Merge pull request #507 from swails/minor_fixes

Small fixes:

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()
@@ -1182,8 +1185,11 @@ class CharmmPsfFile(object):
                 if switchDistance >= nonbondedCutoff:
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                    force.setUseSwitchingFunction(True)
-                    force.setSwitchingDistance(switchDistance)
+                if abs(switchDistance) != switchDistance:
+                    # Detects negatives for both Quantity and float
+                    raise ValueError('switchDistance must be non-negative!')
+                force.setUseSwitchingFunction(True)
+                force.setSwitchingDistance(switchDistance)
 
         else: # periodic
             # Set up box vectors (from inpcrd if available, or fall back to
@@ -1223,8 +1229,11 @@ class CharmmPsfFile(object):
                 if switchDistance >= nonbondedCutoff:
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                    force.setUseSwitchingFunction(True)
-                    force.setSwitchingDistance(switchDistance)
+                if abs(switchDistance) != switchDistance:
+                    # Detects negatives for both Quantity and float
+                    raise ValueError('switchDistance must be non-negative!')
+                force.setUseSwitchingFunction(True)
+                force.setSwitchingDistance(switchDistance)
 
             if ewaldErrorTolerance is not None:
                 force.setEwaldErrorTolerance(ewaldErrorTolerance)

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