New Features

• Updated PROPKA to version 3.0
• Added residue interaction energy extension
• Added protein summary extension
• Combined hbond and hbondwhatit into one extension (hbond) with new command line parameters
• Combined rama, phi, psi into one extension (rama) with new command line parameters.
• Extensions may now add their own command line arguments. Extensions with their own command line arguments will be grouped separately.
• Improved interface for extensions
• Added Opal configuration file.

 Bug Fixes

• Cleaned up white space in several files and some pydev warnings
• Creating print output no longer clears the chain id data from atoms in the data. (Affected resinter plugin)
• Removed possibility of one plug-in affecting the output of another
• Fixed --protonation=new option for propka30
• Improved time reporting for apbs jobs
• Fixed opal runtime reporting
• Fixed misspelled command line options that prevented the use of PEOEPB and TYL06
• Fixed error handling when certain data files are missing
• Fixed LDFLAGS environment variable not being used along with python specific linker flags to link Algorithms.o and _pMC_mult.so
• Fixed possible Attribute error when applying naming scheme.