PDB2PQR 1.1.0 (2006-04) — APBS-PDB2PQR 1.6 documentation

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- The –userff flag has been replaced by opening up the –ff option to user-defined files.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