Allow hexadecimal ATOM id

pdb2pqr/pdb.py

@@ -649,7 +649,15 @@ def __init__(self, line):
         :type line:  str
         """
         super().__init__(line)
-        self.serial = int(line[6:11].strip())
+        try:
+            self.serial = int(line[6:11].strip())
+        except ValueError:
+            try:
+                self.serial = int(line[6:11].strip(), 16)
+            except ValueError:
+                _LOGGER.error(f"Error parsing atom number: {line[6:11].strip()}.")
+                _LOGGER.error("Use integers or VMD's hexadecimal notation")
+                raise ValueError(f"Error parsing atom number: {line[6:11].strip()}. Use integers or VMD's hexadecimal notation")
         self.name = line[12:16].strip()
         self.alt_loc = line[16].strip()
         self.res_name = line[17:20].strip()

pdb2pqr/structures.py

@@ -180,25 +180,21 @@ def from_pqr_line(cls, line):
         else:
             err = f"Unable to parse line: {line}"
             raise ValueError(err)
-        atom.serial = int(words.pop(0))
-        atom.name = words.pop(0)
-        atom.res_name = words.pop(0)
-        token = words.pop(0)
-        try:
-            atom.res_seq = int(token)
-        except ValueError:
-            atom.chain_id = token
-            atom.res_seq = int(words.pop(0))
-        token = words.pop(0)
+        atom.serial = line[6:11].strip()
         try:
-            atom.x = float(token)
-        except ValueError:
-            atom.ins_code = token
-            atom.x = float(words.pop(0))
-        atom.y = float(words.pop(0))
-        atom.z = float(words.pop(0))
-        atom.charge = float(words.pop(0))
-        atom.radius = float(words.pop(0))
+            atom.serial = int(atom.serial)
+        except:
+            atom.serial = int(atom.serial, 16)
+        atom.name = line[12:16].strip()
+        atom.res_name = line[17:21].strip()
+        atom.chain_id = line[21:22]
+        atom.res_seq = int(line[22:26].strip())
+        atom.ins_code = line[26:27]
+        atom.x = float(line[30:38].strip())
+        atom.y = float(line[38:46].strip())
+        atom.z = float(line[46:54].strip()) 
+        atom.charge = float(line[54:62].strip()) 
+        atom.radius = float(line[62:69].strip())
         return atom
 
     @classmethod
@@ -265,7 +261,10 @@ def get_common_string_rep(self, chainflag=False):
         outstr = ""
         tstr = self.type
         outstr += str.ljust(tstr, 6)[:6]
-        tstr = f"{self.serial:d}"
+        if self.serial > 99999:
+            tstr = f"{hex(self.serial)[2:]}" 
+        else:
+            tstr = f"{self.serial:d}"
         outstr += str.rjust(tstr, 5)[:5]
         outstr += " "
         tstr = self.name

tests/core_test.py

@@ -168,6 +168,16 @@ def test_ph_naming(naming_test, tmp_path):
         f"--drop-water --whitespace --with-ph={naming_test['pH']} "
         f"--titration-state-method=propka"
     )
+
+@pytest.mark.parametrize(
+    "input_pdb, expected_pqr",
+    [pytest.param("5urf-assembly1.pdb", "5urf-assembly1.pqr", id="HEX Atom Id")],
+)
+@pytest.mark.long_test
+def test_hex_pdb(input_pdb, expected_pqr, tmp_path):
+    """Tests for HEX ATOM Id."""
+    args = "--log-level=ERROR --ff=AMBER --ffout AMBER"
+    output_pqr = Path(input_pdb).stem + ".pqr"
     common.run_pdb2pqr(
         args=args,
         input_pdb=common.DATA_DIR / input_pdb,