First pass at adding my CHARMM compatibility layer.

Currently gives exactly the same energy as the same files passed through chamber
(which, in turn, was validated to machine precision against CHARMM itself).

wrappers/python/simtk/openmm/app/charmm/__init__.py

+"""
+This package contains code for reading CHARMM structure files for setting up a
+simulation with CHARMM; specifically PSF, PAR, RTF, and STR files
+
+    - PAR : Parameter file (PRM) -- this contains all of the force field
+            parameters (e.g., bond lengths and strengths) for all of the atom
+            types
+
+    - RTF : Residue Topology File -- this file contains the residue
+            connectivity tables as well as a definition of all of the atom
+            types. Also contains an internal coordinate representation of the
+            residues
+
+    - PSF : Protein Structure File -- this is the main file type in CHARMM
+            simulations that defines all of the residues in a system as well as
+            the atom types and connectivity between the atoms
+
+    - STR : Stream file -- Source of additional information and CHARMM commands
+            that can contain RTF and PAR information. Allows users to define
+            additional parameters without 'contaminating' the original force
+            field parameter files
+"""
+
+__all__ = ['psf', 'parameters', 'openmmloader']
+__authors__ = 'Jason Swails'
+__contributors__ = ''
+__license__ = 'GPL v.3'
+__date__ = 'Mar. 31, 2014'
+
+
+__private__ = ['topologyobjects', '_charmmfile']

wrappers/python/simtk/openmm/app/charmm/_charmmfile.py

+"""
+Provides a class for reading CHARMM-style files. The key component to these
+files is that the ! character is a comment character and everything after ! is
+ignored.
+
+Author: Jason M. Swails
+Contributors:
+Date: April 9, 2014
+"""
+from simtk.openmm.app.charmm.exceptions import CharmmFileError
+
+class CharmmFile(object):
+    """
+    A CHARMM file that recognizes the "!" character as a 'comment' token. It
+    can be iterated over and generally treated like a file object, but only
+    spits out strings that have been truncated at its first comment character.
+    
+    There is currently no way to recognize a ! as a _non_ comment character,
+    since allowing an escape character does not seem to be common practice and
+    would likely introduce negative performance implications.
+    """
+
+    def __init__(self, fname, mode='r'):
+        if mode not in ('r', 'w'):
+            raise ValueError('Cannot open CharmmFile with mode "%s"' % mode)
+        if mode == 'r':
+            self.status = 'OLD'
+        else:
+            self.status = 'NEW'
+        try:
+            self._handle = open(fname, mode)
+        except IOError, e:
+            raise CharmmFileError(str(e))
+        self.closed = False
+        self.line_number = 0
+
+    def write(self, *args, **kwargs):
+        return self._handle.write(*args, **kwargs)
+
+    def __iter__(self):
+        # Iterate over the file
+        for line in self._handle:
+            try:
+                idx = line.index('!')
+                end = '\n'
+            except ValueError:
+                # There is no comment...
+                idx = None
+                end = ''
+            yield line[:idx] + end
+
+    def readline(self):
+        self.line_number += 1
+        line = self._handle.readline()
+        try:
+            idx = line.index('!')
+            end = '\n'
+        except ValueError:
+            idx = None
+            end = ''
+        return line[:idx] + end
+
+    def readlines(self):
+        return [line for line in self]
+
+    def read(self):
+        return ''.join(self.readlines())
+
+    def close(self):
+        self._handle.close()
+        self.closed = True
+
+    def rewind(self):
+        """ Return to the beginning of the file """
+        self._handle.seek(0)
+
+    def __del__(self):
+        self.closed or self._handle.close()
+
+# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+class CharmmStreamFile(object):
+    """
+    The stream file is broken down into sections of commands delimited by the
+    strings:
+        read <section> <options>
+        ....
+        ....
+        end
+    This object provides iterators over those sections and a file-like API for
+    dealing with the text.
+    """
+    def __init__(self, fname):
+        self.lines = CharmmFile(fname, 'r').readlines()
+        self.line_number = 0
+
+    def __iter__(self):
+        return iter(self.lines)
+
+    def rewind(self):
+        """ Return to the beginning of the file """
+        self.line_number = 0
+
+    def next_section(self):
+        """
+        Fast-forwards the file to the next CHARMM command section
+
+        Returns: (str, list)
+            - The first string is the line defining the section that's being
+              returned
+            - The list is a list of all lines contained in the section
+              excluding the "read <blah>" and "end" lines.
+
+        Notes:
+            The line pointer will be set to the line defining the 
+        """
+        lines = []
+        while self.line_number < len(self.lines):
+            line = self.lines[self.line_number].strip()
+            if line[:4].lower() == 'read':
+                title = line.strip()
+                self.line_number += 1
+                line = self.lines[self.line_number]
+                while line and not line.strip().lower().startswith('end'):
+                    lines.append(line)
+                    self.line_number += 1
+                    line = self.lines[self.line_number]
+                return title, lines
+            self.line_number += 1
+        # No sections left
+        return None, None
+
+    def __del__(self):
+        pass

wrappers/python/simtk/openmm/app/charmm/exceptions.py

+"""
+This package contains exceptions that may be raised by the CHARMM components of
+the OpenMM Application layer
+
+Author: Jason M. Swails
+Contributors:
+Date: April 9, 2014
+"""
+
+class CharmmPSFError(CharmmError):
+    """ If there is a problem parsing CHARMM PSF files """
+
+class SplitResidueWarning(CharmmWarning):
+    """ For if a residue with the same number but different names is split """
+
+class ResidueError(CharmmError):
+    """ For when there are problems defining a residue """
+
+class CharmmPSFWarning(CharmmWarning):
+    """ For non-fatal PSF parsing issues """
+
+class CharmmFileError(CharmmError):
+    """ If there is a problem parsing CHARMM files """
+
+class MissingParameter(CharmmError):
+    """ If a parameter is missing from a database """
+
+class CmapError(CharmmError):
+    """ For an error arising from CMAP grid incompatibilities """
+
+class BondError(CharmmError):
+    """ Prevent an atom from bonding to itself """