@datagrok/sequence-translator 1.10.1 → 1.10.3

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Files changed (9) hide show
  1. package/CHANGELOG.md +11 -1
  2. package/dist/package-test.js +1 -1
  3. package/dist/package-test.js.map +1 -1
  4. package/dist/package.js +1 -1
  5. package/dist/package.js.map +1 -1
  6. package/package.json +2 -2
  7. package/src/polytool/conversion/pt-synthetic.ts +13 -9
  8. package/test-console-output-1.log +52 -53
  9. package/test-record-1.mp4 +0 -0
package/package.json CHANGED
@@ -1,7 +1,7 @@
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  {
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  "name": "@datagrok/sequence-translator",
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  "friendlyName": "Sequence Translator",
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- "version": "1.10.1",
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+ "version": "1.10.3",
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  "author": {
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  "name": "Davit Rizhinashvili",
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  "email": "drizhinashvili@datagrok.ai"
@@ -22,7 +22,7 @@
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  }
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  ],
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  "dependencies": {
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- "@datagrok-libraries/bio": "^5.60.1",
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+ "@datagrok-libraries/bio": "^5.60.2",
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  "@datagrok-libraries/chem-meta": "^1.2.8",
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  "@datagrok-libraries/tutorials": "^1.6.1",
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  "@datagrok-libraries/utils": "^4.6.5",
package/src/polytool/conversion/pt-synthetic.ts CHANGED
@@ -90,13 +90,15 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
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  // const monomer1 = mLib.getMonomer('PEPTIDE', rule.firstMonomers[0]);
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  // const monomer2 = mLib.getMonomer('PEPTIDE', rule.secondMonomers[0]);
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  let mol: RDMol | null = null;
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+ reactionMembers[1] = reactionMembers[1].replace('[C:1]', '[1*]').replace('[C:2]', '[2*]').replace('[C:3]', '[3*]');
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+
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  let pMolblock = '';
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  try {
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  mol = rdkit.get_mol(reactionMembers[1]);
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  pMolblock = mol?.get_molblock();//molP?.get_v3Kmolblock();//
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  } catch (err: any) {
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  const [errMsg, _errStack] = errInfo(err);
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- grok.shell.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
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+ console.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
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  throw err;
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  } finally {
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  mol?.delete();
@@ -146,16 +148,18 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
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  }
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  function modProduct(product: string): string {
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- const fullMol = product.replace('M RAD', 'M RGP');
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+ const fullMol = product.replace('M RAD', 'M RGP').replace('M ISO', 'M RGP');
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  const lines = fullMol.split('\n');
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- const natoms = Number(lines[3].substring(0, 3));
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- const nbonds = Number(lines[3].substring(3, 6));
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- const rgpShift = 4 + natoms + nbonds;
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+ // const natoms = Number(lines[3].substring(0, 3));
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+ // const nbonds = Number(lines[3].substring(3, 6));
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+ const rgpShift = lines.findIndex((line) => line.startsWith('M RGP'));
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  const fAtom = Number(lines[rgpShift].substring(9, 13));
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  const sAtom = Number(lines[rgpShift].substring(17, 21));
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+ const firstRgroupIndex = Number(lines[rgpShift].substring(13, 17));
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+ const secondRgroupIndex = Number(lines[rgpShift].substring(21, 25));
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- lines[rgpShift] = lines[rgpShift].substring(0, 13) + ' 1' + lines[rgpShift].substring(17, 21) + ' 2';
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+ lines[rgpShift] = lines[rgpShift].substring(0, 13) + ` ${firstRgroupIndex}` + lines[rgpShift].substring(17, 21) + ` ${secondRgroupIndex}`;
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  lines[3 + fAtom] = lines[3 + fAtom].substring(0, 30) + ' R# 0 0 0 0 0 0 0 0 0 0 0 0';
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  lines[3 + sAtom] = lines[3 + sAtom].substring(0, 30) + ' R# 0 0 0 0 0 0 0 0 0 0 0 0';
@@ -185,7 +189,7 @@ function cutReactant(rdkit: RDModule, reactant: string, rxn: RDReaction, monomer
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  molBlock = molP?.get_molblock();//molP?.get_v3Kmolblock();//
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  } catch (err: any) {
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  const [errMsg, _errStack] = errInfo(err);
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- grok.shell.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
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+ console.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
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  throw err;
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  } finally {
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  mols?.delete();
@@ -205,7 +209,7 @@ function getReactionSmirks(rdkit: RDModule, smirks: string): RDReaction {
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  } catch (err: any) {
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  rxn?.delete();
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  const [errMsg, _errStack] = errInfo(err);
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- grok.shell.error(`Can not assemble monomer '${smirks}': ${errMsg}.`);
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+ console.error(`Can not assemble monomer '${smirks}': ${errMsg}.`);
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  throw err;
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  } finally {
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@@ -275,7 +279,7 @@ function getSyntheticMolBlock(rdkit: RDModule, reaction: string,
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  molBlock = molP?.get_molblock();//molP?.get_v3Kmolblock();//
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  } catch (err: any) {
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  const [errMsg, _errStack] = errInfo(err);
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- grok.shell.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
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+ console.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
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  throw err;
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  } finally {
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  rxn?.delete();