@datagrok/sequence-translator 1.6.0 → 1.6.1

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.6.0",
+  "version": "1.6.1",
   "author": {
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"

package/src/polytool/conversion/pt-synthetic.ts

@@ -30,6 +30,7 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
       names = [];
       monomers = [];
       console.error(e);
+      grok.shell.warning(e);
     } finally {
       for (let j = 0; j < names.length; j ++)
         argLib[names[j]] = monomers[j];
@@ -52,12 +53,12 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
 
   const monomerNames = new Array<string>(totalLength);
   const resMonomers = new Array<Monomer>(totalLength);
-  const rawMonomers = new Array<string>(totalLength);
+  const monomers = new Array<string>(totalLength);
 
   const mainRxn = getReactionSmirks(rdkit, reacSmarts);
 
-  const reacCutFirst = `${reactants[0]}>>[C:1]`;
-  const reacCutSecond = `${reactants[1]}>>[C:2]`;
+  const reacCutFirst = `${reactants[0]}>>[C:1]C`;
+  const reacCutSecond = `${reactants[1]}>>[C:2]C`;
 
   const rxnCutFirst = getReactionSmirks(rdkit, reacCutFirst);
   const rxnCutSecond = getReactionSmirks(rdkit, reacCutSecond);
@@ -68,7 +69,7 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
     if (!monomer) throw new MonomerNotFoundError('PEPTIDE', rule.firstMonomers[i]);
 
     const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutFirst, monomer.name);
-    rawMonomers[counter] = sMolBlock;
+    monomers[counter] = sMolBlock;
     monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
     counter++;
   }
@@ -77,7 +78,7 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
     if (!monomer) throw new MonomerNotFoundError('PEPTIDE', rule.secondMonomers[i]);
 
     const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutSecond, monomer.name);
-    rawMonomers[counter] = sMolBlock;
+    monomers[counter] = sMolBlock;
     monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
     counter++;
   }
@@ -97,20 +98,22 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
     mol?.delete();
   }
   //pMolblock = reactionMembers[1]//cutProduct(rdkit, monomer1?.molfile, monomer2?.molfile, mainRxn, monomerName);
-  rawMonomers[counter] = pMolblock;
+  monomers[counter] = pMolblock;
   monomerNames[counter] = monomerName;
 
-  //after RDKit works
-  for (let i = 0; i < totalLength - 1; i ++)
-    rawMonomers[i] = rawMonomers[i].replace('0.0000 C   ', '0.0000 R#  ').replace('M  RGP  2', 'M  RGP  3   1   3');
-  rawMonomers[totalLength - 1] = modProduct(rawMonomers[totalLength - 1]);
+  //after RDKit works - [X:N] is first atom which is exploited
+  for (let i = 0; i < totalLength - 1; i ++) {
+    monomers[i] = monomers[i].replace('    0.0000    0.0000    0.0000 C   ', '    0.0000    0.0000    0.0000 R#  ')
+      .replace('M  RGP  2', 'M  RGP  3   2   3');
+  }
+  monomers[totalLength - 1] = modProduct(monomers[totalLength - 1]);
 
   for (let i = 0; i < totalLength; i ++) {
     const isProduct = i == totalLength - 1 ? true : false;
     const resMonomer: Monomer = {
       [REQ.SYMBOL]: monomerNames[i],
       [REQ.NAME]: monomerNames[i],
-      [REQ.MOLFILE]: rawMonomers[i],
+      [REQ.MOLFILE]: monomers[i],
       [REQ.AUTHOR]: '',
       [REQ.ID]: 0,
       [REQ.RGROUPS]: getNewGroups(isProduct),

package/src/polytool/pt-dialog.ts

@@ -99,8 +99,8 @@ export async function getPolyToolConvertDialog(srcCol?: DG.Column): Promise<DG.D
     const generateHelmInput = ui.input.bool(PT_UI_GET_HELM, {value: true});
     ui.tooltip.bind(generateHelmInput.root, PT_UI_ADD_HELM);
 
-    const chiralityEngineInput = ui.input.bool(PT_UI_USE_CHIRALITY, {value: false});
-    const highlightMonomersInput = ui.input.bool(PT_UI_HIGHLIGHT_MONOMERS, {value: false});
+    const chiralityEngineInput = ui.input.bool(PT_UI_USE_CHIRALITY, {value: true});
+    const highlightMonomersInput = ui.input.bool(PT_UI_HIGHLIGHT_MONOMERS, {value: true});
     let ruleFileList: string[];
     const ruleInputs = new RuleInputs(RULES_PATH, RULES_STORAGE_NAME, '.json', {
       onValueChanged: (value: string[]) => { ruleFileList = value; }

package/src/tests/toAtomicLevel-tests.ts

@@ -85,8 +85,8 @@ category('toAtomicLevel', () => {
     try {
       const molInchi = mol.get_inchi();
       const molInchiKey = rdKitModule.get_inchikey_for_inchi(molInchi);
-      expect(mol.get_num_bonds(), 6);
-      expect(mol.get_num_atoms(), 7);
+      expect(mol.get_num_bonds(), 7);
+      expect(mol.get_num_atoms(), 8);
       // TODO: Check inchi key for the new monomer molfile
       // expect(molInchiKey, 'V2H10N2O3S-UHFFFAOYSA-N');
     } finally {