PDB2PQR 1.8 (2012-01)

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.