pdb2pqr (version 1.2.1, 17 March 2007) | index /Users/baker/coding/manifold/pdb2pqr/trunk/pdb2pqr/pdb2pqr.py

`Driver for PDB2PQR
This module takes a PDB file as input and performs optimizations
before yielding a new PDB-style file as output.
Ported to Python by Todd Dolinsky (todd@ccb.wustl.edu)
Washington University in St. Louis
Parsing utilities provided by Nathan A. Baker (baker@biochem.wustl.edu)
Washington University in St. Louis`

Modules
`` |  |
copy getopt math os | src.pdb src.protein re src.routines | xml.sax src.server string src.structures | sys time src.utilities

Functions
`` |  | getAvailableExtensions(displayflag=0) `Grab available extensions from the extensions directory Parameters displayflag: Display the error message if 1 Returns extensions: A map containing the extensions name and the module instance.` mainCGI() `Main driver for running PDB2PQR from a web page` mainCommand() `Main driver for running program from the command line.` printHeader(atomlist, reslist, charge, ff, warnings, options) `Print the header for the PQR file Parameters: atomlist: A list of atoms that were unable to have charges assigned (list) reslist: A list of residues with non-integral charges (list) charge: The total charge on the protein (float) ff: The forcefield name (string) warnings: A list of warnings generated from routines (list) options: A dictionary of command lnie options (float) Returns header: The header for the PQR file (string)` runPDB2PQR(pdblist, ff, options) `Run the PDB2PQR Suite Parameters pdblist: The list of objects that was read from the PDB file given as input (list) ff: The name of the forcefield (string) options: A dictionary of PDB2PQR options, including: verbose: When 1, script will print information to stdout When 0, no detailed information will be printed (int) debump: When 1, debump heavy atoms (int) opt: When 1, run hydrogen optimization (int) ph: The desired ph of the system (float) outname: The name of the desired output file Returns header: The PQR file header (string) lines: The PQR file atoms (list) missedligandresidues: A list of ligand residue names whose charges could not be assigned (ligand)` usage(rc) `Print usage for this script to stdout. Parameters rc: Exit status (int)`

Data
`` |  | AAPATH = 'dat/AA.xml' ANGLE_CUTOFF = 20.0 BACKBONE = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN'] BONDED_SS_LIMIT = 2.5 BUMP_DIST = 2.0 BUMP_HDIST = 1.5 CELL_SIZE = 2 DIHEDRAL = 57.2958 DIST_CUTOFF = 3.2999999999999998 HDEBUG = 0 HYDPATH = 'dat/HYDROGENS.xml' LIMIT = 500.0 LOADPATH = '/proc/loadavg' LOCALPATH = '/export/home/www/html/pdb2pqr/' LOGPATH = '/export/home/www/html/pdb2pqr//tmp//usage.txt' NAPATH = 'dat/NA.xml' PATCHPATH = 'dat/PATCHES.xml' PEPTIDE_DIST = 1.7 REFRESHTIME = 20 REPAIR_LIMIT = 10 SMALL = 9.9999999999999995e-08 STYLESHEET = 'http://agave.wustl.edu/css/baker.css' TMPDIR = 'tmp/' WEBNAME = 'server.html' WEBSITE = 'http://agave.wustl.edu/pdb2pqr/' __author__ = 'Todd Dolinsky, Nathan Baker' __date__ = '17 March 2007' __version__ = '1.2.1'

Author
`` |  | Todd Dolinsky, Nathan Baker