PDB2PQR 1.8 (2012-01) — APBS-PDB2PQR 1.6 documentation

# 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.