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The –userff flag has been replaced by opening up the –ff option to user-defined files.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)