@datagrok/sequence-translator 1.5.0 → 1.5.1

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.5.0",
+  "version": "1.5.1",
   "author": {
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"

package/src/package.ts

@@ -301,6 +301,9 @@ export async function ptEnumeratorChemApp(): Promise<void> {
 //input: column col
 //input: string separator
 export function applyNotationProviderForCyclized(col: DG.Column<string>, separator: string) {
+  col.setTag('aligned', 'SEQ');
+  col.setTag('alphabet', 'UN');
+  col.setTag('.alphabetIsMultichar', 'true');
   col.meta.units = NOTATION.CUSTOM;
   col.tags[PolyToolTags.dataRole] = 'template';
   col.temp[SeqTemps.notationProvider] = new CyclizedNotationProvider(separator, _package.helmHelper);

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

@@ -179,10 +179,20 @@ export async function getOverriddenLibrary(rules: Rules): Promise<IMonomerLibBas
   const rdkit = await getRdKitModule();
   const argLib: { [symbol: string]: Monomer } = {};
 
+  let names: string [] = [];
+  let monomers: Monomer [] = [];
+
   for (let i = 0; i < rules.reactionRules.length; i++) {
-    const [names, monomers] = getNewMonomers(rdkit, systemMonomerLib, rules.reactionRules[i]);
-    for (let j = 0; j < names.length; j ++)
-      argLib[names[j]] = monomers[j];
+    try {
+      [names, monomers] = getNewMonomers(rdkit, systemMonomerLib, rules.reactionRules[i]);
+    } catch (e: any) {
+      names = [];
+      monomers = [];
+      console.error(e);
+    } finally {
+      for (let j = 0; j < names.length; j ++)
+        argLib[names[j]] = monomers[j];
+    }
   }
 
   const overrideMonomerLibData: MonomerLibData = {[PolymerTypes.PEPTIDE]: argLib};

package/src/polytool/conversion/rule-manager.ts

@@ -37,6 +37,7 @@ export class RulesManager {
   async getView(): Promise<DG.ViewBase> {
     if (!this.v) {
       this.v = DG.View.create();
+      this.v.name = 'Manage Polytool Rules';
       this.v.append(await this.getForm());
     }
 
@@ -94,8 +95,8 @@ export class RulesManager {
     const initCol = DG.Column.fromStrings('monomers', seqs);
     const helmCol = DG.Column.fromStrings('helm', helms);
 
-    initCol.semType = DG.SEMTYPE.MACROMOLECULE;
     applyNotationProviderForCyclized(initCol, '-');
+    initCol.semType = DG.SEMTYPE.MACROMOLECULE;
 
     helmCol.semType = DG.SEMTYPE.MACROMOLECULE;
     helmCol.meta.units = NOTATION.HELM;
@@ -112,7 +113,7 @@ export class RulesManager {
       const code = this.rules.reactionRules[i].code;
       const [firstMonomers, secondMonomers] = getMonomerPairs(this.rules.reactionRules[i]);
       for (let j = 0; j < firstMonomers.length; j++) {
-        const seq = `${firstMonomers[j]}(${code})-A-A-A-A-${secondMonomers[j]}(${code})-A`;
+        const seq = `${firstMonomers[j]}(${code})-A-A-A-A-${secondMonomers[j]}(${code})`;
         seqs.push(seq);
       }
     }