fix: preserve CTER and NTER residue names

pdb2pqr/biomolecule.py

@@ -767,9 +767,13 @@ def apply_name_scheme(self, forcefield_):
                             rname != residue.name
                         ):
                             if len(rname) == 4 and rname[0] in ("C", "N"):
-                                # Remove the C/N prefix to keep the protonation state of the residue
-                                # in the terminal residues
-                                rname = rname[1:]
+                                if rname[1:] == "TER":
+                                    # Preserve explicit terminal names produced by the force field.
+                                    pass
+                                else:
+                                    # Remove the C/N prefix to keep the protonation state of the residue
+                                    # in the terminal residues.
+                                    rname = rname[1:]
                             elif rname.startswith("NEUTRAL-"):
                                 # Remove the NEUTRAL-C and NEUTRAL-N prefixes to keep protonation state
                                 rname = rname[9:]

tests/core_test.py

@@ -5,6 +5,9 @@
 import common
 import pytest
 
+from pdb2pqr import aa
+from pdb2pqr.biomolecule import Biomolecule
+
 # fmt: off
 #: Protein-nucleic acid complexes
 PROTEIN_NUCLEIC_SET = {"4UN3"}
@@ -114,6 +117,38 @@ def test_broken_backbone(input_pdb, tmp_path):
     )
 
 
+@pytest.mark.parametrize(
+    ("forcefield_name", "expected_name"),
+    [
+        pytest.param("CTER", "CTER", id="preserve-cter"),
+        pytest.param("NTER", "NTER", id="preserve-nter"),
+        pytest.param("CGLU", "GLU", id="strip-c-prefix"),
+        pytest.param("NHIS", "HIS", id="strip-n-prefix"),
+    ],
+)
+def test_terminal_forcefield_names_preserve_termini(forcefield_name, expected_name):
+    """Terminal renaming keeps CTER/NTER intact while stripping residue prefixes."""
+
+    class DummyForcefield:
+        def get_names(self, resname, atomname):
+            return forcefield_name, atomname
+
+    atom = type("Atom", (), {"name": "CA", "res_name": None})()
+    residue = object.__new__(aa.Amino)
+    residue.name = "GLU"
+    residue.ffname = "GLU"
+    residue.is_n_term = True
+    residue.is_c_term = False
+    residue.atoms = [atom]
+
+    biomolecule = Biomolecule.__new__(Biomolecule)
+    biomolecule.residues = [residue]
+
+    biomolecule.apply_name_scheme(DummyForcefield())
+
+    assert atom.res_name == expected_name
+
+
 @pytest.mark.parametrize(
     "input_pdb, expected_pqr",
     [pytest.param("cterm_hid.pdb", "cterm_hid_out.pqr", id="C-terminal HID")],