Merge pull request #764 from swails/chambercheck

Add a check and raise an exception if someone tries to use a CHAMBER-style prmtop

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

@@ -173,6 +173,10 @@ class AmberPrmtopFile(object):
          - ewaldErrorTolerance (float=0.0005) The error tolerance to use if nonbondedMethod is Ewald or PME.
         Returns: the newly created System
         """
+        if self._prmtop.chamber:
+            raise ValueError("CHAMBER-style topology file detected. CHAMBER "
+                             "topologies are not supported -- use the native "
+                             "CHARMM files directly.")
         methodMap = {ff.NoCutoff:'NoCutoff',
                      ff.CutoffNonPeriodic:'CutoffNonPeriodic',
                      ff.CutoffPeriodic:'CutoffPeriodic',

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -119,7 +119,7 @@ class PrmtopLoader(object):
         self._raw_data={}
         self._has_nbfix_terms = False
 
-        fIn=open(inFilename)
+        with open(inFilename, 'r') as fIn:
             for line in fIn:
                 if line.startswith('%VERSION'):
                     tag, self._prmtopVersion = line.rstrip().split(None, 1)
@@ -148,7 +148,9 @@ class PrmtopLoader(object):
                         item = line[index:index+iLength]
                         if item:
                             self._raw_data[flag].append(item.strip())
-        fIn.close()
+        # See if this is a CHAMBER-style topology file, which is not supported
+        # for creating Systems
+        self.chamber = 'CTITLE' in self._flags
 
     def _getFormat(self, flag=None):
         if not flag: