AmberTools sometimes installs Python modules.

can cause *weird* errors. Have setup.py trash these files, too.

This walks PATH and sys.path looking for parmed.py and xparmed.py, deleting them
when it finds them.

to use an old version of Python.

ParmedTools.ParmedActions -> parmed.tools.actions

Get rid of legacy Python 2.4 support (didn't quite work all the way back to 2.4,
anyway). Also shift to supporting a single Py2/Py3 code-base with help from the
six module.

tested and is mostly designed for a few specific tasks, such as adding or
removing blocks of atoms from .coor and .vel files.

headers are not where distutils expects them to be. This module is optional, so
don't have a missing dependency kill the install process.

This fixes builds when the Python version is <= 2.6 by simply omitting the
openmm package in that case (since it has Py24/Py25-incompatible syntax).

Register them for automatic file detection.

for tighter integration with Amber.

Fix system creation with the Structure class and assign the nonbonded forces to
the appropriate groups.

numpy cannot be imported.

fortranformat into AmberFormat to handle 'complex' Fortran formats (in standard
prmtops, this includes the FORCE_FIELD_TYPE field in chamber-style topologies).

Updates to chamber topologies to reflect "proper" handling of the
FORCE_FIELD_TYPE section.

Update the setup.py script to install the fortranformat package.

missing an INCREF somewhere...

- Skip the has_key fixer, since it breaks my ArgumentList class (and I don't use
  has_key anywhere else)
- Make the Atom class in charmm/topologyobjects orderable