From ae462842c103d7359ece91be26eada92512a4039 Mon Sep 17 00:00:00 2001
From: Matvey Adzhigirey <matvey.adzhigirey@schrodinger.com>
Date: Tue, 11 Dec 2012 16:20:35 -0800
Subject: [PATCH] replace empty chains with "_" instead "A"

---
 propka/atom.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/propka/atom.py b/propka/atom.py
index 31a83dc..4b71b2a 100644
--- a/propka/atom.py
+++ b/propka/atom.py
@@ -75,7 +75,10 @@ class Atom:
             self.z = float( line[46:54].strip() )
             self.resNumb = int( line[22:26].strip() )
             self.resName = "%-3s" % (line[17:20].strip())
-            self.chainID = max(line[21], 'A') # set chain id to A in case of white space
+            self.chainID = line[21]
+            # Set chain id to "_" if it is just white space.
+            if not self.chainID.strip():
+                self.chainID = '_'
             self.type = line[:6].strip().lower()
 
             if self.resName in ['DA ','DC ','DG ','DT ']: