smiles-js 0.2.1 → 0.2.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "smiles-js",
-  "version": "0.2.1",
+  "version": "0.2.2",
   "description": "A JavaScript library for building molecules using composable fragments",
   "type": "module",
   "main": "src/index.js",

package/src/ring.js

@@ -60,9 +60,7 @@ export function Ring(atom, size, options = {}) {
       for (let i = 0; i < size; i++) {
         const currentAtom = replace[i] !== undefined ? replace[i] : atom;
 
-        if (i === 0) {
-          parts.push(currentAtom + '1');
-        } else if (newSubstituents[i]) {
+        if (newSubstituents[i]) {
           // Remap ring numbers in substituent to avoid conflicts
           const currentSmiles = parts.join('');
           const usedInCurrent = findUsedRingNumbers(currentSmiles);
@@ -83,11 +81,15 @@ export function Ring(atom, size, options = {}) {
           }
 
           // Add substituent at this position
-          if (i === size - 1) {
+          if (i === 0) {
+            parts.push(currentAtom + '1(' + remappedSubstituent + ')');
+          } else if (i === size - 1) {
             parts.push(currentAtom + '(' + remappedSubstituent + ')1');
           } else {
             parts.push(currentAtom + '(' + remappedSubstituent + ')');
           }
+        } else if (i === 0) {
+          parts.push(currentAtom + '1');
         } else if (i === size - 1) {
           parts.push(currentAtom + '1');
         } else {

package/test/ring-composition.test.js

@@ -59,3 +59,16 @@ test('Ring composition counts rings correctly', async () => {
   assert.ok(await isValidSMILES(triphenyl.smiles));
   assert.strictEqual(triphenyl.rings, 3);
 });
+
+test('Phenol composition works correctly', async () => {
+  const benzene = Ring('c', 6);
+  const phenol = benzene.attachAt(1, 'O');
+  assert.ok(await isValidSMILES(phenol.smiles));
+  assert.strictEqual(phenol.smiles, 'c1(O)ccccc1');
+});
+
+test('Para-quinone (2,5-cyclohexadiene-1,4-dione) composition works correctly', async () => {
+  const result = Ring('c', 6).attachAt(1, '=O').attachAt(4, '=O');
+  assert.ok(await isValidSMILES(result.smiles));
+  assert.strictEqual(result.smiles, 'c1(=O)ccc(=O)cc1');
+});

package/test/ring.test.js

@@ -59,7 +59,7 @@ test('Ring counts rings correctly', () => {
 test('Ring.attachAt creates toluene at position 1', async () => {
   const benzene = Ring('c', 6);
   const toluene = benzene.attachAt(1, 'C');
-  assert.strictEqual(toluene.smiles, 'c1ccccc1');
+  assert.strictEqual(toluene.smiles, 'c1(C)ccccc1');
   assert.ok(await isValidSMILES(toluene.smiles));
 });