@datagrok/bio 1.5.8 → 1.6.0

package/src/utils/chem-palette.ts

@@ -1,280 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
-import {MonomerLibrary} from '../monomer-library';
-
-
-export class ChemPalette {
-  cp: StringDictionary = {};
-  isInit: boolean = false;
-  monomerLib: MonomerLibrary | null = null;
-
-  /**
-   * Creates an instance of ChemPalette.
-   *
-   * @param {string} scheme Color scheme to use.
-   * @param {boolean} [grouping=false] Is grouping enabled.
-   * @memberof ChemPalette
-   */
-  private constructor(scheme: string, grouping = false) {
-    if (scheme == 'grok')
-      this.cp = ChemPalette.getDatagrok(grouping);
-  }
-
-  /**
-   * 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.
-   * @param {MonomerLibrary} monomerLib Monomer Library instance
-   */
-  static showTooltip(cell: DG.GridCell, x: number, y: number, monomerLib: MonomerLibrary): void {
-    const s = cell.cell.value as string;
-    let toDisplay = [ui.divText(s)];
-    const [, aarOuter, aarInner] = ChemPalette.getColorAAPivot(s);
-    for (const aar of [aarOuter, aarInner]) {
-      if (monomerLib.monomerNames.includes(aar)) {
-        if (aar in ChemPalette.AANames)
-          toDisplay = [ui.divText(ChemPalette.AANames[aar])];
-
-        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(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);
-  }
-
-  /**
-   * 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
-   */
-  static getInnerOuter(c: string): [string, string] {
-    let isInner = 0;
-    let inner = '';
-    let outer = '';
-
-    for (const char of c) {
-      if (char == '(')
-        isInner++;
-      else if (char == ')')
-        isInner--;
-      else if (isInner)
-        inner += char;
-      else
-        outer += char;
-    }
-
-    return !isNaN(parseInt(inner)) ? [outer, ''] : [outer, inner];
-  }
-
-  static getColorAAPivot(monomer: string = '', scheme: 'grok' = 'grok'): [string, string, string, number] {
-    const chemPaletteInstance = ChemPalette.getPalette(scheme);
-    let [outerMonomer, innerMonomer] = ChemPalette.getInnerOuter(monomer);
-    outerMonomer = (outerMonomer.length > 6 ? `${outerMonomer.slice(0, 3)}...` : outerMonomer);
-    innerMonomer = (innerMonomer.length > 6 ? `${innerMonomer.slice(0, 3)}...` : innerMonomer);
-
-    if (monomer.length == 1 || monomer[1] == '(') {
-      const amino = monomer[0]?.toUpperCase()!;
-      return amino in chemPaletteInstance ?
-        [chemPaletteInstance[amino], amino, innerMonomer, 1]:
-        [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 1];
-    }
-
-    if (monomer[0] == 'd' && monomer[1]! in chemPaletteInstance) {
-      if (monomer.length == 2 || monomer[2] == '(') {
-        const amino = monomer[1]?.toUpperCase()!;
-        return amino in chemPaletteInstance ?
-          [chemPaletteInstance[amino], amino, innerMonomer, 2]:
-          [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 2];
-      }
-    }
-
-    if (monomer.substring(0, 3) in ChemPalette.AAFullNames) {
-      if (monomer.length == 3 || monomer[3] == '(') {
-        const amino = ChemPalette.AAFullNames[monomer.substring(0, 3)];
-        return amino in chemPaletteInstance ?
-          [chemPaletteInstance[amino], amino, innerMonomer, 3]:
-          [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 3];
-      }
-    }
-
-    if (monomer[0]?.toLowerCase() == monomer[0]) {
-      if (monomer.substring(1, 3) in ChemPalette.AAFullNames) {
-        if (monomer.length == 4 || monomer[4] == '(') {
-          const amino = ChemPalette.AAFullNames[monomer.substring(1, 3)];
-          return amino in chemPaletteInstance ?
-            [chemPaletteInstance[amino], amino, innerMonomer, 4]:
-            [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 4];
-        }
-      }
-    }
-
-    return [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 0];
-  }
-
-  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: {[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 undefinedColor = 'rgb(100,100,100)';
-
-  static makePalette(dt: {[key: string]: string[]}, simplified = false, grouping = false): StringDictionary {
-    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: StringDictionary = {
-    '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: StringDictionary = {
-    '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: StringDictionary = {
-    '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: StringDictionary = {
-    '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(grouping = false): StringDictionary {
-    return ChemPalette.makePalette(ChemPalette.grokGroups, false, grouping);
-  }
-
-  static getPalette(scheme: 'grok'): StringDictionary {
-    if (scheme == 'grok')
-      return ChemPalette.getDatagrok();
-    else
-      throw new Error(`ChemPalette: scheme \`${scheme}\` does not exist`);
-  }
-}

package/src/utils/misc.ts

@@ -1,29 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-
-import * as C from './constants';
-
-export function stringToBool(str: string): boolean {
-  return str === 'true' ? true : false;
-}
-
-export function getSeparator(col: DG.Column<string>): string {
-  const separator = col.tags[C.TAGS.SEPARATOR];
-  if (separator)
-    return separator as string;
-
-  const defaultSeparators = ['.', '-', ' '];
-  const categories = col.categories;
-  const catLen = categories.length;
-  for (const potentialSeparator of defaultSeparators) {
-    if (categories.filter((sequence) => sequence.includes(potentialSeparator)).length == catLen)
-      return potentialSeparator;
-  }
-  return separator as string ?? '';
-}
-
-export function getTypedArrayConstructor(
-  maxNum: number): Uint8ArrayConstructor | Uint16ArrayConstructor | Uint32ArrayConstructor {
-  return maxNum < 256 ? Uint8Array :
-    maxNum < 65536 ? Uint16Array :
-      Uint32Array;
-}