smiles-js 2.0.2 → 2.1.0

package/test-integration/mirror.test.js

@@ -0,0 +1,151 @@
+import { describe, test, expect } from 'bun:test';
+import { Ring, Linear, Molecule } from '../src/constructors.js';
+
+describe('Mirror Integration - Linear', () => {
+  test('diethyl ether: CCO mirrored → CCOCC', () => {
+    const half = Linear(['C', 'C', 'O']);
+    const ether = half.mirror();
+    expect(ether.smiles).toBe('CCOCC');
+  });
+
+  test('diethylamine: CCN mirrored → CCNCC', () => {
+    const half = Linear(['C', 'C', 'N']);
+    const result = half.mirror();
+    expect(result.smiles).toBe('CCNCC');
+  });
+
+  test('glycol-like: OCCO mirrored at pivot=3 → OCCOCCCO', () => {
+    const half = Linear(['O', 'C', 'C', 'O']);
+    const result = half.mirror(3);
+    // Left: [O,C,C], Right: reverse of [O,C] → [C,O]
+    expect(result.smiles).toBe('OCCCO');
+  });
+
+  test('symmetric alkene: C=C=O mirrored → C=COC=C', () => {
+    const half = Linear(['C', 'C', 'O'], ['=']);
+    const result = half.mirror();
+    expect(result.smiles).toBe('C=COC=C');
+  });
+
+  test('symmetric chain with phenyl pendant', () => {
+    const half = Linear(['C', 'C', 'O']).attach(
+      1,
+      Ring({ atoms: 'c', size: 6 }),
+    );
+    const result = half.mirror();
+    expect(result.smiles).toBe('C(c1ccccc1)COCC(c2ccccc2)');
+  });
+
+  test('long palindromic chain', () => {
+    const half = Linear(['C', 'C', 'C', 'C', 'N']);
+    const result = half.mirror();
+    expect(result.smiles).toBe('CCCCNCCCC');
+  });
+});
+
+describe('Mirror Integration - Molecule (ABA copolymers)', () => {
+  test('ABA: polyethylene-benzene-polyethylene', () => {
+    const A = Linear(['C', 'C']);
+    const B = Ring({ atoms: 'c', size: 6 });
+    const AB = Molecule([A, B]);
+    const ABA = AB.mirror();
+    expect(ABA.smiles).toBe('CCc1ccccc1CC');
+  });
+
+  test('ABCBA: ethyl-benzene-oxygen-benzene-ethyl', () => {
+    const block = Molecule([
+      Linear(['C', 'C']),
+      Ring({ atoms: 'c', size: 6 }),
+      Linear(['O']),
+    ]);
+    const result = block.mirror();
+    expect(result.smiles).toBe('CCc1ccccc1Oc2ccccc2CC');
+  });
+
+  test('ABA with polystyrene arms', () => {
+    const styrene = Linear(['C', 'C']).attach(
+      2,
+      Ring({ atoms: 'c', size: 6 }),
+    );
+    const core = Linear(['O', 'C', 'O']);
+    const halfBlock = Molecule([styrene, core]);
+    const symmetric = halfBlock.mirror();
+    // styrene-OCO-styrene (with shifted ring numbers)
+    expect(symmetric.type).toBe('molecule');
+    expect(symmetric.components).toHaveLength(3);
+  });
+
+  test('repeat + mirror: homopolymer arm with symmetric core', () => {
+    const arm = Linear(['C', 'C']).repeat(2, 1, 2);
+    const core = Ring({ atoms: 'c', size: 6 });
+    const halfBlock = Molecule([arm, core]);
+    const symmetric = halfBlock.mirror();
+    expect(symmetric.smiles).toBe('CCCCc1ccccc1CCCC');
+  });
+});
+
+describe('Mirror Integration - Ring', () => {
+  test('meta-xylene: methyl at 2, mirror pivot=3', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const mono = benzene.attach(2, Linear(['C']));
+    const result = mono.mirror(3);
+    expect(result.smiles).toBe('c1c(C)cc(C)cc1');
+  });
+
+  test('1,3-disubstituted pyridine: N at 2, mirror pivot=1', () => {
+    const ring = Ring({
+      atoms: 'c',
+      size: 6,
+      substitutions: { 2: 'n' },
+    });
+    const result = ring.mirror(1);
+    expect(result.substitutions[2]).toBe('n');
+    expect(result.substitutions[6]).toBe('n');
+  });
+
+  test('symmetric ring with two pendant groups', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const mono = benzene.attach(2, Linear(['O']));
+    const result = mono.mirror(3);
+    // Attachment at 2 and mirror at 4
+    expect(result.attachments[2]).toHaveLength(1);
+    expect(result.attachments[4]).toHaveLength(1);
+  });
+});
+
+describe('Mirror edge cases', () => {
+  test('mirror preserves immutability', () => {
+    const chain = Linear(['C', 'C', 'O']);
+    const original = chain.smiles;
+    chain.mirror();
+    expect(chain.smiles).toBe(original);
+
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const mono = benzene.attach(2, Linear(['C']));
+    const originalSmiles = mono.smiles;
+    mono.mirror(1);
+    expect(mono.smiles).toBe(originalSmiles);
+
+    const mol = Molecule([Linear(['C']), Linear(['N'])]);
+    const originalMol = mol.smiles;
+    mol.mirror();
+    expect(mol.smiles).toBe(originalMol);
+  });
+
+  test('mirror of single atom is identity', () => {
+    const single = Linear(['N']);
+    expect(single.mirror().smiles).toBe('N');
+  });
+
+  test('mirror of two-atom chain', () => {
+    const two = Linear(['C', 'N']);
+    expect(two.mirror().smiles).toBe('CNC');
+  });
+
+  test('mirror of single-component molecule', () => {
+    const mol = Molecule([Linear(['C', 'C'])]);
+    const result = mol.mirror();
+    expect(result.smiles).toBe('CC');
+    expect(result.components).toHaveLength(1);
+  });
+});

package/test-integration/polymer.test.js

@@ -0,0 +1,148 @@
+import { describe, test, expect } from 'bun:test';
+import { Ring, Linear, Molecule } from '../src/constructors.js';
+
+describe('Polymer repeat() Integration', () => {
+  test('polyethylene trimer: -[CH2CH2]3-', () => {
+    const ethylene = Linear(['C', 'C']);
+    const pe = ethylene.repeat(3, 1, 2);
+    expect(pe.smiles).toBe('CCCCCC');
+  });
+
+  test('polystyrene dimer: styrene with phenyl pendant', () => {
+    const styrene = Linear(['C', 'C']).attach(
+      2,
+      Ring({ atoms: 'c', size: 6 }),
+    );
+    const ps = styrene.repeat(2, 1, 2);
+    expect(ps.smiles).toBe('CC(c1ccccc1)CC(c2ccccc2)');
+  });
+
+  test('polystyrene trimer', () => {
+    const styrene = Linear(['C', 'C']).attach(
+      2,
+      Ring({ atoms: 'c', size: 6 }),
+    );
+    const ps = styrene.repeat(3, 1, 2);
+    expect(ps.smiles).toBe('CC(c1ccccc1)CC(c2ccccc2)CC(c3ccccc3)');
+  });
+
+  test('poly(vinyl alcohol) dimer: -[CH2CH(OH)]2-', () => {
+    const vinylAlcohol = Linear(['C', 'C']).attach(
+      2,
+      Linear(['O']),
+    );
+    const pva = vinylAlcohol.repeat(2, 1, 2);
+    expect(pva.smiles).toBe('CC(O)CC(O)');
+  });
+
+  test('biphenyl: two linked benzene rings', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const biphenyl = benzene.repeat(2, 1, 6);
+    expect(biphenyl.smiles).toBe('c1ccccc1c2ccccc2');
+  });
+
+  test('terphenyl: three linked benzene rings', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const terphenyl = benzene.repeat(3, 1, 6);
+    expect(terphenyl.smiles).toBe('c1ccccc1c2ccccc2c3ccccc3');
+  });
+
+  test('bipyridine: two linked pyridine rings', () => {
+    const pyridine = Ring({
+      atoms: 'c',
+      size: 6,
+      substitutions: { 3: 'n' },
+    });
+    const bipyridine = pyridine.repeat(2, 1, 6);
+    expect(bipyridine.smiles).toBe('c1cnccc1c2cnccc2');
+  });
+
+  test('polyoxymethylene trimer: -[CH2O]3-', () => {
+    const oxymethylene = Linear(['C', 'O']);
+    const pom = oxymethylene.repeat(3, 1, 2);
+    expect(pom.smiles).toBe('COCOCO');
+  });
+
+  test('nylon 6,6 repeating unit dimer', () => {
+    const unit = Molecule([
+      Linear(['N', 'C'], [null, '=']),
+      Linear(['C', 'C', 'C', 'C']),
+      Linear(['C', 'N'], ['=', null]),
+      Linear(['C', 'C', 'C', 'C', 'C', 'C']),
+    ]);
+    const dimer = unit.repeat(2, 1, 1);
+    expect(dimer.type).toBe('molecule');
+    expect(dimer.components).toHaveLength(2);
+    expect(dimer.smiles).toBe('N=CCCCC=CNCCCCCCN=CCCCC=CNCCCCCC');
+  });
+});
+
+describe('Polymer fusedRepeat() Integration', () => {
+  test('naphthalene: 2 fused aromatic rings', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const naphthalene = benzene.fusedRepeat(2, 4);
+    expect(naphthalene.type).toBe('fused_ring');
+    expect(naphthalene.rings).toHaveLength(2);
+    expect(naphthalene.rings[0].ringNumber).toBe(1);
+    expect(naphthalene.rings[1].ringNumber).toBe(2);
+  });
+
+  test('anthracene: 3 fused aromatic rings', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const anthracene = benzene.fusedRepeat(3, 4);
+    expect(anthracene.type).toBe('fused_ring');
+    expect(anthracene.rings).toHaveLength(3);
+  });
+
+  test('tetracene: 4 fused aromatic rings', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const tetracene = benzene.fusedRepeat(4, 4);
+    expect(tetracene.type).toBe('fused_ring');
+    expect(tetracene.rings).toHaveLength(4);
+  });
+
+  test('fused cyclohexane dimer (decalin-like)', () => {
+    const cyclohexane = Ring({ atoms: 'C', size: 6 });
+    const decalin = cyclohexane.fusedRepeat(2, 4);
+    expect(decalin.type).toBe('fused_ring');
+    expect(decalin.rings).toHaveLength(2);
+  });
+
+  test('fused 5-membered rings (pentalene-like)', () => {
+    const cp = Ring({ atoms: 'C', size: 5 });
+    const pentalene = cp.fusedRepeat(2, 3);
+    expect(pentalene.type).toBe('fused_ring');
+    expect(pentalene.rings).toHaveLength(2);
+  });
+});
+
+describe('Polymer edge cases', () => {
+  test('repeat n=1 returns clone, not original', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const clone = benzene.repeat(1, 1, 6);
+    expect(clone.smiles).toBe('c1ccccc1');
+    expect(clone).not.toBe(benzene);
+  });
+
+  test('fusedRepeat n=1 returns ring clone', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const clone = benzene.fusedRepeat(1, 4);
+    expect(clone.smiles).toBe('c1ccccc1');
+    expect(clone.type).toBe('ring');
+    expect(clone).not.toBe(benzene);
+  });
+
+  test('large repeat count (n=10)', () => {
+    const ethylene = Linear(['C', 'C']);
+    const pe10 = ethylene.repeat(10, 1, 2);
+    expect(pe10.smiles).toBe('C'.repeat(20));
+  });
+
+  test('repeat preserves immutability of original', () => {
+    const benzene = Ring({ atoms: 'c', size: 6 });
+    const original = benzene.smiles;
+    benzene.repeat(5, 1, 6);
+    benzene.fusedRepeat(3, 4);
+    expect(benzene.smiles).toBe(original);
+  });
+});

package/todo

@@ -1,4 +1,2 @@
-repeat
-mirror
 HOSE integration
 Bile acid sequestrants