smiles-js 2.0.3 → 2.2.0

package/test-integration/adjuvant-analgesics.test.js

@@ -23,6 +23,12 @@ describe('Gabapentin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(GABAPENTIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(GABAPENTIN_SMILES);
     const code = ast.toCode('v');
@@ -30,14 +36,14 @@ describe('Gabapentin Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(GABAPENTIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -64,9 +70,15 @@ describe('Pregabalin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(PREGABALIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(PREGABALIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -92,9 +104,15 @@ describe('Amitriptyline Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(AMITRIPTYLINE_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(AMITRIPTYLINE_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -121,9 +139,15 @@ describe('Duloxetine Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(DULOXETINE_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(DULOXETINE_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -150,9 +174,15 @@ describe('Carbamazepine Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(CARBAMAZEPINE_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(CARBAMAZEPINE_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -179,9 +209,15 @@ describe('Valproic Acid Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(VALPROIC_ACID_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(VALPROIC_ACID_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);

package/test-integration/cholesterol-drugs.test.js

@@ -12,6 +12,7 @@ const EZETIMIBE_SMILES = 'C[C@H]1[C@@H](O)[C@H](O[C@H]1c2ccc(F)cc2)c3ccc(O)cc3C(
 const FENOFIBRATE_SMILES = 'CC(C)OC(=O)C(C)(C)Oc1ccc(cc1)C(=O)c2ccc(Cl)cc2';
 const GEMFIBROZIL_SMILES = 'CC1=CC(C)=CC=C1CCCC(C)(C)C(=O)O';
 const PITAVASTATIN_SMILES = 'CC(C)c1nc(nc(c1/C=C/[C@@H](O)C[C@@H](O)CC(=O)O)c2ccc(F)cc2)NC(=O)C3CC3';
+const CHOLESTEROL_SMILES = 'C[C@H](CCCC(C)C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C';
 
 describe('Atorvastatin Integration Test', () => {
   test('parses atorvastatin', () => {
@@ -27,6 +28,12 @@ describe('Atorvastatin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(ATORVASTATIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(ATORVASTATIN_SMILES);
     const code = ast.toCode('v');
@@ -34,14 +41,14 @@ describe('Atorvastatin Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(ATORVASTATIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -67,6 +74,12 @@ describe('Simvastatin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(SIMVASTATIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(SIMVASTATIN_SMILES);
     const code = ast.toCode('v');
@@ -74,14 +87,14 @@ describe('Simvastatin Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(SIMVASTATIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -107,6 +120,12 @@ describe('Rosuvastatin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(ROSUVASTATIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(ROSUVASTATIN_SMILES);
     const code = ast.toCode('v');
@@ -114,14 +133,14 @@ describe('Rosuvastatin Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(ROSUVASTATIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -147,6 +166,12 @@ describe('Pravastatin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(PRAVASTATIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(PRAVASTATIN_SMILES);
     const code = ast.toCode('v');
@@ -154,14 +179,14 @@ describe('Pravastatin Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(PRAVASTATIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -187,6 +212,12 @@ describe('Lovastatin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(LOVASTATIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(LOVASTATIN_SMILES);
     const code = ast.toCode('v');
@@ -194,14 +225,14 @@ describe('Lovastatin Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(LOVASTATIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -227,6 +258,12 @@ describe('Fluvastatin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(FLUVASTATIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(FLUVASTATIN_SMILES);
     const code = ast.toCode('v');
@@ -234,14 +271,14 @@ describe('Fluvastatin Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(FLUVASTATIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -267,6 +304,12 @@ describe('Ezetimibe Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(EZETIMIBE_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(EZETIMIBE_SMILES);
     const code = ast.toCode('v');
@@ -274,14 +317,14 @@ describe('Ezetimibe Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(EZETIMIBE_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -307,6 +350,12 @@ describe('Fenofibrate Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(FENOFIBRATE_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(FENOFIBRATE_SMILES);
     const code = ast.toCode('v');
@@ -314,14 +363,14 @@ describe('Fenofibrate Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(FENOFIBRATE_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -347,6 +396,12 @@ describe('Gemfibrozil Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(GEMFIBROZIL_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(GEMFIBROZIL_SMILES);
     const code = ast.toCode('v');
@@ -354,14 +409,14 @@ describe('Gemfibrozil Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(GEMFIBROZIL_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -387,6 +442,12 @@ describe('Pitavastatin Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(PITAVASTATIN_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(PITAVASTATIN_SMILES);
     const code = ast.toCode('v');
@@ -394,14 +455,14 @@ describe('Pitavastatin Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(PITAVASTATIN_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
 
     const varMatch = code.match(/export const (v\d+) = /g);
@@ -412,3 +473,49 @@ describe('Pitavastatin Integration Test', () => {
     expect(reconstructed.smiles).toBe(PITAVASTATIN_SMILES);
   });
 });
+
+describe('Cholesterol Integration Test', () => {
+  test('parses cholesterol', () => {
+    const ast = parse(CHOLESTEROL_SMILES);
+    const obj = ast.toObject();
+    expect(obj).toMatchSnapshot();
+    expect(ast.smiles).toBe(CHOLESTEROL_SMILES);
+  });
+
+  test('generates valid code via toCode()', () => {
+    const ast = parse(CHOLESTEROL_SMILES);
+    const code = ast.toCode('v');
+    expect(code).toMatchSnapshot();
+  });
+
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(CHOLESTEROL_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
+  test('generated code is valid JavaScript', () => {
+    const ast = parse(CHOLESTEROL_SMILES);
+    const code = ast.toCode('v');
+    const executableCode = stripExports(code);
+
+    let factory;
+    expect(() => {
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
+    }).not.toThrow();
+    expect(typeof factory).toBe('function');
+  });
+
+  test('codegen round-trip: generated code produces valid SMILES', () => {
+    const ast = parse(CHOLESTEROL_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    const executableCode = stripExports(code);
+
+    const varMatch = code.match(/export const (v\d+) = /g);
+    const lastVar = varMatch ? varMatch[varMatch.length - 1].match(/export const (v\d+)/)[1] : 'v1';
+
+    const reconstructed = executeCode(executableCode, lastVar);
+
+    expect(reconstructed.smiles).toBe(CHOLESTEROL_SMILES);
+  });
+});

package/test-integration/cholesterol.test.js

@@ -0,0 +1,112 @@
+import { describe, test, expect } from 'bun:test';
+import { parse } from '../src/parser/index.js';
+import { codegenRoundTrip } from './utils.js';
+
+const CHOLESTEROL_SMILES = 'C[C@H](CCCC(C)C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C';
+
+describe('Cholesterol - Divide and Conquer', () => {
+  // Cholesterol SMILES:
+  // C[C@H](CCCC(C)C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
+  //
+  // The failure: ring 4 is being dropped
+  // Expected: ...CC=C4[C@@]3(CC[C@@H](C4)O)C)C
+  // Received: ...CC=C[C@@]3(CC[C@@H](C)O)C)C
+
+  // Level 1: Simple ring closures
+  test('simple ring', () => {
+    const s = 'C1CCCCC1';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 2: Two fused rings (decalin-like)
+  test('two fused rings', () => {
+    const s = 'C1CCC2CCCCC2C1';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 3: Ring closure inside a branch - the core pattern
+  test('ring closure in branch: C1CCC(C1)C', () => {
+    const s = 'C1CCC(C1)C';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 4: Two ring numbers, one closing in a branch
+  test('two rings, one closing in branch: C1CC2CCC(C2)C1', () => {
+    const s = 'C1CC2CCC(C2)C1';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 5: Ring opening and closing with different numbers in nested context
+  test('ring 4 opens and closes in branch: C4CCC(C4)', () => {
+    const s = 'C4CCC(C4)';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 6: The specific pattern from cholesterol - ring opens, then closes inside a parenthesized branch
+  test('ring open at atom, close inside branch argument: CC=C4C(CC(C4)O)', () => {
+    const s = 'CC=C4C(CC(C4)O)';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 7: Closer to cholesterol D-ring pattern
+  test('cholesterol D-ring pattern: CC=C4C(CCC(C4)O)C', () => {
+    const s = 'CC=C4C(CCC(C4)O)C';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 8: Add ring 3 fused with ring 4
+  test('fused rings 3+4: C3CC=C4C3(CCC(C4)O)C', () => {
+    const s = 'C3CC=C4C3(CCC(C4)O)C';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 9: The C/D ring system from cholesterol (without stereo)
+  test('C/D ring system: C2CC=C4C(CC2)(CCC(C4)O)C', () => {
+    const s = 'C2CC=C4C(CC2)(CCC(C4)O)C';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 10: Three fused rings (A/B/C ring without stereo)
+  test('three fused rings: C1CCC2C1CCC3CC=C4C3(CCC(C4)O)C', () => {
+    const s = 'C1CCC2C1CCC3C2CC=C4C3(CCC(C4)O)C';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 11: Isolate multiple branches on same atom with ring closures
+  test('two branches with ring closures: C1C(C1)(C2)CC2', () => {
+    const s = 'C1C(C1)(C2)CC2';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 12: Minimal failing pattern - ring closure in second branch
+  test('ring close in second branch: C4CC(C)(C4)', () => {
+    const s = 'C4CC(C)(C4)';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 13: Full cholesterol (no stereo) to isolate stereo vs ring issue
+  test('cholesterol without stereochemistry', () => {
+    const s = 'CC(CCCC(C)C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C';
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+
+  // Level 14: Full cholesterol with stereochemistry
+  test('full cholesterol', () => {
+    const s = CHOLESTEROL_SMILES;
+    expect(parse(s).smiles).toBe(s);
+    expect(codegenRoundTrip(s).smiles).toBe(s);
+  });
+});

package/test-integration/dexamethasone.test.js

@@ -24,6 +24,12 @@ describe('Dexamethasone Integration Test', () => {
     expect(code).toMatchSnapshot();
   });
 
+  test('generates valid verbose code via toCode()', () => {
+    const ast = parse(DEXAMETHASONE_SMILES);
+    const code = ast.toCode('v', { verbose: true });
+    expect(code).toMatchSnapshot();
+  });
+
   test('generated code is valid JavaScript', () => {
     const ast = parse(DEXAMETHASONE_SMILES);
     const code = ast.toCode('v');
@@ -31,14 +37,14 @@ describe('Dexamethasone Integration Test', () => {
 
     let factory;
     expect(() => {
-      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', executableCode);
+      factory = createFunction('Ring', 'Linear', 'FusedRing', 'Molecule', 'RawFragment', 'Fragment', executableCode);
     }).not.toThrow();
     expect(typeof factory).toBe('function');
   });
 
   test('codegen round-trip: generated code produces valid SMILES', () => {
     const ast = parse(DEXAMETHASONE_SMILES);
-    const code = ast.toCode('v');
+    const code = ast.toCode('v', { verbose: true });
     const executableCode = stripExports(code);
     const varMatch = code.match(/export const (v\d+) = /g);
     const lastVar = varMatch[varMatch.length - 1].match(/export const (v\d+)/)[1];