PDB2PQR 1.1.0 (2006-04)

New features

  • Structural data files have been moved to XML format. This should make it easier for users and developers to contribute to the project.
  • Added an extensions directory for small scripts. Scripts in this directory will be automatically loaded into PDB2PQR has command line options for post-processing, and can be easily customized.
  • Code has been greatly cleaned so as to minimize values hard-coded into functions and to allow greater customizability via external XML files. This includes a more object-oriented hierarchy of structures.
  • Improved detection of the termini of chains.
  • Assign-only now does just that - only assigns parameters to atoms without additions, debumping, or optimizations.
  • Added a –clean command line option which does no additions, optimizations, or forcefield assignment, but simply aligns the PDB columns on output. Useful for using post-processing scripts like those in the extensions directory without modifying the original input file.
  • The –userff flag has been replaced by opening up the –ff option to user-defined files.
  • Pydoc documentation is now included in html/pydoc.
  • A programmer’s guide has been included to explain programming decisions and ease future development.
  • A –ffout flag has been added to allow users to output a PQR file in the naming scheme of the desired forcefield.
  • User guide FAQ updated.
  • The efficiency of the hydrogen bonding detection script (–hbond) has been greatly improved.
  • Increased the number of options available to users via the PDB2PQR web server.

Bug fixes

  • Updated psize.py to use centers and radii when calculating grid sizes (thanks to John Mongan)
  • Fixed bug where PDB2PQR could not read PropKa results from chains with more than 1000 residues (thanks to Michael Widmann)