[Pdb2pqr-announce] PDB2PQR 1.9.0

[Nathan B. <nat...@gm...>]

Dear PDB2PQR users --

We are excited to announce the release of PDB2PQR 1.9.  Details of this
release are provided below.

As usual, you can download the release from
http://www.poissonboltzmann.org/pdb2pqr/d or start using it immediately via
the web at http://nbcr-222.ucsd.edu/pdb2pqr.

I would like to extend a special thanks to Kyle Monson and Nadya Williams
for their hard work in getting this release ready.

Thank you for your continued support of APBS and PDB2PQR.

Sincerely,

The APBS/PDB2PQR Development Team


PDB2PQR 1.9.0 Notable new features: Binary builds.

Binary builds do not require python or numpy be installed to use.
Everything needed to run PDB2PQR is included. Just unpack and use.

OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.

Linux binaries require CentOS 6 or newer and have been tested on Ubuntu
12.04 LTS and Linux Mint 13. If you are running 64-bit Linux use the 64-bit
libraries. In some cases the needed 32-bit system libraries will not be
installed on a 64-bit system.

Windows binaries are 32 bit and were built and tested on Windows 7 64-bit
but should work on Windows XP, Vista, and 8 both 32 and 64-bit systems.
Windows support

PDB2PQR can now be compiled and run on Windows using MinGW32. See
http://mingw.org/ for details.
Compilation with Scons

PDB2PQR now uses Scons for compilations. With this comes improved automated
testing.

Please see http://www.poissonboltzmann.org/pdb2pqr/release-history for the
complete release history
NEW FEATURES

   - A ligand file with duplicate atoms will cause pdb2pqr to stop instead
   of issue a warning. Trust us, this is a feature, not a bug!
   - Improved error reporting.
   - Added support for reference command line option for PROPKA.
   - Added newresinter plugin to provide alternate methods for calculating
   interaction energies between residues.
   - Mol2 file handling is now case insensitive with atom names.
   - PROPKA with a pH of 7 is now specified by default on the web service.
   - Compilation is now done with scons.
   - Verbose output now includes information on all patches applied during
   a run.
   - Added stderr and stdout to web error page.
   - Added warning to water optimization when other water is ignored.
   - Command line used to generate a pqr is now duplicated in the comments
   of the output.
   - Added support for NUMMDL in parser.
   - Added complete commandline feature test. Use complete-test target.
   - Added propka support for phosphorous sp3. - Thanks to Dr. Stefan
   Henrich
   - Added a PyInstaller spec file. Standalone pdb2pqr builds are now
   possible.

BUG FIXES

   - Rolled back change that prevented plugins from interfering with each
   other. Large proteins would cause a stack overflow when trying to do a deep
   copy.
   - Updated INSTALL file to reflect no more need for Fortran.
   - Fixed apbs input file to match what web interface produces.
   - Fixed user specified mobile ion species not being passed to apbs input
   file.
   - Removed ambiguous A, ADE, C, CYT, G, GUA, T, THY, U, URA as possible
   residue names.
   - Removed eval from pdb parsing routines.
   - Updated web links to refer to http://www.poissonboltzmann.org where
   appropriate.
   - Fixed hbond extension output to include insertion code in residue name.
   - Fixed debumping routines not including water in their checks. Fixes
   bad debump of ASN B 20 in 1gm9 when run with pH 7.0.
   - Fixed debumping failing to use best angle for a specific dihedral
   angle when no tested angles are without conflict.
   - Fixed debumping using asymmetrical cutoffs and too large cutoffs in
   many checks involving hydrogen.
   - Fixed debumping accumulating rounding error while checking angles.
   - Fixed inconsistencies in pdb parsing. - Thanks to Dr. Stefan Henrich
   - Fixed problems with propka handling of aromatic carbon/nitrogen. -
   Thanks to Dr. Stefan Henrich
   - Fixed case where certain apbs compile options would break web
   visualization.
   - Fixed improper handling of paths with a '.' or filenames with more
   than one '.' in them.

CHANGES

   - Removed numpy from contrib. The user is expected to have numpy
   installed and available to python at configuration.
   - Support for numeric dropped.

KNOWN BUGS

   - If more than one extension is run from the command line and one of the
   extensions modifies the protein data structure it could affect the output
   of the other extension. The only included extensions that exhibit this
   problem are resinter and newresinter.