PDB2PQR 1.1.0 (2006-04)
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New features
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* Structural data files have been moved to XML format.  This should make it easier for users and developers to contribute to the project.
* Added an extensions directory for small scripts.  Scripts in this directory will be automatically loaded into PDB2PQR has command line options for post-processing, and can be easily customized.
* Code has been greatly cleaned so as to minimize values hard-coded into functions and to allow greater customizability via external XML files.  This includes a more object-oriented hierarchy of structures.
* Improved detection of the termini of chains.
* Assign-only now does just that - only assigns parameters to atoms without additions, debumping, or optimizations.
* Added a --clean command line option which does no additions, optimizations, or forcefield assignment, but simply aligns the PDB columns on output.  Useful for using post-processing scripts like those in the extensions directory without modifying the original input file.
* The --userff flag has been replaced by opening up the --ff option to user-defined files.
* Pydoc documentation is now included in html/pydoc.
* A programmer's guide has been included to explain programming decisions and ease future development.
* A --ffout flag has been added to allow users to output a PQR file in the naming scheme of the desired forcefield.
* User guide FAQ updated.
* The efficiency of the hydrogen bonding detection script (--hbond) has been greatly improved.
* Increased the number of options available to users via the PDB2PQR web server.

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Bug fixes
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* Updated psize.py to use centers and radii when calculating grid sizes (thanks to John Mongan) 
* Fixed bug where PDB2PQR could not read PropKa results from chains with more than 1000 residues (thanks to Michael Widmann)
