Parmed

This release has improved support for converting between different formats, including OpenMM, Amber, CHARMM, and GROMACS.

It has numerous bug fixes, and all users are encouraged to upgrade to this version.

This is a minor bugfix release:
- Fixes a nuisance parsing some PDB files with insertion codes and ANISOU records (762)

There are a number of improvements and bug fixes including:
- Improved atomic number determination for mol2 files (695)
- Fix OFF file writing for solvent boxes (702)
- Fix bug in storing angle types for CHARMM systems (704)
- Eliminate severe performance degradation of OpenMM simulations with the NetCDF reporter (722)
- Support loading molecules from the `rdkit` package
- Update for small changes to OpenMM API
- Support native visualization through the nglview backend
- Support reading SDF-format files (through rdkit)

And many other small improvements.

This is a major new stable release of ParmEd since version 1.1. An abbreviated list of changes and improvements are listed below:
- Unified object model built on `Structure` that facilitates file format translations and integration with OpenMM
- Support for reading and writing GROMACS topology and GRO files
- Automatic file loading based on file contents (rather than filename extension)
- Read many new file formats, including Mol2, GROMACS topology, GRO, PDBx/mmCIF, Amber OFF libraries, Amber parameter and leaprc files, CHARMM residue templates, OpenMM XML files, and more
- Expressive selection syntax for slicing substructures and views of `Structure`
- Flexible molecule splitting functionality within `Structure`
- Support Python 2 and Python 3 in the same code base through the `six` module
- Overhauled the coordinate and unit cell handling functionality, creating a unified interface for all objects based on the n-dimensional array in `numpy`
- C++-accelerated Amber topology file reader
- Abstract file reader capable of reading compressed and remote files (and remote compressed files)
- Convenient `Structure.save` method that converts between different file formats automatically
- Added `gromber` action to ParmEd interpreter to facilitate converting from GROMACS to AMBER file formats
- Added ability to instantiate parametrized `Structure` from OpenMM Topology and System objects
- Added robust unit handling and dimensional analysis through the `unit` package that is part of OpenMM
- New package organization -- there is now a single subpackage `parmed` that contains all of the modules and packages. `chemistry` has been renamed `parmed` and `ParmedTools` has been moved to `parmed.tools`
- Renamed scripts from `parmed.py` and `xparmed.py` to `parmed` and `xparmed`.
- New, extensive API documentation generated automatically by Sphinx
- Many bug fixes and stability improvements
- Added serialization support (so that the objects in ParmEd can now be pickled)

This release brings some substantial changes and API stability. The major changes here that will affect users upgrading from older versions are
1. Python 2.7 or later is now required. Support for earlier versions of Python has been discontinued.
2. The `numpy` package is now required and is used for coordinate and unit cell handling
3. OpenMM support requires version 6.3 or later of the OpenMM library
4. The following packages have been renamed:
- `chemistry` -> `parmed`
- `ParmedTools` -> `parmed.tools`
- `ParmedTools.ParmedActions` -> `parmed.tools.actions`

Making the above substitutions should be sufficient to fix existing scripts or programs to work with the newest version of ParmEd.

This is a major upgrade from the last release (version 1.1), and is also a substantial update from the version released with AmberTools 15. There have been over

This code is tested on Python 2.7, 3.3, and 3.4, and is expected to work for any later versions of Python 3.

Many big changes are enumerated below:
- New package organization [1]
- Support for reading and writing Gromacs topology files
- Unified object model, permitting interconversion between file formats and integration with OpenMM for all of them
- Support for reading more file formats (Amber OFF file, residue templates from CHARMM, mol2 files, PDBx/mmCIF -files, Gromacs GRO and topology files, and many more)
- Flexible and powerful Structure manipulation features (fancy indexing of Structure, splitting, merging, and replicating Structure)
- Accelerated Amber topology file reader
- Arbitrary unit handling and dimensional analysis
- Support Python 2 and Python 3 in the same code base without doing source code conversion
- API and user documentation generated by Sphinx (http://parmed.github.io/ParmEd)

and many more...

[1] This release introduces a new Python package layout compared to previous releases. In particular, the `chemistry` package has been renamed to `parmed`, and the `ParmedTools` package has been renamed to `parmed.tools`.

A special thanks to Lee-Ping Wang and David Mobley for their help adding Gromacs support.