From 52f58c7aa8b0437eaec34a06b2985c470849bd6c Mon Sep 17 00:00:00 2001
From: Venkata Nainala <mailcs76@gmail.com>
Date: Sun, 7 Jun 2026 16:58:30 +0200
Subject: [PATCH 1/2] fix(search): correct citations tagType on welcome page
 button

Align the citations tab search button with Enter key handling and the
backend tag handler by using tagType=citations and activeTab=citations.
---
 resources/views/livewire/welcome.blade.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/resources/views/livewire/welcome.blade.php b/resources/views/livewire/welcome.blade.php
index 2b38b6c1..bf659e5d 100644
--- a/resources/views/livewire/welcome.blade.php
+++ b/resources/views/livewire/welcome.blade.php
@@ -206,7 +206,7 @@ class="h-full w-full border-transparent py-2 pl-8 pr-3 text-sm text-gray-900 pla
                                             </div>
                                             <div class="flex items-center md:ml-1">
                                                 <button type="submit"
-                                                    @click="window.location.href = '/search?q=' + encodeURIComponent(query) + '&tagType=citation&type=tags&activeTab=citation'"
+                                                    @click="window.location.href = '/search?q=' + encodeURIComponent(query) + '&tagType=citations&type=tags&activeTab=citations'"
                                                     class="rounded-md bg-secondary-dark px-3.5 py-1.5 text-base font-semibold leading-7 text-white shadow-sm hover:bg-secondary-light focus-visible:outline focus-visible:outline-2 focus-visible:outline-offset-2 focus-visible:outline-indigo-600 mr-3"><svg
                                                         xmlns="http://www.w3.org/2000/svg" fill="none"
                                                         viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor"

From 55320fb244ffbc5d7a5794710cf557eae960d686 Mon Sep 17 00:00:00 2001
From: Venkata Nainala <mailcs76@gmail.com>
Date: Sun, 7 Jun 2026 16:58:32 +0200
Subject: [PATCH 2/2] fix(search): detect SMILES ring notation instead of
 molecular formula

Ring-closure SMILES such as C1CCCCC1 were misclassified as molecular
formulas because the element-token regex matched before the SMILES check.
Reject consecutive same-element tokens so these queries use RDKit search.
---
 app/Actions/Coconut/SearchMolecule.php     | 32 ++++++++++++++++++--
 tests/Unit/SearchMoleculeQueryTypeTest.php | 35 ++++++++++++++++++++++
 2 files changed, 64 insertions(+), 3 deletions(-)
 create mode 100644 tests/Unit/SearchMoleculeQueryTypeTest.php

diff --git a/app/Actions/Coconut/SearchMolecule.php b/app/Actions/Coconut/SearchMolecule.php
index e6964b49..3b47ca1b 100644
--- a/app/Actions/Coconut/SearchMolecule.php
+++ b/app/Actions/Coconut/SearchMolecule.php
@@ -120,9 +120,9 @@ private function determineQueryType($query)
             return 'parttialinchikey';
         }
 
-        // Check for molecular formula (must match pattern and not contain SMILES-specific characters)
-        // Molecular formulas contain only element symbols and numbers (e.g., C6H12O6, H2O)
-        if (preg_match('/^([A-Z][a-z]?\d*)+$/', $query) && ! preg_match('/[()@\[\]\/\\\\=#\-+]/', $query)) {
+        // Molecular formulas use condensed notation (e.g., C6H12O6, H2O), not SMILES chains
+        // like C1CCCCC1 or CCO where the same element appears in consecutive tokens.
+        if ($this->looksLikeMolecularFormula($query)) {
             return 'molecularformula';
         }
 
@@ -139,6 +139,32 @@ private function determineQueryType($query)
         return 'text';
     }
 
+    /**
+     * True when the query looks like a Hill-order molecular formula, not a SMILES string.
+     */
+    private function looksLikeMolecularFormula(string $query): bool
+    {
+        if (! preg_match('/^([A-Z][a-z]?\d*)+$/', $query) || preg_match('/[()@\[\]\/\\\\=#\-+]/', $query)) {
+            return false;
+        }
+
+        preg_match_all('/[A-Z][a-z]?\d*/', $query, $matches);
+
+        $previousElement = null;
+        foreach ($matches[0] as $token) {
+            preg_match('/^([A-Z][a-z]?)/', $token, $elementMatch);
+            $element = $elementMatch[1];
+
+            if ($element === $previousElement) {
+                return false;
+            }
+
+            $previousElement = $element;
+        }
+
+        return true;
+    }
+
     /**
      * Apply status filter to SQL query.
      * Only adds a filter when status is 'approved' or 'revoked'.
diff --git a/tests/Unit/SearchMoleculeQueryTypeTest.php b/tests/Unit/SearchMoleculeQueryTypeTest.php
new file mode 100644
index 00000000..00b07040
--- /dev/null
+++ b/tests/Unit/SearchMoleculeQueryTypeTest.php
@@ -0,0 +1,35 @@
+<?php
+
+namespace Tests\Unit;
+
+use App\Actions\Coconut\SearchMolecule;
+use PHPUnit\Framework\TestCase;
+use ReflectionMethod;
+
+class SearchMoleculeQueryTypeTest extends TestCase
+{
+    /**
+     * @dataProvider queryTypeProvider
+     */
+    public function test_determine_query_type(string $query, string $expectedType): void
+    {
+        $search = new SearchMolecule;
+        $method = new ReflectionMethod(SearchMolecule::class, 'determineQueryType');
+        $method->setAccessible(true);
+
+        $this->assertSame($expectedType, $method->invoke($search, $query));
+    }
+
+    public static function queryTypeProvider(): array
+    {
+        return [
+            'cyclohexane smiles' => ['C1CCCCC1', 'smiles'],
+            'benzene smiles' => ['c1ccccc1', 'smiles'],
+            'molecular formula' => ['C6H12', 'molecularformula'],
+            'glucose formula' => ['C6H12O6', 'molecularformula'],
+            'water formula' => ['H2O', 'molecularformula'],
+            'cnp identifier' => ['CNP0228556', 'identifier'],
+            'compound name' => ['caffeine', 'text'],
+        ];
+    }
+}