Small fixes:

    - Adjust CharmmPsfFile parser to accept multiple blank lines before the
      NATOM record (I saw 1 PSF file like this... not sure how common it really
      is)
    - Removed the shebang line from element.py and removed execute permissions--
      it should never be executed directly (evidenced by the fact that the
      original shebang line was wrong and would never work, anyway).
    - Fix a test to determine if a Bond is part of an Angle in the PSF data
      structures.

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -158,10 +158,13 @@ class CharmmPsfFile(object):
         title = list()
         for i in range(ntitle):
             title.append(psf.readline().rstrip())
-        # Skip the blank line
-        psf.readline()
+        # Skip all blank lines. Most of the time there is only 1, but I've seen
+        # a file that has 2
+        line = psf.readline().strip()
+        while not line:
+            line = psf.readline().strip()
         # Next is the number of atoms
-        natom = conv(psf.readline().strip(), int, 'natom')
+        natom = conv(line, int, 'natom')
         # Parse all of the atoms
         residue_list = ResidueList()
         atom_list = AtomList()

wrappers/python/simtk/openmm/app/element.py

-#!/bin/env python
-
 """
 element.py: Used for managing elements.
 

wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py

@@ -12,7 +12,7 @@ Copyright (c) 2014 the Authors
 
 Author: Jason M. Swails
 Contributors:
-Date: April 18, 2014
+Date: July 3, 2014
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the "Software"),
@@ -501,7 +501,7 @@ class Angle(object):
         """ See if a bond or an atom is in this angle """
         if isinstance(thing, Bond):
             return self.atom2 in thing and (self.atom1 in thing or
-                                            self.atom2 in thing)
+                                            self.atom3 in thing)
         # Otherwise assume it's an atom
         return self.atom1 is thing or self.atom2 is thing or self.atom3 is thing