Biskit 2.4 released

This Biskit release was long overdue. Even though I didn't have much time to work on Biskit for most of the last two years, a lot of changes, improvements and bug-fixes have accumulated. If you are still using version 2.3.1, I highly recommend to switch. Please fetch your installation package from the SourceForge project site:

https://sourceforge.net/projects/biskit

Note: If you are installing from source (python setup.py install) , you will first need to install some other packages. See Short instruction for details (not yet adapted to the latest version). Most dependencies (except biggles and pypvm) should be resolved automatically, if you install from the Python Package Index PyPI using the pip package installer (although I haven't tested that).

http://pypi.python.org/pypi/biskit/2.4

Users of Debian-based Linux (Ubuntu, Mint Linux, etc) should install the Biskit Debian package. I haven't submitted this package to Debian (that would require some additional polishing). Simply point your Ubuntu Software Center, or GDebi or whatever local package manager you are using to this file. This will resolve Python as well as non-Python dependencies. The Biggles plotting module is now included in the list of dependencies and will be installed automatically. 

Marc-Michael Blum has built a Fink package for installing Biskit on Mac OS-X (Thanks!). Please follow his instructions: Mac OS X installation.

Biskit interfaces with many (optional) third-party programs that need to be installed separately. See Helper applications.

New features

• TM-align: structure alignment wrapper and integration into PDBModel

  - new class: TMAlign
  - new method in PDBModel: structureFit()

• Reduce: a wrapper for the reduce program to optimize hydrogen bonding networks, assign protonation states to His and add hydrogens to a structure.
• AtomCharger: maps partial atomic charges from Amber prep/topologyfiles into the residues of a given structure.
• Delphi: wrapper (and more) for automatted calculations of  electrostatic potentials with the DelPhi Poisson-Boltzmann solver
• DelphiBindingEnergy: workflow for the calculation of electrostatic free energies of binding (with Delphi) for a given complex
• Support for DNA and RNA residues in entropy and other calculations
• BioModel: extract and apply the biological relevant unit from PDB file (by Alexander Gryzlov)

There are many smaller improvements and changes. Some of them are listed in the README.txt

Things that are broken

Unfortunately, there are also some things that will NOT work right now:

• The new version of HMMer and modifications to Pfam have killed the Biskit wrapper which probably would need to be re-written almost from scratch -- the PDBDope.addConservation doesn't currently work
• The Fold-X wrapper is very outdated and has not been updated to the latest versions
• PSI-blast searching may not be working with the latest NCBITools/BioPython version. The Mod module soon needs to be updated to the new blast+ tool set.
  
• The API documentation is still pointing to Johan's three year old version on a Swedish server. Until we put a new version onine, you can use the epydoc tool to generate your own. 
  

Good luck!