Python: module src.psize

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

`psize class
Get dimensions and other information from a PQR file.
Originally written by Dave Sept
Additional APBS-specific features added by Nathan Baker
Ported to Python/Psize class by Todd Dolinsky and subsequently
hacked 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
`` |  |
string | sys |  |

Classes
`` |  | Psize
class Psize
`` |  | Methods defined here: __init__(self) getCenter(self) getCharge(self) getCoarseGridDims(self) getConstant(self, name) `Get a constant value; raises KeyError if constant not found` getFineGridDims(self) getFineGridPoints(self) getFocus(self) getLength(self) getMax(self) getMin(self) getProcGrid(self) getSmallest(self) parseInput(self, filename) `Parse input structure file in PDB or PQR format` parseLines(self, lines) `Parse the lines` parseString(self, structure) `Parse the input structure as a string in PDB or PQR format` printResults(self) `Return a string with the formatted results` runPsize(self, filename) `Parse input PQR file and set parameters` setAll(self) `Set up all of the things calculated individually above` setCenter(self, maxlen, minlen) `Compute molecule center` setCoarseGridDims(self, olen) `Compute coarse mesh dimensions` setConstant(self, name, value) `Set a constant to a value; returns 0 if constant not found` setFineGridDims(self, olen, clen) `Compute fine mesh dimensions` setFineGridPoints(self, flen) `Compute mesh grid points, assuming 4 levels in MG hierarchy` setFocus(self, flen, np, clen) `Calculate the number of levels of focusing required for each processor subdomain` setLength(self, maxlen, minlen) `Compute molecule dimensions` setProcGrid(self, n, nsmall) `Calculate the number of processors required to span each dimension` setSmallest(self, n) `Compute parallel division in case memory requirement above ceiling Find the smallest dimension and see if the number of grid points in that dimension will fit below the memory ceiling Reduce nsmall until an nsmall^3 domain will fit into memory`

Functions
`` |  | log(...) `log(x[, base]) -> the logarithm of x to the given base. If the base not specified, returns the natural logarithm (base e) of x.` main() usage()

Data
`` |  | stdout = <open file '<stdout>', mode 'w' at 0x513068>