apbs-pdb2pqr: APBS 1.4.2.1

APBS 1.4.2.1 CHANGELOG These are notes for APBS version 1.4.2.1.

• Binary releases may be found on GitHub and on SourceForge.

• Actually included PB-AM binary, examples and documentation -- note that this is Linux and OS X only!
• Fixed Windows build so that it is not a Debug build, and ensured that no DLLs are missing

• Poisson-Boltzmann Semi-Analytical Method (PB-AM) packaged and built with APBS
  • the binary is called mpe and colocated with the apbs binary
  • documentation is with the APBS documentation, and called PBE_Manual_V1.docx
  • examples are located with APBS examples in a pb-am directory
• New Geometric flow API and improvements in speed (#235)
• Support for BinaryDX file format (#216)
• SOR solver added for mg-auto input file option
• DXMath improvements (#168, #216)
• Test suite improvements
  • APBS build in Travis-CI
  • Geometric Flow tests added
  • Protein RNA tests enabled (#149)
  • Intermetiate result testing (#64)
• Example READMEs onverted to markdown and updated with latest results

• OpenMPI (mg-para) functionality restored (#190)
• Fixed parsing PQR files that contained records other than ATOM and HETATM (#77, #214)
• Geometric Flow boundary indexing bug fixed
• Build fixes:
  • Out of source CMake builds are again working
  • Python library may be built (#372)
  • CentOS 5 binary builds for glibc compatibility
  • Pull requests merged
• Removed irrelevant warning messages (#378)

The following packages are treated as submodules in APBS:

• Geometric Flow has been moved to it's own repository
• FETk has been cloned so that we have could effect updates
• PB-SAM lives here

Added chat feature for users. This can also be found from the support tab on http://www.poissonboltzmann.org/.

• 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