> {
+  const pi = DG.TaskBarProgressIndicator.create('Creating embedding...');
 
   activityColumnName = activityColumnName ?? inferActivityColumnsName(table);
 
   const axesNames = ['~X', '~Y', '~MW'];
   const columnData = alignedSequencesColumn.toList().map((v, _) => AlignedSequenceEncoder.clean(v));
 
-  const embcols = await createDimensinalityReducingWorker({data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
+  const embcols = await createDimensinalityReducingWorker(
+    {data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
 
   const columns = Array.from(
-    embcols as Coordinates,
-    (v: Float32Array, k) => (DG.Column.fromFloat32Array(axesNames[k], v)),
-  );
-
-  function _getMW(sequences = columnData) {
-    const mw: Float32Array = new Float32Array(sequences.length).fill(0);
-    let currentSequence;
-
-    for (let i = 0; i < sequences.length; ++i) {
-      currentSequence = sequences[i];
-      mw[i] = currentSequence == null ? 0 : getSequenceMolecularWeight(currentSequence);
-    }
+    embcols as Coordinates, (v: Float32Array, k) => DG.Column.fromFloat32Array(axesNames[k], v));
+
+  function _getMW(sequences: string[]) {
+    const mw: Float32Array = new Float32Array(sequences.length);
+
+    mw.map((_, index) => getSequenceMolecularWeight(sequences[index] ?? ''));
+
     return mw;
   }
 
-  columns.push(DG.Column.fromFloat32Array('~MW', _getMW()));
+  columns.push(DG.Column.fromFloat32Array('~MW', _getMW(columnData)));
 
   const edf = DG.DataFrame.fromColumns(columns);
 
@@ -103,11 +93,11 @@ export async function createPeptideSimilaritySpaceViewer(
       table.columns.insert(newCol);
   }
 
-  const viewerOptions = {x: '~X', y: '~Y', color: activityColumnName ?? '~MW', size: '~MW'};
-  const viewer = DG.Viewer.scatterPlot(table, viewerOptions);
-
-  if (view !== null)
-    view.addViewer(viewer);
+  const viewerOptions = {
+    x: '~X', y: '~Y', color: activityColumnName ?? '~MW', size: '~MW', title: 'Peptide Space', showYSelector: false,
+    showXSelector: false, showColorSelector: false, showSizeSelector: false,
+  };
+  const viewer = table.plot.scatter(viewerOptions);
 
   pi.close();
   return viewer;

package/src/utils/split-aligned.ts

@@ -1,4 +1,4 @@
-import * as DG from 'datagrok-api/dg';
+// import * as DG from 'datagrok-api/dg';
 
 /**
  * Split aligned sequence string into separate parts containing amino acid residues.
@@ -8,65 +8,65 @@ import * as DG from 'datagrok-api/dg';
  * @param {boolean} [filter=true] Filter out columns with all the same residues.
  * @return {[DG.DataFrame, number[]]} DataFrame containing split sequence and a list of invalid indexes.
  */
-export function splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean = true): [DG.DataFrame, number[]] {
-  const splitPeptidesArray: string[][] = [];
-  let currentSplitPeptide: string[];
-  let modeMonomerCount = 0;
-  let currentLength;
-  const colLength = peptideColumn.length;
+// export function splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean = true): [DG.DataFrame, number[]] {
+//   const splitPeptidesArray: string[][] = [];
+//   let currentSplitPeptide: string[];
+//   let modeMonomerCount = 0;
+//   let currentLength;
+//   const colLength = peptideColumn.length;
 
-  // splitting data
-  const monomerLengths: {[index: string]: number} = {};
-  for (let i = 0; i < colLength; i++) {
-    currentSplitPeptide = peptideColumn.get(i).split('-').map((value: string) => value ? value : '-');
-    splitPeptidesArray.push(currentSplitPeptide);
-    currentLength = currentSplitPeptide.length;
-    monomerLengths[currentLength + ''] =
-      monomerLengths[currentLength + ''] ? monomerLengths[currentLength + ''] + 1 : 1;
-  }
-  //@ts-ignore: what I do here is converting string to number the most effective way I could find. parseInt is slow
-  modeMonomerCount = 1 * Object.keys(monomerLengths).reduce((a, b) => monomerLengths[a] > monomerLengths[b] ? a : b);
+//   // splitting data
+//   const monomerLengths: {[index: string]: number} = {};
+//   for (let i = 0; i < colLength; i++) {
+//     currentSplitPeptide = peptideColumn.get(i).split('-').map((value: string) => value ? value : '-');
+//     splitPeptidesArray.push(currentSplitPeptide);
+//     currentLength = currentSplitPeptide.length;
+//     monomerLengths[currentLength + ''] =
+//       monomerLengths[currentLength + ''] ? monomerLengths[currentLength + ''] + 1 : 1;
+//   }
+//   //@ts-ignore: what I do here is converting string to number the most effective way I could find. parseInt is slow
+//   modeMonomerCount = 1 * Object.keys(monomerLengths).reduce((a, b) => monomerLengths[a] > monomerLengths[b] ? a : b);
 
-  // making sure all of the sequences are of the same size
-  // and marking invalid sequences
-  let nTerminal: string;
-  const invalidIndexes: number[] = [];
-  let splitColumns: string[][] = Array.from({length: modeMonomerCount}, (_) => []);
-  modeMonomerCount--; // minus N-terminal
-  for (let i = 0; i < colLength; i++) {
-    currentSplitPeptide = splitPeptidesArray[i];
-    nTerminal = currentSplitPeptide.pop()!; // it is guaranteed that there will be at least one element
-    currentLength = currentSplitPeptide.length;
-    if (currentLength !== modeMonomerCount)
-      invalidIndexes.push(i);
+//   // making sure all of the sequences are of the same size
+//   // and marking invalid sequences
+//   let nTerminal: string;
+//   const invalidIndexes: number[] = [];
+//   let splitColumns: string[][] = Array.from({length: modeMonomerCount}, (_) => []);
+//   modeMonomerCount--; // minus N-terminal
+//   for (let i = 0; i < colLength; i++) {
+//     currentSplitPeptide = splitPeptidesArray[i];
+//     nTerminal = currentSplitPeptide.pop()!; // it is guaranteed that there will be at least one element
+//     currentLength = currentSplitPeptide.length;
+//     if (currentLength !== modeMonomerCount)
+//       invalidIndexes.push(i);
 
-    for (let j = 0; j < modeMonomerCount; j++)
-      splitColumns[j].push(j < currentLength ? currentSplitPeptide[j] : '-');
+//     for (let j = 0; j < modeMonomerCount; j++)
+//       splitColumns[j].push(j < currentLength ? currentSplitPeptide[j] : '-');
 
-    splitColumns[modeMonomerCount].push(nTerminal);
-  }
-  modeMonomerCount--; // minus C-terminal
+//     splitColumns[modeMonomerCount].push(nTerminal);
+//   }
+//   modeMonomerCount--; // minus C-terminal
 
-  //create column names list
-  const columnNames = Array.from({length: modeMonomerCount}, (_, index) => `${index + 1 < 10 ? 0 : ''}${index + 1 }`);
-  columnNames.splice(0, 0, 'N-terminal');
-  columnNames.push('C-terminal');
+//   //create column names list
+//   const columnNames = Array.from({length: modeMonomerCount}, (, index) => `${index + 1 < 10 ? 0 : ''}${index + 1 }`);
+//   columnNames.splice(0, 0, 'N-terminal');
+//   columnNames.push('C-terminal');
 
-  // filter out the columns with the same values
-  if (filter) {
-    splitColumns = splitColumns.filter((positionArray, index) => {
-      const isRetained = new Set(positionArray).size > 1;
-      if (!isRetained)
-        columnNames.splice(index, 1);
+//   // filter out the columns with the same values
+//   if (filter) {
+//     splitColumns = splitColumns.filter((positionArray, index) => {
+//       const isRetained = new Set(positionArray).size > 1;
+//       if (!isRetained)
+//         columnNames.splice(index, 1);
 
-      return isRetained;
-    });
-  }
+//       return isRetained;
+//     });
+//   }
 
-  return [
-    DG.DataFrame.fromColumns(splitColumns.map((positionArray, index) => {
-      return DG.Column.fromList('string', columnNames[index], positionArray);
-    })),
-    invalidIndexes,
-  ];
-}
+//   return [
+//     DG.DataFrame.fromColumns(splitColumns.map((positionArray, index) => {
+//       return DG.Column.fromList('string', columnNames[index], positionArray);
+//     })),
+//     invalidIndexes,
+//   ];
+// }