@datagrok/sequence-translator 1.0.17 → 1.1.0

package/src/hardcode-to-be-eliminated/salts.ts

@@ -1,2 +0,0 @@
-export const SALTS_CSV = `DISPLAY,MOLWEIGHT
-no Data Added,100`;

package/src/hardcode-to-be-eliminated/sources.ts

@@ -1,3 +0,0 @@
-export const SOURCES = `DISPLAY
-NO DATA
-`;

package/src/hardcode-to-be-eliminated/users.ts

@@ -1,3 +0,0 @@
-export const USERS_CSV = `DISPLAY
-NO DATA
-`;

package/src/main-tab/main-tab.ts

@@ -1,210 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import * as rxjs from 'rxjs';
-import $ from 'cash-dom';
-
-import {convertSequence, undefinedInputSequence, isValidSequence} from '../sdf-tab/sequence-codes-tools';
-
-// todo: elminate completely
-import {map} from '../hardcode-to-be-eliminated/map';
-import {MODIFICATIONS} from '../hardcode-to-be-eliminated/const';
-
-// todo: unify with lib bio monomers works
-import {sequenceToSmiles, sequenceToMolV3000} from '../utils/structures-works/from-monomers';
-import {drawMolecule} from '../utils/structures-works/draw-molecule';
-
-import {download} from '../utils/helpers';
-
-const defaultInput = 'fAmCmGmAmCpsmU'; // todo: capitalize constants
-const sequenceWasCopied = 'Copied'; // todo: wrap hardcoded literals into constants
-const tooltipSequence = 'Copy sequence';
-
-export async function getMainTab(onSequenceChanged: (seq: string) => void): Promise<HTMLDivElement> {
-  const onInput: rxjs.Subject<string> = new rxjs.Subject<string>();
-
-  async function updateTableAndMolecule(sequence: string, inputFormat: string): Promise<void> {
-    moleculeImgDiv.innerHTML = '';
-    outputTableDiv.innerHTML = '';
-    const pi = DG.TaskBarProgressIndicator.create('Rendering table and molecule...');
-
-    try {
-      sequence = sequence.replace(/\s/g, '');
-      const output = isValidSequence(sequence, null);
-      inputFormatChoiceInput.value = output.synthesizer![0];
-      const outputSequenceObj = convertSequence(sequence, output);
-      const tableRows = [];
-
-      for (const key of Object.keys(outputSequenceObj).slice(1)) {
-        const indexOfFirstNotValidChar = ('indexOfFirstNotValidChar' in outputSequenceObj) ?
-          JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).indexOfFirstNotValidChar :
-          -1;
-
-        tableRows.push({
-          'key': key,
-          'value': ('indexOfFirstNotValidChar' in outputSequenceObj) ?
-            ui.divH([
-              ui.divText(sequence.slice(0, indexOfFirstNotValidChar), {style: {color: 'grey'}}),
-              ui.tooltip.bind(
-                ui.divText(sequence.slice(indexOfFirstNotValidChar), {style: {color: 'red'}}),
-                'Expected format: ' + JSON.parse(outputSequenceObj.indexOfFirstNotValidChar!).synthesizer +
-                '. See tables with valid codes on the right',
-              ),
-            ]) : //@ts-ignore
-            ui.link(outputSequenceObj[key], () => navigator.clipboard.writeText(outputSequenceObj[key])
-              .then(() => grok.shell.info(sequenceWasCopied)), tooltipSequence, ''),
-        });
-      }
-
-      outputTableDiv.append(
-        ui.div([
-          DG.HtmlTable.create(tableRows, (item: { key: string; value: string; }) =>
-            [item.key, item.value], ['Code', 'Sequence']).root,
-        ])
-      );
-
-      if (outputSequenceObj.type !== undefinedInputSequence && outputSequenceObj.Error !== undefinedInputSequence) {
-        const formCanvasWidth = 500;
-        const formCanvasHeight = 170;
-        const molfile = sequenceToMolV3000(
-          inputSequenceField.value.replace(/\s/g, ''), false, true,
-          output.synthesizer![0]
-        );
-        await drawMolecule(moleculeImgDiv, formCanvasWidth, formCanvasHeight, molfile);
-      } else {
-        moleculeImgDiv.innerHTML = '';
-      }
-    } finally {
-      pi.close();
-    }
-  }
-
-  const inputFormatChoiceInput = ui.choiceInput('Input format: ', 'Janssen GCRS Codes', Object.keys(map));
-  inputFormatChoiceInput.onInput((format: string) => {
-    updateTableAndMolecule(inputSequenceField.value.replace(/\s/g, ''), format);
-  });
-  const moleculeImgDiv = ui.block([]);
-  const outputTableDiv = ui.div([]);
-  const inputSequenceField = ui.textInput('', defaultInput, (sequence: string) => {
-    // Send event to DG.debounce()
-    onInput.next(sequence);
-  });
-
-  DG.debounce<string>(onInput, 300).subscribe((sequence) => {
-    updateTableAndMolecule(sequence, inputFormatChoiceInput.value!);
-    onSequenceChanged(sequence);
-  });
-
-  const asoGapmersGrid = DG.Viewer.grid(
-    DG.DataFrame.fromObjects([
-      {'Name': '2\'MOE-5Me-rU', 'BioSpring': '5', 'Janssen GCRS': 'moeT'},
-      {'Name': '2\'MOE-rA', 'BioSpring': '6', 'Janssen GCRS': 'moeA'},
-      {'Name': '2\'MOE-5Me-rC', 'BioSpring': '7', 'Janssen GCRS': 'moe5mC'},
-      {'Name': '2\'MOE-rG', 'BioSpring': '8', 'Janssen GCRS': 'moeG'},
-      {'Name': '5-Methyl-dC', 'BioSpring': '9', 'Janssen GCRS': '5mC'},
-      {'Name': 'ps linkage', 'BioSpring': '*', 'Janssen GCRS': 'ps'},
-      {'Name': 'dA', 'BioSpring': 'A', 'Janssen GCRS': 'A, dA'},
-      {'Name': 'dC', 'BioSpring': 'C', 'Janssen GCRS': 'C, dC'},
-      {'Name': 'dG', 'BioSpring': 'G', 'Janssen GCRS': 'G, dG'},
-      {'Name': 'dT', 'BioSpring': 'T', 'Janssen GCRS': 'T, dT'},
-      {'Name': 'rA', 'BioSpring': '', 'Janssen GCRS': 'rA'},
-      {'Name': 'rC', 'BioSpring': '', 'Janssen GCRS': 'rC'},
-      {'Name': 'rG', 'BioSpring': '', 'Janssen GCRS': 'rG'},
-      {'Name': 'rU', 'BioSpring': '', 'Janssen GCRS': 'rU'},
-    ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
-  );
-
-  const omeAndFluoroGrid = DG.Viewer.grid(
-    DG.DataFrame.fromObjects([
-      {'Name': '2\'-fluoro-U', 'BioSpring': '1', 'Axolabs': 'Uf', 'Janssen GCRS': 'fU'},
-      {'Name': '2\'-fluoro-A', 'BioSpring': '2', 'Axolabs': 'Af', 'Janssen GCRS': 'fA'},
-      {'Name': '2\'-fluoro-C', 'BioSpring': '3', 'Axolabs': 'Cf', 'Janssen GCRS': 'fC'},
-      {'Name': '2\'-fluoro-G', 'BioSpring': '4', 'Axolabs': 'Gf', 'Janssen GCRS': 'fG'},
-      {'Name': '2\'OMe-rU', 'BioSpring': '5', 'Axolabs': 'u', 'Janssen GCRS': 'mU'},
-      {'Name': '2\'OMe-rA', 'BioSpring': '6', 'Axolabs': 'a', 'Janssen GCRS': 'mA'},
-      {'Name': '2\'OMe-rC', 'BioSpring': '7', 'Axolabs': 'c', 'Janssen GCRS': 'mC'},
-      {'Name': '2\'OMe-rG', 'BioSpring': '8', 'Axolabs': 'g', 'Janssen GCRS': 'mG'},
-      {'Name': 'ps linkage', 'BioSpring': '*', 'Axolabs': 's', 'Janssen GCRS': 'ps'},
-    ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
-  );
-
-  const overhangModificationsGrid = DG.Viewer.grid(
-    DG.DataFrame.fromColumns([
-      DG.Column.fromStrings('Name', Object.keys(MODIFICATIONS)),
-    ])!, {showRowHeader: false, showCellTooltip: false, allowEdit: false},
-  );
-  updateTableAndMolecule(defaultInput, inputFormatChoiceInput.value!);
-
-  const codesTablesDiv = ui.splitV([
-    ui.box(ui.h2('ASO Gapmers'), {style: {maxHeight: '40px'}}),
-    asoGapmersGrid.root,
-    ui.box(ui.h2('2\'-OMe and 2\'-F siRNA'), {style: {maxHeight: '40px'}}),
-    omeAndFluoroGrid.root,
-    ui.box(ui.h2('Overhang modifications'), {style: {maxHeight: '40px'}}),
-    overhangModificationsGrid.root,
-  ], {style: {maxWidth: '350px'}});
-
-  const appMainDescription = ui.info([
-    ui.divText('How to convert one sequence:', {style: {'font-weight': 'bolder'}}),
-    ui.divText('Paste sequence into the text field below'),
-    ui.divText('\n How to convert many sequences:', {style: {'font-weight': 'bolder'}}),
-    ui.divText('1. Drag & drop an Excel or CSV file with sequences into Datagrok'),
-    ui.divText('2. Right-click on the column header, then see the \'Convert\' menu'),
-    ui.divText('This will add the result column to the right of the table'),
-  ], 'Convert oligonucleotide sequences between Nucleotides, BioSpring, Axolabs, Mermade 12 and GCRS representations.');
-
-  $(codesTablesDiv).hide();
-  const switchInput = ui.switchInput('Codes', false, (v: boolean) => (v) ?
-    $(codesTablesDiv).show() :
-    $(codesTablesDiv).hide(),
-  );
-
-  const downloadMolFileIcon = ui.iconFA('download', async () => {
-    const clearSequence = inputSequenceField.value.replace(/\s/g, '');
-    const result = sequenceToMolV3000(inputSequenceField.value.replace(/\s/g, ''), false, false,
-      inputFormatChoiceInput.value!);
-    download(clearSequence + '.mol', encodeURIComponent(result));
-  }, 'Save .mol file');
-
-  const copySmilesIcon = ui.iconFA('copy', () => {
-    navigator.clipboard.writeText(
-      sequenceToSmiles(inputSequenceField.value.replace(/\s/g, ''), false, inputFormatChoiceInput.value!),
-    ).then(() => grok.shell.info(sequenceWasCopied));
-  }, 'Copy SMILES');
-
-  const topPanel = [
-    downloadMolFileIcon,
-    copySmilesIcon,
-    switchInput.root, // todo: remove from top panel
-  ];
-
-  const v = grok.shell.v;
-  const tabControl = grok.shell.sidebar;
-  tabControl.onTabChanged.subscribe((_) => {
-    v.setRibbonPanels([(tabControl.currentPane.name == 'MAIN') ? topPanel : []]);
-  });
-  v.setRibbonPanels([topPanel]);
-
-  return ui.box(
-    ui.splitH([
-      ui.splitV([
-        ui.panel([
-          appMainDescription,
-          ui.div([
-            ui.h1('Input sequence'),
-            ui.div([], 'input-base'),
-            inputSequenceField.root,
-          ], 'inputSequence'),
-          ui.div([inputFormatChoiceInput], {style: {padding: '5px 0'}}),
-          ui.block([
-            ui.h1('Output'),
-            outputTableDiv,
-          ]),
-          moleculeImgDiv,
-        ], 'sequence'),
-      ]),
-      codesTablesDiv,
-    ], {style: {height: '100%', width: '100%'}}),
-  );
-}

package/src/sdf-tab/sdf-tab.ts

@@ -1,163 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-import * as rxjs from 'rxjs';
-import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
-
-import $ from 'cash-dom';
-
-import {download} from '../utils/helpers';
-
-import {sequenceToMolV3000} from '../utils/structures-works/from-monomers';
-import {linkStrandsV3000} from '../utils/structures-works/mol-transformations';
-import {getFormat} from './sequence-codes-tools';
-
-import {drawMolecule} from '../utils/structures-works/draw-molecule';
-
-function getMolfileForImg(
-  ss: string, as: string,
-  as2: string | null = null,
-  invertSS: boolean, invertAS: boolean, invertAS2: boolean,
-  useChiral: boolean
-): string {
-  const formatAs = getFormat(as);
-  const formatSs = getFormat(ss);
-  let formatAs2: string | null = null;
-  let molAS2: string | null = null;
-
-  let molSS = '';
-  let molAS = '';
-  try {
-    // a workaround to get the SS depicted in case AS is empty
-    molSS = sequenceToMolV3000(ss, invertSS, false, formatSs!);
-    molAS = sequenceToMolV3000(as, invertAS, false, formatAs!);
-  } catch (err) {
-    const errStr = errorToConsole(err);
-    console.error(errStr);
-  }
-
-  if (as2 !== null && as2 !== '') {
-    formatAs2 = getFormat(as2!);
-    molAS2 = sequenceToMolV3000(as2, invertAS2!, false, formatAs2!);
-  }
-
-  const antiStrands = molAS2 === null ? [molAS] : [molAS, molAS2];
-  const resultingMolfile = linkStrandsV3000({senseStrands: [molSS], antiStrands: antiStrands}, useChiral);
-  return resultingMolfile;
-}
-
-export function saveSdf(as: string, ss: string,
-  oneEntity: boolean, useChiral: boolean,
-  invertSS: boolean, invertAS: boolean,
-  as2: string | null = null, invertAS2: boolean | null
-): void {
-  const formatAs = getFormat(as);
-  const formatSs = getFormat(ss);
-  let formatAs2: string | null = null;
-  let molAS2: string | null = null;
-
-  const molSS = sequenceToMolV3000(ss, invertSS, false, formatSs!);
-  const molAS = sequenceToMolV3000(as, invertAS, false, formatAs!);
-
-  if (as2 !== null && as2 !== '') {
-    formatAs2 = getFormat(as2!);
-    molAS2 = sequenceToMolV3000(as2, invertAS2!, false, formatAs2!);
-  }
-
-  let result: string;
-  if (oneEntity) {
-    const antiStrands = molAS2 === null ? [molAS] : [molAS, molAS2];
-    result = linkStrandsV3000({senseStrands: [molSS], antiStrands: antiStrands}, useChiral) + '\n$$$$\n';
-  } else {
-    result =
-    molSS + '\n' +
-    `> <Sequence>\nSense Strand\n$$$$\n` +
-    molAS + '\n' +
-    `> <Sequence>\nAnti Sense\n$$$$\n`;
-
-    if (molAS2) {
-      result += molAS2+ '\n' +
-      `> <Sequence>\nAnti Sense 2\n$$$$\n`;
-    }
-  }
-
-  // construct date-time in the form yyyy-mm-dd_hh-mm-ss
-  const date = new Date();
-  function pad(x: number): string {
-    return (x >= 10) ? x.toString() : '0' + x.toString();
-  }
-  const dateString: string = date.getFullYear() + '-' + pad(date.getMonth() + 1) +
-                      '-' + pad(date.getDate()) + '_' + pad(date.getHours()) + '-' +
-                      pad(date.getMinutes()) + '-' + pad(date.getSeconds());
-
-  download(`SequenceTranslator-${dateString}.sdf`, encodeURIComponent(result));
-}
-
-/** UI of the SDF tab on the application's view */
-export function getSdfTab(): HTMLDivElement {
-  const onInput: rxjs.Subject<string> = new rxjs.Subject<string>();
-
-  // inputs
-  const inputColHeader = ui.h1('Sequences');
-  const ssInput = ui.textInput('Sense Strand', '', () => { onInput.next(); });
-  ssInput.root.style.color = 'red';
-  const asInput = ui.textInput('Anti Sense', '', () => { onInput.next(); });
-  const as2Input = ui.textInput('Anti Sense 2', '', () => { onInput.next(); });
-  const saveEntity = ui.boolInput('Save as one entity', true);
-  const useChiralInput = ui.boolInput('Use chiral', true);
-
-  // default values
-  const straight = '5 prime -> 3 prime';
-  const inverse = '3 prime -> 5 prime';
-  let invertSS = false;
-  let invertAS = false;
-  const invertAS2 = false;
-
-  // choice inputs
-  const ssDirection = ui.choiceInput('SS direction', straight, [straight, inverse]);
-  ssDirection.onChanged(() => { invertSS = ssDirection.value === inverse; });
-  const asDirection = ui.choiceInput('AS direction', straight, [straight, inverse]);
-  asDirection.onChanged(() => { invertAS = asDirection.value === inverse; });
-  const as2Direction = ui.choiceInput('AS 2 direction', straight, [straight, inverse]);
-  as2Direction.onChanged(() => { invertAS = asDirection.value === inverse; });
-
-  // molecule image
-  const moleculeImgDiv = ui.block([]);
-  DG.debounce<string>(onInput, 300).subscribe(async () => {
-    let molfile = '';
-    try {
-      molfile = getMolfileForImg(
-        ssInput.value, asInput.value, as2Input.value, invertSS, invertAS, invertAS2, useChiralInput.value!
-      );
-    } catch (err) {
-      const errStr = errorToConsole(err);
-      console.error(errStr);
-    }
-    // todo: calculate relative numbers
-    const canvasWidth = 500;
-    const canvasHeight = 170;
-    // todo: remove div with image if molfile empty
-    await drawMolecule(moleculeImgDiv, canvasWidth, canvasHeight, molfile);
-  });
-
-  const saveButton = ui.buttonsInput([
-    ui.bigButton('Save SDF', () =>
-      saveSdf(
-        asInput.value, ssInput.value, saveEntity.value!,
-        useChiralInput.value!, invertSS, invertAS, as2Input.value, invertAS2)
-    )
-  ]);
-  //@ts-ignore
-  // the above line is recommended by Dmitry because saveButton has wrong return
-  // type
-  const form1 = ui.form([inputColHeader, ssInput, asInput, as2Input, saveButton]);
-  form1.className = 'ui-form ui-form-wide';
-  const form2 = ui.form([ssDirection, asDirection, as2Direction, saveEntity, useChiralInput]);
-  form2.className = 'ui-form ui-form-wide';
-
-  const body = ui.divV([ui.divH([ui.block([form1]), form2]), moleculeImgDiv]);
-  $(form1).find('textarea').css('flex-grow', '1');
-  $(form1).find('label').css('max-width', '140px');
-
-  return body;
-}