src.inputgen | index /Users/baker/coding/manifold/pdb2pqr/trunk/pdb2pqr/src/inputgen.py

`inputgen class
Create an APBS input file using psize data
Written by Todd Dolinsky based on original sed script by Nathan Baker
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
Nathan A. Baker (baker@biochem.wustl.edu)
Todd Dolinsky (todd@ccb.wustl.edu)
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
Washington University in St. Louis
Jens Nielsen (Jens.Nielsen@ucd.ie)
University College Dublin
Additional contributing authors listed in documentation and supporting
package licenses.
Copyright (c) 2003-2007. Washington University in St. Louis.
All Rights Reserved.
This file is part of PDB2PQR.
PDB2PQR is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
PDB2PQR is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with PDB2PQR; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
----------------------------`

Modules

``

src.psize | string | sys |

Classes

``

Elec
Input

class Elec
`` | `An object for the ELEC section of an APBS input file`

Methods defined here:

__init__(self, size, method, asyncflag)
  `Initialize the variables that can be set in this object
  Users can modify any of these variables (that's why
  they're here!)`

__str__(self)
  `Return the elec statement as a string. Check the method
  to see which keywords to use.`

class Input
`` | `The input class. Each input object is one APBS input file.`

Methods defined here:

__init__(self, pqrpath, size, method, asyncflag)
  `Initialize the input file class. Each input file contains
  a PQR name, a list of elec objects, and a list of strings
  containing print statements. For starters assume two
  ELEC statements are needed, one for the inhomgenous and
  the other for the homogenous dielectric calculations.
  Users can edit the elec statements and the print statements.
  This assumes you have already run psize, either by
  size.runPsize(/path/to/pqr) or
  size.parseString(string)
  size.setAll()
  Parameters
  pqrpath: The path to the PQR file (string)
  size: The Psize object (psize)
  method: The method (para, auto, manual, async) to use
  asyncflag: 1 if async is desired, 0 otherwise`

__str__(self)
  `Return the text of the input file`

printInputFiles(self)
  `Make the input file(s) associated with this object`

Functions

``

main()

splitInput(filename)
  `Split the parallel input file into multiple async file names
  Parameters
  filename: The path to the original parallel input
  file (string)`

usage()
  `Display the usage information for this script`