[Pdb2pqr-announce] APBS 1.4.2 now available

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

Dear APBS & PDB2PQR users --

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Thank you for your continued support of APBS and PDB2PQR!

Sincerely,

The APBS & PDB2PQR Development Team

---------- Forwarded message ---------
From: APBS & PDB2PQR Biomolecular Solvation Software <
nat...@gm...>
Date: Fri, Jan 8, 2016 at 7:41 PM
Subject: APBS 1.4.2 now available
To: Nathan <nat...@ic...>


APBS 1.4.2 is now available View this email in your browser
<http://us11.campaign-archive1.com/?u=a5808042b2b3ea90ee3603cd8&id=f32947e2b6&e=cbebd7d419>
APBS
1.4.2 is now available
------------------------------

Dear APBS and PDB2PQR users:

We are pleased to announce the release of APBS 1.4.2 which is now available
on GitHub
<http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=9a1baad17f&e=cbebd7d419>
and SourceForge
<http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=77d115c85f&e=cbebd7d419>.
New features and bug fixes for this release are described below.  The
latest information about APBS and PDB2PQR can always be found at
http://www.poissonboltzmann.org/
<http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=ed8a78d648&e=cbebd7d419>
.

Thank you for your continued support of APBS!

Sincerely,

The APBS & PDB2PQR Development Team
------------------------------
New Features

   - Poisson-Boltzmann Semi-Analytical Method (PB-SAM) packaged and built
   with APBS
   - New Geometric flow API and improvements in speed (#235
   <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=b6e24daad1&e=cbebd7d419>
   )
   - Support for BinaryDX file format (#216
   <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=173ddd0bde&e=cbebd7d419>
   )
   - SOR solver added for mg-auto input file option
   - DXMath improvements (#168
   <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=53e3362d88&e=cbebd7d419>
   , #216
   <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=012e20cdf4&e=cbebd7d419>
   )
   - Test suite improvements
      - APBS build in Travis-CI
      - Geometric Flow tests added
      - Protein RNA tests enabled (#149
      <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=5d69d102ef&e=cbebd7d419>
      )
      - Intermetiate result testing (#64
      <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=709a649568&e=cbebd7d419>
      )
   - Example READMEs onverted to markdown and updated with latest results

Bug Fixes

   - OpenMPI (mg-para) functionality restored (#190
   <http://poissonboltzmann.us11.list-manage1.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=f6cfc353ba&e=cbebd7d419>
   )
   - Fixed parsing PQR files that contained records other than *ATOM* and
   *HETATM* (#77
   <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=0c07b2c433&e=cbebd7d419>
   , #214
   <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=c3b3b00013&e=cbebd7d419>
   )
   - Geometric Flow boundary indexing bug fixed
   - Build fixes:
      - Out of source CMake builds are again working
      - Python library may be built (#372
      <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=6c35d8d775&e=cbebd7d419>
      )
      - CentOS 5 binary builds for glibc compatibility
      - Pull requests merged
   - Removed irrelevant warning messages (#378
   <http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=eefca7cc05&e=cbebd7d419>
   )

Notes

The following packages are treated as submodules in APBS:

   - Geometric Flow has been moved to its own repository
   <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=b7e0599ca8&e=cbebd7d419>
   - FETk has been cloned
   <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=13baff3b2b&e=cbebd7d419>
so
   that we have could effect updates
   - PB-SAM lives here
   <http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=bd09191b31&e=cbebd7d419>

We have added a chat feature
<http://poissonboltzmann.us11.list-manage2.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=31e3a5c86a&e=cbebd7d419>
for
users. This can also be found from the support tab on
http://www.poissonboltzmann.org/
<http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=68bc8771d1&e=cbebd7d419>
.
Known Bugs

   - Travis CI Linux builds are breaking because Geometric Flow relies on
   C++11 and Travis boxen have an old GCC that doth not support C++11. This is
   also an issue for CentOS 5
   - BEM is temprarily disabled due to build issues
   - Geometric Flow build is currently broken on Windows using Visual Studio

<http://poissonboltzmann.us11.list-manage.com/track/click?u=a5808042b2b3ea90ee3603cd8&id=fac3dbf2ae&e=cbebd7d419>
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