Merge remote-tracking branch 'upstream/master'

pdbfixer/pdbfixer.py

@@ -1104,7 +1104,7 @@ class PDBFixer(object):
                 element = atom.element
                 typeName = 'extra_'+element.symbol
                 if element not in atomTypes:
-                    atomTypes[element] = (typeName, 0.0, element)
+                    atomTypes[element] = app.ForceField._AtomType(typeName, '', 0.0, element)
                     forcefield._atomTypes[typeName] = atomTypes[element]
                     if water:
                         # Select a reasonable vdW radius for this atom type.

pdbfixer/tests/test_build_and_simulate.py

@@ -12,7 +12,7 @@ import tempfile
 from threading import Timer
 
 #from a solution on stackoverflow
-class Watchdog:
+class Watchdog(BaseException):
     def __init__(self, timeout, userHandler=None):  # timeout in seconds
         self.timeout = timeout
         self.handler = userHandler if userHandler is not None else self.defaultHandler