[fix.stereo.λ.D8+] exclude aromatic bonds from E/Z unknowns

Kekulized aromatic rings were being audited as ordinary double bonds, so valid explicitly assigned chiral ligands were blocked by a fabricated UNSPECIFIED E/Z verdict. RDKit aromatic atom witnesses now exclude ring bonds while preserving exocyclic and ordinary stereogenic double bonds; a focused regression seals the boundary.

Author: ivanicu

src/app.frontend.facets.molstar-rdkit.editable/fep-workbench/fep-workbench.ts

@@ -7,7 +7,7 @@ import { decideWorkbenchBoot } from './workbench-boot';
 import { escapeHtml, markPipelineReadyDom, renderOperationConfirmationDom, renderPreparationControlsDom, renderPreparationPolicyDom, renderRunHistoryDom, renderRunJobsDom, setSafeText } from './workbench-dom';
 import { acknowledgedPreparationReceipt, campaignScientificRefFrom, contentRef, fullJobId, operationBindingFromReceipt, preparationReceiptBinding, runReceiptFromData, runReceiptMatchesData, runReceiptState, type AcknowledgedPreparationReceipt, type AnyPreparationReceipt as PreparationReceipt, type ArtifactRef, type CampaignScientificRef, type ContentRef, type PreparationReceipt as DurablePreparationReceipt, type PlannerOutputReceipt, type PlannerReceipt, type RunReceipt, type RunReceiptState } from './workbench-receipts';
 import { globalPhysicalReceiptKey, RECEIPT_KEYS, WorkbenchReceiptStore, type ReceiptStorage } from './workbench-receipt-store';
-import { OperationCoordinator, aggregateArmMatches, canonicalJson, chemistryEvidenceFrom, chemistryEvidenceView, exactOperationBindingMatches, executionEligibilityFrom, sameExactRef, type ExactAggregateArm, type ExactOperationBinding, type ExactRunBinding, type OperationScope } from './workbench-state';
+import { OperationCoordinator, aggregateArmMatches, canonicalJson, chemistryEvidenceFrom, chemistryEvidenceView, exactOperationBindingMatches, executionEligibilityFrom, isPotentialEzBond, sameExactRef, type ExactAggregateArm, type ExactOperationBinding, type ExactRunBinding, type OperationScope } from './workbench-state';
 import { aggregatePanelViewFrom, preparationPolicyGate, preparationPolicyViewFrom, runHistoryViewFrom, runJobsViewFrom } from './workbench-view-model';
 import { workbenchShellMarkup } from './workbench-shell';
 import { DemoCompounds, FallbackEdges, FallbackNetwork } from './workbench-fixture';
@@ -159,8 +159,10 @@ async function atomInfo(smiles: string): Promise<AtomInfo> {
         try{
             const stereo=JSON.parse(mol.get_stereo_tags()) as {CIP_atoms?:Array<[number,string]>;CIP_bonds?:Array<[number,number,string]>};cipAtoms=Array.isArray(stereo.CIP_atoms)?stereo.CIP_atoms:[];cipBonds=Array.isArray(stereo.CIP_bonds)?stereo.CIP_bonds:[];
             const json=JSON.parse(mol.get_json()) as {defaults?:{atom?:{impHs?:number}};molecules?:Array<{atoms?:Array<{impHs?:number}>;extensions?:Array<{name?:string;cipRanks?:number[]}>}>},molecule=json.molecules?.[0],atoms=molecule?.atoms||[],ranks=molecule?.extensions?.find(extension=>extension.name==='rdkitRepresentation')?.cipRanks||[],defaultHydrogens=Number(json.defaults?.atom?.impHs||0);
+            const aromaticAtoms=new Set<number>();let aromaticQuery:ReturnType<typeof RDKit.get_qmol>|null=null;
+            try{aromaticQuery=RDKit.get_qmol('[a]');const matches=aromaticQuery?JSON.parse(mol.get_substruct_matches(aromaticQuery)) as Array<{atoms?:number[]}>:[];if(Array.isArray(matches))matches.forEach(match=>match.atoms?.forEach(index=>aromaticAtoms.add(index)));}finally{aromaticQuery?.delete();}
             const substituentKeys=(atomIndex:number,partnerIndex:number):string[]=>{const keys=bonds.filter(bond=>bond.left===atomIndex||bond.right===atomIndex).map(bond=>bond.left===atomIndex?bond.right:bond.left).filter(index=>index!==partnerIndex).map(index=>`A:${String(ranks[index]??`${symbols[index]}:${index}`)}`),implicitHydrogens=Number(atoms[atomIndex]?.impHs??defaultHydrogens);for(let index=0;index<implicitHydrogens;index++)keys.push('H');return keys;};
-            potentialEzBonds=bonds.filter(bond=>bond.order===2&&!cipBonds.some(([left,right])=>(left===bond.left&&right===bond.right)||(left===bond.right&&right===bond.left))).filter(bond=>{const left=substituentKeys(bond.left,bond.right),right=substituentKeys(bond.right,bond.left);return left.length===2&&right.length===2&&left[0]!==left[1]&&right[0]!==right[1];}).map(bond=>[bond.left,bond.right]);
+            potentialEzBonds=bonds.filter(bond=>isPotentialEzBond(bond,aromaticAtoms)&&!cipBonds.some(([left,right])=>(left===bond.left&&right===bond.right)||(left===bond.right&&right===bond.left))).filter(bond=>{const left=substituentKeys(bond.left,bond.right),right=substituentKeys(bond.right,bond.left);return left.length===2&&right.length===2&&left[0]!==left[1]&&right[0]!==right[1];}).map(bond=>[bond.left,bond.right]);
         }catch{stereoAvailable=false;}
         const result = { symbols, molblock, canonicalSmiles, charges, atomStereo, bonds, cycleRank, stereoAvailable, cipAtoms, cipBonds, potentialEzBonds }; atomInfoCache.set(smiles, result); return result;
     }

src/app.frontend.facets.molstar-rdkit.editable/fep-workbench/workbench-state.spec.ts

@@ -1,7 +1,14 @@
 import { describe, expect, it } from '@jest/globals';
-import { CHEMISTRY_DIMENSIONS, OperationCoordinator, aggregateArmMatches, campaignsVisibleToCopy, canonicalJson, chemistryEvidenceFrom, chemistryEvidenceView, exactOperationBindingMatches, exactRunBindingMatches, executionEligibilityFrom, sameExactRef, type ChemistryDimension, type ChemistryVerdict, type ExactOperationBinding, type ExactRunBinding } from './workbench-state';
+import { CHEMISTRY_DIMENSIONS, OperationCoordinator, aggregateArmMatches, campaignsVisibleToCopy, canonicalJson, chemistryEvidenceFrom, chemistryEvidenceView, exactOperationBindingMatches, exactRunBindingMatches, executionEligibilityFrom, isPotentialEzBond, sameExactRef, type ChemistryDimension, type ChemistryVerdict, type ExactOperationBinding, type ExactRunBinding } from './workbench-state';
 
 describe('FEP workbench operation ownership', () => {
+    it('excludes kekulized aromatic bonds from unknown E/Z candidates', () => {
+        const aromaticAtoms = new Set([0, 1, 2, 3, 4, 5]);
+        expect(isPotentialEzBond({ left: 0, right: 1, order: 2 }, aromaticAtoms)).toBe(false);
+        expect(isPotentialEzBond({ left: 5, right: 6, order: 2 }, aromaticAtoms)).toBe(true);
+        expect(isPotentialEzBond({ left: 6, right: 7, order: 1 }, aromaticAtoms)).toBe(false);
+    });
+
     it('invalidates competitors while allowing the transition owner to continue', () => {
         const coordinator = new OperationCoordinator('tab-a');
         const owner = coordinator.begin('restore');

src/app.frontend.facets.molstar-rdkit.editable/fep-workbench/workbench-state.ts

@@ -317,3 +317,11 @@ export function chemistryEvidenceView(value: unknown): ChemistryEvidenceView {
         ledger,
     };
 }
+
+/** Kekulized mol blocks encode aromatic rings as alternating 1/2 bonds. */
+export function isPotentialEzBond(
+    bond: { left: number; right: number; order: number },
+    aromaticAtoms: ReadonlySet<number>,
+): boolean {
+    return bond.order === 2 && !(aromaticAtoms.has(bond.left) && aromaticAtoms.has(bond.right));
+}