@datagrok/sequence-translator 1.0.17 → 1.1.0

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>