From 26c72eb80172b4d312b5540e325115b63f62e656 Mon Sep 17 00:00:00 2001
From: nightcityblade <nightcityblade@gmail.com>
Date: Wed, 1 Apr 2026 23:10:12 +0800
Subject: [PATCH 1/2] fix: correct DT5 patch applyto from 'T' to 'DT' in
 PATCHES.xml

Fixes #456
---
 pdb2pqr/dat/PATCHES.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pdb2pqr/dat/PATCHES.xml b/pdb2pqr/dat/PATCHES.xml
index 2069701c..4cd04c86 100644
--- a/pdb2pqr/dat/PATCHES.xml
+++ b/pdb2pqr/dat/PATCHES.xml
@@ -579,7 +579,7 @@ OF THE POSSIBILITY OF SUCH DAMAGE.
   </patch>
   <patch>
      <name>DT5</name>
-     <applyto>T</applyto>
+     <applyto>DT</applyto>
      <remove>O1P</remove>
      <remove>P</remove>
      <remove>O2P</remove>

From 25074830efb63a35a0b0d26e3b9ee361c2ee3604 Mon Sep 17 00:00:00 2001
From: nightcityblade <nightcityblade@gmail.com>
Date: Wed, 8 Apr 2026 11:07:35 +0800
Subject: [PATCH 2/2] test: cover DT5 patch reference residue

---
 tests/patches_test.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 tests/patches_test.py

diff --git a/tests/patches_test.py b/tests/patches_test.py
new file mode 100644
index 00000000..5c2341d0
--- /dev/null
+++ b/tests/patches_test.py
@@ -0,0 +1,20 @@
+from pathlib import Path
+
+from pdb2pqr.definitions import Definition
+
+
+def test_dt5_patch_applies_to_dt_reference() -> None:
+    dat_dir = Path(__file__).resolve().parents[1] / "pdb2pqr" / "dat"
+
+    with (
+        (dat_dir / "AA.xml").open() as aa_file,
+        (dat_dir / "NA.xml").open() as na_file,
+        (dat_dir / "PATCHES.xml").open() as patch_file,
+    ):
+        definition = Definition(aa_file, na_file, patch_file)
+
+    assert "DT" in definition.map
+    assert "DT5" in definition.map
+    assert "P" not in definition.map["DT5"].map
+    assert "O1P" not in definition.map["DT5"].map
+    assert "H5T" in definition.map["DT5"].map