@datagrok/sequence-translator 1.10.0 → 1.10.2

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.10.0",
+  "version": "1.10.2",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -22,7 +22,7 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.60.0",
+    "@datagrok-libraries/bio": "^5.60.2",
     "@datagrok-libraries/chem-meta": "^1.2.8",
     "@datagrok-libraries/tutorials": "^1.6.1",
     "@datagrok-libraries/utils": "^4.6.5",

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

@@ -20,8 +20,8 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
   const rdkit = await getRdKitModule();
   const argLib: { [symbol: string]: Monomer } = {};
 
-  let names: string [] = [];
-  let monomers: Monomer [] = [];
+  let names: (string | null) [] = [];
+  let monomers: (Monomer | null) [] = [];
 
   for (let i = 0; i < rules.reactionRules.length; i++) {
     try {
@@ -32,8 +32,11 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
       console.error(e);
       grok.shell.warning(e);
     } finally {
-      for (let j = 0; j < names.length; j ++)
-        argLib[names[j]] = monomers[j];
+      for (let j = 0; j < names.length; j ++) {
+        if (names[j] == null || monomers[j] == null)
+          continue;
+        argLib[names[j]!] = monomers[j]!;
+      }
     }
   }
 
@@ -44,16 +47,16 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
   return overriddenMonomerLib;
 }
 
-export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleReaction): [string[], Monomer[]] {
+export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleReaction): [(string | null)[], (Monomer | null)[]] {
   const reacSmarts = rule.reaction;
   const monomerName = rule.name;
   const totalLength = rule.firstMonomers.length + rule.secondMonomers.length + 1;
   const reactionMembers = rule.reaction.split('>>');
   const reactants = reactionMembers[0].split('.');
 
-  const monomerNames = new Array<string>(totalLength);
-  const resMonomers = new Array<Monomer>(totalLength);
-  const monomers = new Array<string>(totalLength);
+  const monomerNames = new Array<string | null>(totalLength);
+  const resMonomers = new Array<Monomer | null>(totalLength);
+  const monomers = new Array<string | null>(totalLength);
 
   const mainRxn = getReactionSmirks(rdkit, reacSmarts);
 
@@ -66,20 +69,21 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
   let counter = 0;
   for (let i = 0; i < rule.firstMonomers.length; i++) {
     const monomer = mLib.getMonomer('PEPTIDE', rule.firstMonomers[i]);
-    if (!monomer) throw new MonomerNotFoundError('PEPTIDE', rule.firstMonomers[i]);
 
-    const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutFirst, monomer.name);
-    monomers[counter] = sMolBlock;
-    monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    if (monomer) {
+      const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutFirst, monomer.name);
+      monomers[counter] = sMolBlock;
+      monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    }
     counter++;
   }
   for (let i = 0; i < rule.secondMonomers.length; i++) {
     const monomer = mLib.getMonomer('PEPTIDE', rule.secondMonomers[i]);
-    if (!monomer) throw new MonomerNotFoundError('PEPTIDE', rule.secondMonomers[i]);
-
-    const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutSecond, monomer.name);
-    monomers[counter] = sMolBlock;
-    monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    if (monomer) {
+      const sMolBlock = cutReactant(rdkit, monomer.molfile, rxnCutSecond, monomer.name);
+      monomers[counter] = sMolBlock;
+      monomerNames[counter] = `${monomer.symbol}_${monomerName}`;
+    }
     counter++;
   }
 
@@ -92,7 +96,7 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
     pMolblock = mol?.get_molblock();//molP?.get_v3Kmolblock();//
   } catch (err: any) {
     const [errMsg, _errStack] = errInfo(err);
-    grok.shell.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
+    console.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
     throw err;
   } finally {
     mol?.delete();
@@ -103,17 +107,21 @@ export function getNewMonomers(rdkit: RDModule, mLib: IMonomerLib, rule: RuleRea
 
   //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');
+    if (monomers[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]);
+  monomers[totalLength - 1] = modProduct(monomers[totalLength - 1]!);
 
   for (let i = 0; i < totalLength; i ++) {
     const isProduct = i == totalLength - 1 ? true : false;
+    if (!monomers[i] || !monomerNames[i])
+      continue;
     const resMonomer: Monomer = {
-      [REQ.SYMBOL]: monomerNames[i],
-      [REQ.NAME]: monomerNames[i],
-      [REQ.MOLFILE]: monomers[i],
+      [REQ.SYMBOL]: monomerNames[i]!,
+      [REQ.NAME]: monomerNames[i]!,
+      [REQ.MOLFILE]: monomers[i]!,
       [REQ.AUTHOR]: '',
       [REQ.ID]: 0,
       [REQ.RGROUPS]: getNewGroups(isProduct),
@@ -177,7 +185,7 @@ function cutReactant(rdkit: RDModule, reactant: string, rxn: RDReaction, monomer
     molBlock = molP?.get_molblock();//molP?.get_v3Kmolblock();//
   } catch (err: any) {
     const [errMsg, _errStack] = errInfo(err);
-    grok.shell.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
+    console.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
     throw err;
   } finally {
     mols?.delete();
@@ -197,7 +205,7 @@ function getReactionSmirks(rdkit: RDModule, smirks: string): RDReaction {
   } catch (err: any) {
     rxn?.delete();
     const [errMsg, _errStack] = errInfo(err);
-    grok.shell.error(`Can not assemble monomer '${smirks}': ${errMsg}.`);
+    console.error(`Can not assemble monomer '${smirks}': ${errMsg}.`);
     throw err;
   } finally {
 
@@ -267,7 +275,7 @@ function getSyntheticMolBlock(rdkit: RDModule, reaction: string,
     molBlock = molP?.get_molblock();//molP?.get_v3Kmolblock();//
   } catch (err: any) {
     const [errMsg, _errStack] = errInfo(err);
-    grok.shell.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
+    console.error(`Can not assemble monomer '${monomerName}': ${errMsg}.`);
     throw err;
   } finally {
     rxn?.delete();

package/src/tests/toAtomicLevel-tests.ts

@@ -80,9 +80,8 @@ category('toAtomicLevel', () => {
     const reactionRule = rules.reactionRules.find((r) => r.name == 'GGaz')!;
 
     const [newSymbols, newMonomers] = getNewMonomers(rdKitModule, systemMonomerLib, reactionRule);
-    expect(newSymbols[0], 'azG_GGaz');
-
-    const mol = rdKitModule.get_mol(newMonomers[0].molfile);
+    expect(newSymbols?.[0], 'azG_GGaz');
+    const mol = rdKitModule.get_mol(newMonomers[0]!.molfile);
     try {
       const molInchi = mol.get_inchi();
       const molInchiKey = rdKitModule.get_inchikey_for_inchi(molInchi);