@datagrok/peptides 0.3.0 → 0.5.6

package/src/utils/chem-palette.ts

@@ -2,243 +2,351 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-
+/**
+ * Chem palette class.
+ *
+ * @export
+ * @class ChemPalette
+ */
 export class ChemPalette {
-    cp: {[key: string]: string} = {};
+  cp: {[key: string]: string} = {};
 
-    constructor(scheme: string) {
-      if (scheme == 'grok') {
-        this.cp = ChemPalette.getDatagrok();
-      }
+  /**
+   * Creates an instance of ChemPalette.
+   *
+   * @param {string} scheme Color scheme to use.
+   * @param {boolean} [grouping=false] Is grouping enabled.
+   * @memberof ChemPalette
+   */
+  constructor(scheme: string, grouping = false) {
+    if (scheme == 'grok') {
+      this.cp = ChemPalette.getDatagrok(grouping);
     }
+  }
 
-    showTooltip(cell:DG.GridCell, x:number, y:number) {
-      const s = cell.cell.value as string;
-      let toDisplay = [ui.divText(s)];
-      // eslint-disable-next-line no-unused-vars
-      const [_c, aar, _p] = this.getColorAAPivot(s);
-      if (aar in ChemPalette.AASmiles) {
-        if (s in ChemPalette.AANames) {
-          toDisplay = [ui.divText(ChemPalette.AANames[s])];
-        }
-        if (s in ChemPalette.AAFullNames) {
-          toDisplay = [ui.divText(ChemPalette.AANames[ChemPalette.AAFullNames[s]])];
-        }
-        const sketch = grok.chem.svgMol(ChemPalette.AASmiles[aar]);
-        toDisplay.push(sketch);
+  /**
+   * Renders 2D representation of a amino acid residue in a tooltip.
+   *
+   * @param {DG.GridCell} cell Grid cell to show tooltip over.
+   * @param {number} x x coordinate of the mouse pointer.
+   * @param {number} y y coordinate of the mouse pointer.
+   */
+  showTooltip(cell: DG.GridCell, x: number, y: number) {
+    const s = cell.cell.value as string;
+    let toDisplay = [ui.divText(s)];
+    const [, aar] = this.getColorAAPivot(s);
+    if (aar in ChemPalette.AASmiles) {
+      if (s in ChemPalette.AANames) {
+        toDisplay = [ui.divText(ChemPalette.AANames[s])];
       }
-      ui.tooltip.show(ui.divV(toDisplay), x, y);
+      if (s in ChemPalette.AAFullNames) {
+        toDisplay = [ui.divText(ChemPalette.AANames[ChemPalette.AAFullNames[s]])];
+      }
+      const options = {
+        autoCrop: true,
+        autoCropMargin: 0,
+        suppressChiralText: true,
+      };
+      const sketch = grok.chem.svgMol(ChemPalette.AASmiles[aar], undefined, undefined, options);
+      toDisplay.push(sketch);
     }
+    ui.tooltip.show(ui.divV(toDisplay), x, y);
+  }
+
+  /**
+   * Get color for the provided amino acid residue.
+   * @param {string} c Amino acid residue string.
+   * @returns {string} Color.
+   */
+  getColor(c: string): string {
+    const [color] = this.getColorPivot(c);
+    return color;
+  }
 
-    getColor( c: string) {
-    // eslint-disable-next-line no-unused-vars
-      const [color, _] = this.getColorPivot(c);
-      return color;
+  /**
+   * Get color for the provided amino acid residue pivot
+   * @param {string} [c=''] Amino acid residue string.
+   * @returns {[string, string, number]}
+   */
+  getColorAAPivot(c: string = ''): [string, string, number] {
+    if (c.length == 1 || c[1] == '(') {
+      const amino = c[0]?.toUpperCase()!;
+      return amino in this.cp?
+        [this.cp[amino], amino, 1]:
+        [ChemPalette.undefinedColor, '', 1];
     }
 
-    getColorAAPivot(c = ''): [string, string, number] {
-      if (c.length == 1 || c[1] == '(') {
-        const amino = c[0]?.toUpperCase()!;
+    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, 1]:
-          [ChemPalette.undefinedColor, '', 1];
+          [this.cp[amino], amino, 2]:
+          [ChemPalette.undefinedColor, '', 2];
       }
+    }
 
-      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];
-        }
+    if (c.substr(0, 3) in ChemPalette.AAFullNames) {
+      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];
       }
+    }
 
-      if (c.substr(0, 3) in ChemPalette.AAFullNames) {
-        if (c.length == 3 || c[3] == '(') {
-          const amino = ChemPalette.AAFullNames[c.substr(0, 3)];
+    if (c[0]?.toLowerCase() == c[0]) {
+      if (c.substr(1, 3) in ChemPalette.AAFullNames) {
+        if (c.length == 4 || c[4] == '(') {
+          const amino = ChemPalette.AAFullNames[c.substr(1, 3)];
           return amino in this.cp?
-            [this.cp[amino], amino, 3]:
-            [ChemPalette.undefinedColor, '', 3];
+            [this.cp[amino], amino, 4]:
+            [ChemPalette.undefinedColor, '', 4];
         }
       }
+    }
 
-      if (c[0]?.toLowerCase() == c[0]) {
-        if (c.substr(1, 3) in ChemPalette.AAFullNames) {
-          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];
-          }
-        }
-      }
+    return [ChemPalette.undefinedColor, '', 0];
+  }
 
-      return [ChemPalette.undefinedColor, '', 0];
-    }
+  /**
+   * Get color pivot.
+   *
+   * @param c
+   * @returns
+   */
+  getColorPivot(c = ''): [string, number] {
+    //TODO: merge with getColorAAPivot?
+    const [color,, pivot] = this.getColorAAPivot(c);
+    return [color, pivot];
+  };
 
-    getColorPivot(c = ''): [string, number] {
-      // eslint-disable-next-line no-unused-vars
-      const [color, _, pivot] = this.getColorAAPivot(c);
-      return [color, pivot];
-    };
-
-    static colourPalette: {[key: string]: string[]} = {
-      'orange': ['rgb(255,187,120)', 'rgb(245,167,100)', 'rgb(235,137,70)', 'rgb(205, 111, 71)'],
-      'all_green': ['rgb(44,160,44)', 'rgb(74,160,74)', 'rgb(23,103,57)', 'rgb(30,110,96)', 'rgb(60,131,95)',
-        'rgb(24,110,79)', 'rgb(152,223,138)', 'rgb(182, 223, 138)', 'rgb(152, 193, 138)'],
-      'all_blue': ['rgb(31,119,180)', 'rgb(23,190,207)', 'rgb(122, 102, 189)', 'rgb(158,218,229)', 'rgb(141, 124, 217)',
-        'rgb(31, 120, 150)'],
-      'magenta': ['rgb(162,106,192)', 'rgb(197,165,224)', 'rgb(208,113,218)'],
-      'red': ['rgb(214,39,40)', 'rgb(255,152,150)'],
-      'st_blue': ['rgb(23,190,207)', 'rgb(158,218,229)', 'rgb(31,119,180)'],
-      'dark_blue': ['rgb(31,119,180)', 'rgb(31, 120, 150)'],
-      'light_blue': ['rgb(23,190,207)', 'rgb(158,218,229)', 'rgb(108, 218, 229)', 'rgb(23,190,227)'],
-      'lilac_blue': ['rgb(124,102,211)', 'rgb(149,134,217)', 'rgb(97, 81, 150)'],
-      'dark_green': ['rgb(23,103,57)', 'rgb(30,110,96)', 'rgb(60,131,95)', 'rgb(24,110,79)'],
-      'green': ['rgb(44,160,44)', 'rgb(74,160,74)'],
-      'light_green': ['rgb(152,223,138)', 'rgb(182, 223, 138)', 'rgb(152, 193, 138)'],
-      'st_green': ['rgb(44,160,44)', 'rgb(152,223,138)', 'rgb(39, 174, 96)', 'rgb(74,160,74)'],
-      'pink': ['rgb(247,182,210)'],
-      'brown': ['rgb(140,86,75)', 'rgb(102, 62, 54)'],
-      '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)'],
-    }
+  /**
+   * Color palette
+   *
+   * @static
+   * @type {{[key: string]: string[]}}
+   * @memberof ChemPalette
+   */
+  static colourPalette: {[key: string]: string[]} = {
+    'orange': ['rgb(255,187,120)', 'rgb(245,167,100)', 'rgb(235,137,70)', 'rgb(205, 111, 71)'],
+    'all_green': ['rgb(44,160,44)', 'rgb(74,160,74)', 'rgb(23,103,57)', 'rgb(30,110,96)', 'rgb(60,131,95)',
+      'rgb(24,110,79)', 'rgb(152,223,138)', 'rgb(182, 223, 138)', 'rgb(152, 193, 138)'],
+    'all_blue': ['rgb(31,119,180)', 'rgb(23,190,207)', 'rgb(122, 102, 189)', 'rgb(158,218,229)', 'rgb(141, 124, 217)',
+      'rgb(31, 120, 150)'],
+    'magenta': ['rgb(162,106,192)', 'rgb(197,165,224)', 'rgb(208,113,218)'],
+    'red': ['rgb(214,39,40)', 'rgb(255,152,150)'],
+    'st_blue': ['rgb(23,190,207)', 'rgb(158,218,229)', 'rgb(31,119,180)'],
+    'dark_blue': ['rgb(31,119,180)', 'rgb(31, 120, 150)'],
+    'light_blue': ['rgb(23,190,207)', 'rgb(158,218,229)', 'rgb(108, 218, 229)', 'rgb(23,190,227)'],
+    'lilac_blue': ['rgb(124,102,211)', 'rgb(149,134,217)', 'rgb(97, 81, 150)'],
+    'dark_green': ['rgb(23,103,57)', 'rgb(30,110,96)', 'rgb(60,131,95)', 'rgb(24,110,79)'],
+    'green': ['rgb(44,160,44)', 'rgb(74,160,74)'],
+    'light_green': ['rgb(152,223,138)', 'rgb(182, 223, 138)', 'rgb(152, 193, 138)'],
+    'st_green': ['rgb(44,160,44)', 'rgb(152,223,138)', 'rgb(39, 174, 96)', 'rgb(74,160,74)'],
+    'pink': ['rgb(247,182,210)'],
+    'brown': ['rgb(140,86,75)', 'rgb(102, 62, 54)'],
+    '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)'],
+  }
 
-    // static grokGroups: [string[], string][] = [
-    //   [['C', 'U'], 'yellow'],
-    //   [['G', 'P'], 'red'],
-    //   [['A', 'V', 'I', 'L', 'M', 'F', 'Y', 'W'], 'all_green'],
-    //   [['R', 'H', 'K'], 'light_blue'],
-    //   [['D', 'E'], 'dark_blue'],
-    //   [['S', 'T', 'N', 'Q'], 'orange'],
-    // ];
-    static grokGroups: {[key: string]: string[]} = {
-      'yellow': ['C', 'U'],
-      'red': ['G', 'P'],
-      'all_green': ['A', 'V', 'I', 'L', 'M', 'F', 'Y', 'W'],
-      'light_blue': ['R', 'H', 'K'],
-      'dark_blue': ['D', 'E'],
-      'orange': ['S', 'T', 'N', 'Q'],
-    }
+  /**
+   * Grok color scheme groups.
+   *
+   * @static
+   * @type {{[key: string]: string[]}}
+   * @memberof ChemPalette
+   */
+  static grokGroups: {[key: string]: string[]} = {
+    'yellow': ['C', 'U'],
+    'red': ['G', 'P'],
+    'all_green': ['A', 'V', 'I', 'L', 'M', 'F', 'Y', 'W'],
+    'light_blue': ['R', 'H', 'K'],
+    'dark_blue': ['D', 'E'],
+    'orange': ['S', 'T', 'N', 'Q'],
+  }
 
-    static leskGroups: {[key: string]: string[]} = {
-      'orange': ['G', 'A', 'S', 'T'],
-      'all_green': ['C', 'V', 'I', 'L', 'P', 'F', 'Y', 'M', 'W'],
-      'magenta': ['N', 'Q', 'H'],
-      'red': ['D', 'E'],
-      'all_blue': ['K', 'R'],
-    }
+  /**
+   * Lesk color scheme groups.
+   *
+   * @static
+   * @type {{[key: string]: string[]}}
+   * @memberof ChemPalette
+   */
+  static leskGroups: {[key: string]: string[]} = {
+    'orange': ['G', 'A', 'S', 'T'],
+    'all_green': ['C', 'V', 'I', 'L', 'P', 'F', 'Y', 'M', 'W'],
+    'magenta': ['N', 'Q', 'H'],
+    'red': ['D', 'E'],
+    'all_blue': ['K', 'R'],
+  }
 
-    static undefinedColor = 'rgb(100,100,100)'
+  /**
+   * Undefined color.
+   *
+   * @static
+   * @memberof ChemPalette
+   */
+  static undefinedColor = 'rgb(100,100,100)';
 
-    static makePalette(dt: {[key: string]: string[]}, simplified = false) {
-      const palette: { [key: string]: string } = {};
-      for (const [color, monomers] of Object.entries(dt)) {
-        monomers.forEach((monomer, index) => {
-          palette[monomer] = ChemPalette.colourPalette[color][simplified ? 0 : index];
-        });
-      }
-      return palette;
+  /**
+   * Create palette.
+   *
+   * @param dt
+   * @param simplified Is simplified.
+   * @param grouping Is grouping enabled.
+   * @returns
+   */
+  static makePalette(dt: {[key: string]: string[]}, simplified = false, grouping = false) {
+    const palette: { [key: string]: string } = {};
+    const groups = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ';
+    let currentGroup = 0;
+    for (const [color, monomers] of Object.entries(dt)) {
+      monomers.forEach((monomer, index) => {
+        palette[grouping ? groups[currentGroup] : monomer] = ChemPalette.colourPalette[color][simplified ? 0 : index];
+      });
+      currentGroup++;
     }
+    return palette;
+  }
 
-    static AANames: {[key: string]: string} = {
-      'G': 'Glycine',
-      'L': 'Leucine',
-      'Y': 'Tyrosine',
-      'S': 'Serine',
-      'E': 'Glutamic acid',
-      'Q': 'Glutamine',
-      'D': 'Aspartic acid',
-      'N': 'Asparagine',
-      'F': 'Phenylalanine',
-      'A': 'Alanine',
-      'K': 'Lysine',
-      'R': 'Arginine',
-      'H': 'Histidine',
-      'C': 'Cysteine',
-      'V': 'Valine',
-      'P': 'Proline',
-      'W': 'Tryptophan',
-      'I': 'Isoleucine',
-      'M': 'Methionine',
-      'T': 'Threonine',
-    }
+  /**
+   * Amino acid residue names.
+   *
+   * @static
+   * @type {{[key: string]: string}}
+   * @memberof ChemPalette
+   */
+  static AANames: {[key: string]: string} = {
+    'G': 'Glycine',
+    'L': 'Leucine',
+    'Y': 'Tyrosine',
+    'S': 'Serine',
+    'E': 'Glutamic acid',
+    'Q': 'Glutamine',
+    'D': 'Aspartic acid',
+    'N': 'Asparagine',
+    'F': 'Phenylalanine',
+    'A': 'Alanine',
+    'K': 'Lysine',
+    'R': 'Arginine',
+    'H': 'Histidine',
+    'C': 'Cysteine',
+    'V': 'Valine',
+    'P': 'Proline',
+    'W': 'Tryptophan',
+    'I': 'Isoleucine',
+    'M': 'Methionine',
+    'T': 'Threonine',
+  }
 
-    static AASmiles: {[key: string]: string} = {
-      'G': 'NCC(=O)O',
-      'L': 'N[C@H](CC(C)C)C(=O)O',
-      'Y': 'NC(CC1=CC=C(O)C=C1)C(=O)O',
-      'S': 'NC(CO)C(=O)O',
-      'E': 'N[C@@H](CCC(O)=O)C(=O)O',
-      'Q': 'N[C@@H](CCC(N)=O)C(=O)O',
-      'D': 'N[C@@H](CC(O)=O)C(=O)O',
-      'N': 'N[C@@H](CC(N)=O)C(=O)O',
-      'F': 'NC(CC1=CC=CC=C1)C(=O)O',
-      'A': 'N[C@H](C)C(=O)O',
-      'K': 'NC(CCCCN)C(=O)O',
-      'R': 'N[C@H](CCCNC(=N)C)C(=O)O',
-      'H': 'NC(CC1=CN=C[N]1)C(=O)O',
-      'C': 'N[C@@H](CS)C(=O)O',
-      'V': 'NC(C(C)C)C(=O)O',
-      'P': 'N(CCC1)C1C(=O)O',
-      'W': 'N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O',
-      '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 SMILES.
+   *
+   * @static
+   * @type {{[key: string]: string}}
+   * @memberof ChemPalette
+   */
+  static AASmiles: {[key: string]: string} = {
+    'G': 'NCC(=O)O',
+    'L': 'N[C@H](CC(C)C)C(=O)O',
+    'Y': 'NC(CC1=CC=C(O)C=C1)C(=O)O',
+    'S': 'NC(CO)C(=O)O',
+    'E': 'N[C@@H](CCC(O)=O)C(=O)O',
+    'Q': 'N[C@@H](CCC(N)=O)C(=O)O',
+    'D': 'N[C@@H](CC(O)=O)C(=O)O',
+    'N': 'N[C@@H](CC(N)=O)C(=O)O',
+    'F': 'NC(CC1=CC=CC=C1)C(=O)O',
+    'A': 'N[C@H](C)C(=O)O',
+    'K': 'NC(CCCCN)C(=O)O',
+    'R': 'N[C@H](CCCNC(=N)C)C(=O)O',
+    'H': 'NC(CC1=CN=C[N]1)C(=O)O',
+    'C': 'N[C@@H](CS)C(=O)O',
+    'V': 'NC(C(C)C)C(=O)O',
+    'P': 'N(CCC1)C1C(=O)O',
+    'W': 'N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O',
+    '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',
+  }
 
-    static AASmilesTruncated: {[key: string]: string} = {
-      'G': '*C*',
-      'L': 'CC(C)C[C@H](*)*',
-      'Y': 'C1=CC(=CC=C1CC(*)*)O',
-      'S': 'OCC(*)C*',
-      'E': '*[C@@H](CCC(O)=O)*',
-      'Q': '*N[C@@H](CCC(N)=O)*',
-      'D': '*[C@@H](CC(O)=O)*',
-      'N': '*[C@@H](CC(N)=O)*',
-      'F': 'C1=CC=C(C=C1)CC(*)*',
-      'A': 'C[C@H](*)*',
-      'K': 'C(CCN)CC(*)*',
-      'R': '*[C@H](CCCNC(=N)C)*',
-      'H': 'C1=C(NC=N1)CC(*)*',
-      'C': 'C([C@@H](*)*)S',
-      'V': 'CC(C)C(*)*',
-      'P': 'C1CCN(*)C1*',
-      'W': '*[C@@H](Cc1c2ccccc2n([H])c1)*',
-      'I': 'CC[C@H](C)[C@H](*)*',
-      'M': 'CSCCC(*)*',
-      'T': 'CC(O)C(*)*',
-    }
+  /**
+   * Amino acid residue truncated SMILES.
+   *
+   * @static
+   * @type {{[key: string]: string}}
+   * @memberof ChemPalette
+   */
+  static AASmilesTruncated: {[key: string]: string} = {
+    'G': '*C*',
+    'L': 'CC(C)C[C@H](*)*',
+    'Y': 'C1=CC(=CC=C1CC(*)*)O',
+    'S': 'OCC(*)C*',
+    'E': '*[C@@H](CCC(O)=O)*',
+    'Q': '*N[C@@H](CCC(N)=O)*',
+    'D': '*[C@@H](CC(O)=O)*',
+    'N': '*[C@@H](CC(N)=O)*',
+    'F': 'C1=CC=C(C=C1)CC(*)*',
+    'A': 'C[C@H](*)*',
+    'K': 'C(CCN)CC(*)*',
+    'R': '*[C@H](CCCNC(=N)C)*',
+    'H': 'C1=C(NC=N1)CC(*)*',
+    'C': 'C([C@@H](*)*)S',
+    'V': 'CC(C)C(*)*',
+    'P': 'C1CCN(*)C1*',
+    'W': '*[C@@H](Cc1c2ccccc2n([H])c1)*',
+    'I': 'CC[C@H](C)[C@H](*)*',
+    'M': 'CSCCC(*)*',
+    'T': 'CC(O)C(*)*',
+  }
 
-    static AAFullNames: {[key: string]: string} = {
-      'Ala': 'A',
-      'Arg': 'R',
-      'Asn': 'N',
-      'Asp': 'D',
-      'Cys': 'C',
-      'Gln': 'Q',
-      'Glu': 'E',
-      'Gly': 'G',
-      'His': 'H',
-      'Ile': 'I',
-      'Leu': 'L',
-      'Lys': 'K',
-      'Met': 'M',
-      'Phe': 'F',
-      'Pro': 'P',
-      'Ser': 'S',
-      'Thr': 'T',
-      'Trp': 'W',
-      'Tyr': 'Y',
-      'Val': 'V',
-    }
+  /**
+   * Amino acid residue full names.
+   *
+   * @static
+   * @type {{[key: string]: string}}
+   * @memberof ChemPalette
+   */
+  static AAFullNames: {[key: string]: string} = {
+    'Ala': 'A',
+    'Arg': 'R',
+    'Asn': 'N',
+    'Asp': 'D',
+    'Cys': 'C',
+    'Gln': 'Q',
+    'Glu': 'E',
+    'Gly': 'G',
+    'His': 'H',
+    'Ile': 'I',
+    'Leu': 'L',
+    'Lys': 'K',
+    'Met': 'M',
+    'Phe': 'F',
+    'Pro': 'P',
+    'Ser': 'S',
+    'Thr': 'T',
+    'Trp': 'W',
+    'Tyr': 'Y',
+    'Val': 'V',
+  }
 
-    static getDatagrok() {
-      return ChemPalette.makePalette(ChemPalette.grokGroups);
-    }
+  /**
+   * Get Datagrok palette.
+   *
+   * @param grouping Is grouping enabled?
+   * @returns
+   */
+  static getDatagrok(grouping = false) {
+    return ChemPalette.makePalette(ChemPalette.grokGroups, false, grouping);
+  }
 
-    static getLesk() {
-      return ChemPalette.makePalette(ChemPalette.leskGroups);
-    }
+  /**
+   * Get Lesk palette.
+   *
+   * @param grouping Is grouping enabled?
+   * @returns
+   */
+  static getLesk() {
+    return ChemPalette.makePalette(ChemPalette.leskGroups);
+  }
 }