adhoc fix for 6uwi

jamesmkrieger · Nov 8, 2023 · 96ba836 · 96ba836
1 parent 27e38ba
commit 96ba836
Showing 1 changed file with 10 additions and 1 deletion.
diff --git a/prody/proteins/ciffile.py b/prody/proteins/ciffile.py
@@ -6,6 +6,7 @@
 
 from collections import OrderedDict
 import os.path
+from numbers import Integral
 import numpy as np
 
 from prody.atomic import AtomGroup
@@ -19,6 +20,8 @@
 from .cifheader import getCIFHeaderDict
 from .header import buildBiomolecules, assignSecstr, isHelix, isSheet
 
+from string import ascii_uppercase
+
 __all__ = ['parseMMCIFStream', 'parseMMCIF', 'parseCIF']
 
 
@@ -300,6 +303,7 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
     doneAtomBlock = False
     start = 0
     stop = 0
+    warnedAltloc = False
     while not doneAtomBlock:
         line = lines[i]
         if line[:11] == '_atom_site.':
@@ -432,7 +436,12 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
 
         alt = line.split()[fields['label_alt_id']]
         if alt not in which_altlocs and which_altlocs != 'all':
-            continue
+            try:
+                alt = ascii_uppercase[int(alt)]
+            except TypeError:
+                if not warnedAltloc:
+                    LOGGER.warn('alt {0} not in which_altlocs {1}'.format(alt, which_altlocs))
+                continue
 
         if alt == '.':
             alt = ' '