@datagrok/sequence-translator 1.0.17 → 1.1.4

package/src/utils/sdf-save-table.ts

@@ -1,56 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-import {COL_NAMES, GENERATED_COL_NAMES, SEQUENCE_TYPES} from '../autostart/constants';
-import {differenceOfTwoArrays, download} from '../utils/helpers';
-import * as grok from 'datagrok-api/grok';
-import {SYNTHESIZERS} from '../hardcode-to-be-eliminated/map';
-import {sequenceToMolV3000} from '../utils/structures-works/from-monomers';
-import {parseStrandsFromDuplexCell, parseStrandsFromTriplexOrDimerCell} from './parse';
-import {linkStrandsV3000} from '../utils/structures-works/mol-transformations';
-
-export async function sdfSaveTable(table: DG.DataFrame, onError: (rowI: number, err: any) => void) {
-  if (GENERATED_COL_NAMES.some((colName) => !table.columns.contains(colName))) {
-    const absentColNames = differenceOfTwoArrays(GENERATED_COL_NAMES, table.columns.names()).join(`', '`);
-    grok.shell.warning(`File saved without columns '${absentColNames}'`);
-  }
-
-  const sequenceCol = table.getCol(COL_NAMES.SEQUENCE);
-  const typeCol = table.getCol(COL_NAMES.TYPE);
-
-  let resultStr = '';
-  const rowCount = table.rowCount;
-  for (let i = 0; i < rowCount; i++) {
-    try {
-      let rowStr = '';
-      const format = SYNTHESIZERS.GCRS; //getFormat(sequenceCol.get(i))!;
-      if (typeCol.get(i) == SEQUENCE_TYPES.SENSE_STRAND) {
-        rowStr += `${sequenceToMolV3000(sequenceCol.get(i), false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
-      } else if (typeCol.get(i) == SEQUENCE_TYPES.ANTISENSE_STRAND) {
-        rowStr += `${sequenceToMolV3000(sequenceCol.get(i), true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
-      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
-        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
-        const as = `${sequenceToMolV3000(obj.AS, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
-        const ss = `${sequenceToMolV3000(obj.SS, false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
-        rowStr += `${linkStrandsV3000({senseStrands: [ss], antiStrands: [as]}, true)}\n\n`;
-      } else if ([SEQUENCE_TYPES.TRIPLEX, SEQUENCE_TYPES.DIMER].includes(typeCol.get(i))) {
-        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
-        const as1 = `${sequenceToMolV3000(obj.AS1, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
-        const as2 = `${sequenceToMolV3000(obj.AS2, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
-        const ss = `${sequenceToMolV3000(obj.SS, false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
-        rowStr += `${linkStrandsV3000({senseStrands: [ss], antiStrands: [as1, as2]}, true)}\n\n`;
-      }
-
-      for (const col of table.columns) {
-        if (col.name != COL_NAMES.SEQUENCE)
-          rowStr += `> <${col.name}>\n${col.get(i)}\n\n`;
-      }
-
-      rowStr += '$$$$\n';
-
-      resultStr += rowStr;
-    } catch (err: any) {
-      onError(i, err);
-    }
-  }
-
-  download(`${table.name}.sdf`, encodeURIComponent(resultStr));
-}

package/src/utils/structures-works/draw-molecule.ts

@@ -1,84 +0,0 @@
-/* Do not change these import lines to match external modules in webpack configuration */
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
-
-import $ from 'cash-dom';
-
-import {extractAtomDataV3000} from './mol-transformations';
-
-/** Draw molecule on the canvas and append it to the specified div, with the
- * option of zoom-in */
-export async function drawMolecule(
-  moleculeImgDiv: HTMLDivElement,
-  canvasWidth: number, canvasHeight: number,
-  molfile: string
-): Promise<void> {
-  // clear the div's content if any
-  async function drawMolfileOnCanvas(canvas: HTMLCanvasElement): Promise<void> {
-    await grok.functions.call('Chem:canvasMol', {
-      x: 0, y: 0, w: canvas.width, h: canvas.height, canvas: canvas,
-      molString: molfile, scaffoldMolString: '',
-      options: {normalizeDepiction: false, straightenDepiction: false}
-    });
-  };
-
-  async function drawZoomedInMolecule(): Promise<void> {
-    try {
-      const dialogDivStyle = {
-        overflowX: 'scroll',
-      };
-      const dialogDiv = ui.div([], {style: dialogDivStyle});
-
-      // dialogDiv size required, but now available before dialog show()
-      const atomCoordinates = extractAtomDataV3000(molfile);
-      // const cw: number = $(window).width() * 0.80; // dialogDiv.clientWidth
-      const clientHeight: number = $(window).height() * 0.70; // dialogDiv.clientHeight
-      const molWidth: number = Math.max(...atomCoordinates.x) - Math.min(...atomCoordinates.x);
-      const molHeight: number = Math.max(...atomCoordinates.y) - Math.min(...atomCoordinates.y);
-
-      // const wR: number = cw / molWidth;
-      const hR: number = clientHeight / molHeight;
-      const r: number = hR; // Math.max(wR, hR);
-      const dialogCanvasWidth = r * molWidth;
-      const dialogCanvasHeight = r * molHeight;
-
-      const dialogCanvas = ui.canvas(
-        dialogCanvasWidth * window.devicePixelRatio, dialogCanvasHeight * window.devicePixelRatio
-      );
-      dialogCanvas.style.width = `${dialogCanvasWidth}px`;
-      dialogCanvas.style.height = `${dialogCanvasHeight}px`;
-      await drawMolfileOnCanvas(dialogCanvas);
-
-      dialogDiv.appendChild(dialogCanvas);
-      ui.dialog('Molecule')
-        .add(dialogDiv)
-        .showModal(true);
-    } catch (err) {
-      const errStr = errorToConsole(err);
-      console.error(errStr);
-    }
-  };
-
-  // clear div's content if any
-  moleculeImgDiv.innerHTML = '';
-
-  if (molfile !== '') {
-    const canvas = ui.canvas(canvasWidth * window.devicePixelRatio, canvasHeight * window.devicePixelRatio);
-
-    // Draw zoomed-out molecule
-    canvas.style.width = `${canvasWidth}px`;
-    canvas.style.height = `${canvasHeight}px`;
-    canvas.style.borderStyle = 'solid';
-    canvas.style.borderColor = 'blue';
-    drawMolfileOnCanvas(canvas);
-
-    // Dialog with zoomed-in molecule
-    $(canvas).on('click', drawZoomedInMolecule);
-    $(canvas).on('mouseover', () => $(canvas).css('cursor', 'grab')); // for some reason 'zoom-in' value wouldn't work
-    $(canvas).on('mouseout', () => $(canvas).css('cursor', 'default'));
-
-    moleculeImgDiv.append(canvas);
-  }
-}

package/src/utils/structures-works/from-monomers.ts

@@ -1,266 +0,0 @@
-// import {map, SYNTHESIZERS, TECHNOLOGIES, MODIFICATIONS, DELIMITER} from './map';
-import {map, SYNTHESIZERS, TECHNOLOGIES, DELIMITER} from '../../hardcode-to-be-eliminated/map';
-import {isValidSequence} from '../../sdf-tab/sequence-codes-tools';
-import {sortByStringLengthInDescendingOrder} from '../helpers';
-import {getMonomerWorks} from '../../package';
-import {getNucleotidesMol} from './mol-transformations';
-
-import {standardPhosphateLinkSmiles, MODIFICATIONS} from '../../hardcode-to-be-eliminated/const';
-import {getMonomerLib} from '../../package';
-// todo: remove
-// const NAME = 'name';
-const CODES = 'codes';
-// const SMILES = 'smiles';
-const MOL = 'molfile';
-
-export function sequenceToMolV3000(
-  sequence: string, inverted: boolean = false, oclRender: boolean = false,
-  format: string
-): string {
-  const monomerNameFromCode = getCodeToNameMap(sequence, format);
-  let codes = sortByStringLengthInDescendingOrder(Object.keys(monomerNameFromCode));
-  let i = 0;
-  const codesList = [];
-  const links = ['s', 'ps', '*'];
-  const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
-  const dropdowns = Object.keys(MODIFICATIONS);
-  codes = codes.concat(dropdowns).concat(DELIMITER);
-  while (i < sequence.length) {
-    const code = codes.find((s: string) => s === sequence.slice(i, i + s.length))!;
-    i += code.length;
-    inverted ? codesList.unshift(code) : codesList.push(code);
-  }
-
-  const monomers: string[] = [];
-
-  for (let i = 0; i < codesList.length; i++) {
-    if (links.includes(codesList[i]) ||
-      includesStandardLinkAlready.includes(codesList[i]) ||
-      (i < codesList.length - 1 && links.includes(codesList[i + 1]))
-    ) {
-      const aa = monomerNameFromCode[codesList[i]];
-      if (aa !== undefined)
-        monomers.push(aa);
-      else
-        monomers.push(codesList[i]);
-    } else {
-      const aa = monomerNameFromCode[codesList[i]];
-      if (aa !== undefined)
-        monomers.push(aa);
-      else
-        monomers.push(codesList[i]);
-      monomers.push('p linkage');
-    }
-  }
-
-  const lib = getMonomerLib();
-  const mols: string [] = [];
-  for (let i = 0; i < monomers.length; i++) {
-    const mnmr = lib?.getMonomer('RNA', monomers[i]);
-    mols.push(mnmr?.molfile!);
-  }
-
-
-  return getNucleotidesMol(mols);
-  //return getMonomerWorks()?.getAtomicLevel(monomers, 'RNA')!;
-}
-
-export function sequenceToMolV3000_new(
-  sequence: string, inverted: boolean = false, oclRender: boolean = false,
-  format: string,
-): string {
-  const monomerNameFromCode = getCodeToNameMap(sequence, format);
-  let codes = sortByStringLengthInDescendingOrder(Object.keys(monomerNameFromCode));
-  let i = 0;
-  const codesList = [];
-  const links = ['s', 'ps', '*'];
-  const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
-  const dropdowns = Object.keys(MODIFICATIONS);
-  codes = codes.concat(dropdowns).concat(DELIMITER);
-  while (i < sequence.length) {
-    const code = codes.find((s: string) => s === sequence.slice(i, i + s.length))!;
-    i += code.length;
-    inverted ? codesList.unshift(code) : codesList.push(code);
-  }
-
-  const monomers: string[] = [];
-
-  for (let i = 0; i < codesList.length; i++) {
-    if (links.includes(codesList[i]) ||
-      includesStandardLinkAlready.includes(codesList[i]) ||
-      (i < codesList.length - 1 && links.includes(codesList[i + 1]))
-    )
-      monomers.push(monomerNameFromCode[codesList[i]]);
-    else {
-      monomers.push(monomerNameFromCode[codesList[i]]);
-      monomers.push('p linkage');
-    }
-  }
-
-  return getMonomerWorks()?.getAtomicLevel(monomers, 'RNA')!;
-}
-
-export function sequenceToSmiles(sequence: string, inverted: boolean = false, format: string): string {
-  const obj = getObjectWithCodesAndSmiles(sequence, format);
-  let codes = sortByStringLengthInDescendingOrder(Object.keys(obj));
-  let i = 0;
-  let smiles = '';
-  const codesList = [];
-  const links = ['s', 'ps', '*'];
-  const includesStandardLinkAlready = ['e', 'h', /*'g',*/ 'f', 'i', 'l', 'k', 'j'];
-  const dropdowns = Object.keys(MODIFICATIONS);
-  codes = codes.concat(dropdowns).concat(DELIMITER);
-  while (i < sequence.length) {
-    const code = codes.find((s: string) => s == sequence.slice(i, i + s.length))!;
-    i += code.length;
-    inverted ? codesList.unshift(code) : codesList.push(code);
-  }
-  for (let i = 0; i < codesList.length; i++) {
-    if (dropdowns.includes(codesList[i])) {
-      smiles += (i >= codesList.length / 2) ?
-        MODIFICATIONS[codesList[i]].right + standardPhosphateLinkSmiles :
-        MODIFICATIONS[codesList[i]].left + standardPhosphateLinkSmiles;
-    } else {
-      if (links.includes(codesList[i]) ||
-        includesStandardLinkAlready.includes(codesList[i]) ||
-        (i < codesList.length - 1 && links.includes(codesList[i + 1]))
-      )
-        smiles += obj[codesList[i]];
-      else
-        smiles += obj[codesList[i]] + standardPhosphateLinkSmiles;
-    }
-  }
-  smiles = smiles.replace(/OO/g, 'O');
-  return (
-    (
-      links.includes(codesList[codesList.length - 1]) &&
-      codesList.length > 1 &&
-      !includesStandardLinkAlready.includes(codesList[codesList.length - 2])
-    ) ||
-    dropdowns.includes(codesList[codesList.length - 1]) ||
-    includesStandardLinkAlready.includes(codesList[codesList.length - 1])
-  ) ?
-    smiles :
-    smiles.slice(0, smiles.length - standardPhosphateLinkSmiles.length + 1);
-}
-
-function getCodeToNameMap(sequence: string, format: string) {
-  const obj: { [code: string]: string } = {};
-  const NAME = 'name';
-  if (format == null) {
-    for (const synthesizer of Object.keys(map)) {
-      for (const technology of Object.keys(map[synthesizer])) {
-        for (const code of Object.keys(map[synthesizer][technology]))
-          obj[code] = map[synthesizer][technology][code][NAME]!;
-      }
-    }
-  } else {
-    for (const technology of Object.keys(map[format])) {
-      for (const code of Object.keys(map[format][technology]))
-        obj[code] = map[format][technology][code][NAME]!;
-      // obj[code] = map[format][technology][code].SMILES;
-    }
-  }
-  obj[DELIMITER] = '';
-  // TODO: create object based from synthesizer type to avoid key(codes) duplicates
-  const output = isValidSequence(sequence, format);
-  if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12))
-    obj['g'] = map[SYNTHESIZERS.MERMADE_12][TECHNOLOGIES.SI_RNA]['g'][NAME]!;
-  else if (output.synthesizer!.includes(SYNTHESIZERS.AXOLABS))
-    obj['g'] = map[SYNTHESIZERS.AXOLABS][TECHNOLOGIES.SI_RNA]['g'][NAME]!;
-  return obj;
-}
-
-function getObjectWithCodesAndSmiles(sequence: string, format: string) {
-  const obj: { [code: string]: string } = {};
-  if (format == null) {
-    for (const synthesizer of Object.keys(map)) {
-      for (const technology of Object.keys(map[synthesizer])) {
-        for (const code of Object.keys(map[synthesizer][technology]))
-          obj[code] = map[synthesizer][technology][code].SMILES;
-      }
-    }
-  } else {
-    for (const technology of Object.keys(map[format])) {
-      for (const code of Object.keys(map[format][technology]))
-        obj[code] = map[format][technology][code].SMILES;
-    }
-  }
-  obj[DELIMITER] = '';
-  // TODO: create object based from synthesizer type to avoid key(codes) duplicates
-  const output = isValidSequence(sequence, format);
-  if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12))
-    obj['g'] = map[SYNTHESIZERS.MERMADE_12][TECHNOLOGIES.SI_RNA]['g'].SMILES;
-  else if (output.synthesizer!.includes(SYNTHESIZERS.AXOLABS))
-    obj['g'] = map[SYNTHESIZERS.AXOLABS][TECHNOLOGIES.SI_RNA]['g'].SMILES;
-  return obj;
-}
-
-function getObjectWithCodesAndMolsFromFile(sequence: string, format: string, libFileContent: string) {
-  const obj: { [code: string]: string } = {};
-  // todo: type
-  const lib: any[] = JSON.parse(libFileContent); //consider using library
-
-  for (const item of lib) {
-    for (const synthesizer of Object.keys(item[CODES])) {
-      if (synthesizer === format) {
-        for (const technology of Object.keys(item[CODES][synthesizer])) {
-          const codes = item[CODES][synthesizer][technology];
-          let mol: string = item[MOL];
-          // todo: find another solution
-          mol = mol.replace(/ R /g, ' O ');
-
-          for (const code of codes)
-            obj[code] = mol;
-        }
-      }
-    }
-  }
-
-  obj[DELIMITER] = '';
-  // TODO: create object based on synthesizer type to avoid key(codes) duplicates
-  const output = isValidSequence(sequence, format);
-  if (output.synthesizer!.includes(SYNTHESIZERS.MERMADE_12)) {
-    // todo: remove as quickfix, optimize access to 'g'
-    for (const item of lib) {
-      for (const synthesizer of Object.keys(item[CODES])) {
-        for (const technology of Object.keys(item[CODES][synthesizer])) {
-          const codes = item[CODES][synthesizer][technology];
-          for (const code of codes) {
-            const condition =
-              (code === 'g') &&
-              (synthesizer === SYNTHESIZERS.MERMADE_12) &&
-              (technology === TECHNOLOGIES.SI_RNA);
-            if (condition) {
-              let mol: string = item[MOL];
-              // todo: find another solution
-              mol = mol.replace(/ R /g, ' O ');
-              obj[code] = mol;
-            }
-          }
-        }
-      }
-    }
-  } else if (output.synthesizer!.includes(SYNTHESIZERS.AXOLABS)) {
-    for (const item of lib) {
-      for (const synthesizer of Object.keys(item[CODES])) {
-        for (const technology of Object.keys(item[CODES][synthesizer])) {
-          const codes = item[CODES][synthesizer][technology];
-          for (const code of codes) {
-            const condition =
-              (code === 'g') &&
-              (synthesizer === SYNTHESIZERS.AXOLABS) &&
-              (technology === TECHNOLOGIES.SI_RNA);
-            if (condition) {
-              let mol: string = item[MOL];
-              // todo: find another solution
-              mol = mol.replace(/ R /g, ' O ');
-              obj[code] = mol;
-            }
-          }
-        }
-      }
-    }
-  }
-  return obj;
-}

package/test-SequenceTranslator-6288c2fbe346-695b7b55.html

@@ -1,259 +0,0 @@
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-</style></head><body><div id="jesthtml-content"><header><h1 id="title">SequenceTranslator Test Report. Datagrok version datagrok/datagrok:latest SHA=6288c2fbe346. Commit 695b7b55.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-12-19 15:46:37</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts</div><div class="suite-time warn">15.201s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">4.324s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:62:11)
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/test-node.ts:28:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:40:11
-    at Generator.next (&lt;anonymous&gt;)
-    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:34:71
-    at new Promise (&lt;anonymous&gt;)
-    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:30:12)
-    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:38:23)
-    at Promise.then.completed (/home/runner/work/public/public/packages/SequenceTranslator/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing SequenceTranslator package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:72:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 2 : SequenceTranslator.sequence-translator.usCfCfUfGfAf : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.usAfsusgsgsg : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.UfUfUfsCfsuacg : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.susususauasu : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.CfGfCfsGfsCf : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.acacacsacsac : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.cccgggusug : OK
-Test result : Success : 0 : SequenceTranslator.sequence-translator.UfAfCfGfGfCfAfUf : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)cuCfuUfsc : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)usAfsucuCfuUfAfgcugUfgCfacususu : OK
-Test result : Success : 1 : SequenceTranslator.sequence-translator.(invabasic)asacgGfuGfCfAfacucuauuca : OK
-</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:74:11
-    at Generator.next (&lt;anonymous&gt;)
-    at fulfilled (/home/runner/work/public/public/packages/SequenceTranslator/src/__jest__/remote.test.ts:31:58)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message"/></div></div></div></div></body></html>