From 9088f145a3db802d43a8c74e2d9ce14178dc38fe Mon Sep 17 00:00:00 2001
From: Nathan Baker <nathanandrewbaker@gmail.com>
Date: Sat, 20 Nov 2021 19:40:20 -0800
Subject: [PATCH] Fixes #250.

---
 docs/source/releases.rst | 9 +++++++++
 pdb2pqr/biomolecule.py   | 2 +-
 pdb2pqr/main.py          | 2 +-
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/docs/source/releases.rst b/docs/source/releases.rst
index 2ac9869a..59b68154 100644
--- a/docs/source/releases.rst
+++ b/docs/source/releases.rst
@@ -2,6 +2,15 @@
 Release history
 ###############
 
+***************
+Current version
+***************
+
+Fixes
+=====
+
+* Fix bug for application of pKa predictions to proteins with more than 999 residues (`#250 <https://github.com/Electrostatics/pdb2pqr/issues/250>`_).
+
 ******************
 3.3.1 (2021-11-13)
 ******************
diff --git a/pdb2pqr/biomolecule.py b/pdb2pqr/biomolecule.py
index 5c482eb2..8518255b 100644
--- a/pdb2pqr/biomolecule.py
+++ b/pdb2pqr/biomolecule.py
@@ -822,7 +822,7 @@ def apply_pka_values(self, force_field, ph, pkadic):
                             _LOGGER.warning(warn)
                         else:
                             self.apply_patch("NEUTRAL-CTERM", residue)
-            key = f"{resname:<3} {resnum:>3} {chain_id}"
+            key = f"{resname} {resnum} {chain_id}"
             key = key.strip()
             if key in pkadic:
                 value = pkadic[key]
diff --git a/pdb2pqr/main.py b/pdb2pqr/main.py
index 082fc260..0216e543 100644
--- a/pdb2pqr/main.py
+++ b/pdb2pqr/main.py
@@ -637,7 +637,7 @@ def non_trivial(args, biomolecule, ligand, definition, is_cif):
             biomolecule.apply_pka_values(
                 forcefield_.name,
                 args.ph,
-                {row["group_label"]: row["pKa"] for row in pka_df},
+                {f"{row['res_name']} {row['res_num']} {row['chain_id']}": row["pKa"] for row in pka_df},
             )
 
         _LOGGER.info("Adding hydrogens to biomolecule.")