psize

Get dimensions and other information from a PQR file.

Todo

This code should be moved to the APBS code base.

Code author: Dave Sept

Code author: Nathan Baker

Code author: Todd Dolinksy

Code author: Yong Huang

class pdb2pqr.psize.Psize(cfac=1.7, fadd=20.0, space=0.5, gmemfac=200, gmemceil=400, ofrac=0.1, redfac=0.25)[source]

Class for parsing input files and suggesting settings.

__init__(cfac=1.7, fadd=20.0, space=0.5, gmemfac=200, gmemceil=400, ofrac=0.1, redfac=0.25)[source]

Initialize.

Parameters

  • cfac (float) – factor by which to expand molecular dimensions to get coarse grid dimensions

  • fadd (float) – amount (in Angstroms) to add to molecular dimensions to get the fine grid dimensions

  • space (float) – desired fine mesh resolution (in Angstroms)

  • gmemfac (float) – number of bytes per grid point required for a sequential multigrid calculation

  • gmemceil (float) – maximum memory (in MB) allowed for sequential multigrid calculation. Adjust this value to force the script to perform faster calculations (which require more parallelism).

  • ofrac (float) – overlap factor between mesh partitions in parallel focusing calculation

  • redfac (float) – the maximum factor by which a domain dimension can be reduced during focusing

get_smallest() → List[int][source]

Get Smallest

run_psize(filename)[source]

Parse input PQR file and set parameters.

Parameters

filename (str) – path of PQR file

pdb2pqr.psize.get_cli_args(args_str: Optional[str] = None) → argparse.Namespace[source]

Build argument parser.

Parameters

args_str (str) – String representation of command line arguments

Returns

argument parser

Return type

Namespace

pdb2pqr.psize.main()[source]

Main driver for module.