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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.psize</title>
<meta charset="utf-8">
</head><body bgcolor="#f0f0f8">
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
<tr bgcolor="#7799ee">
<td valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong><a href="src.html"><font color="#ffffff">src</font></a>.psize</strong></big></big> (4 June 2008)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/psize.py">/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/psize.py</a></font></td></tr></table>
<p><tt>psize class<br>
<br>
Get dimensions and other information from a PQR file.<br>
<br>
Originally written by Dave Sept<br>
Additional APBS-specific features added by Nathan Baker<br>
Ported to Python/<a href="#Psize">Psize</a> class by Todd Dolinsky and subsequently<br>
hacked by Nathan Baker<br>
<br>
----------------------------<br>
<br>
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of<br>
Poisson-Boltzmann electrostatics calculations<br>
<br>
Copyright (c) 2002-2011, Jens Erik Nielsen, University College Dublin; <br>
Nathan A. Baker, Battelle Memorial Institute, Developed at the Pacific <br>
Northwest National Laboratory, operated by Battelle Memorial Institute, <br>
Pacific Northwest Division for the U.S. Department Energy.; <br>
Paul Czodrowski & Gerhard Klebe, University of Marburg.<br>
<br>
All rights reserved.<br>
<br>
Redistribution and use in source and binary forms, with or without modification, <br>
are permitted provided that the following conditions are met:<br>
<br>
* Redistributions of source code must retain the above copyright notice, <br>
this list of conditions and the following disclaimer.<br>
* Redistributions in binary form must reproduce the above copyright notice, <br>
this list of conditions and the following disclaimer in the documentation <br>
and/or other materials provided with the distribution.<br>
* Neither the names of University College Dublin, Battelle Memorial Institute,<br>
Pacific Northwest National Laboratory, US Department of Energy, or University<br>
of Marburg nor the names of its contributors may be used to endorse or promote<br>
products derived from this software without specific prior written permission.<br>
<br>
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND <br>
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED <br>
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. <br>
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, <br>
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, <br>
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, <br>
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF <br>
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE <br>
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED <br>
OF THE POSSIBILITY OF SUCH DAMAGE.<br>
<br>
----------------------------</tt></p>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#aa55cc">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
<tr><td bgcolor="#aa55cc"><tt> </tt></td><td> </td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="getopt.html">getopt</a><br>
</td><td width="25%" valign=top><a href="string.html">string</a><br>
</td><td width="25%" valign=top><a href="sys.html">sys</a><br>
</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
<tr><td bgcolor="#ee77aa"><tt> </tt></td><td> </td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="src.psize.html#Psize">Psize</a>
</font></dt></dl>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Psize">class <strong>Psize</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>Master class for parsing input files and suggesting settings<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Psize-__init__"><strong>__init__</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getCenter"><strong>getCenter</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getCharge"><strong>getCharge</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getCoarseGridDims"><strong>getCoarseGridDims</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getConstant"><strong>getConstant</strong></a>(self, name)</dt><dd><tt>Get a constant value; raises KeyError if constant not found</tt></dd></dl>
<dl><dt><a name="Psize-getFineGridDims"><strong>getFineGridDims</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getFineGridPoints"><strong>getFineGridPoints</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getFocus"><strong>getFocus</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getLength"><strong>getLength</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getMax"><strong>getMax</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getMin"><strong>getMin</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getProcGrid"><strong>getProcGrid</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-getSmallest"><strong>getSmallest</strong></a>(self)</dt></dl>
<dl><dt><a name="Psize-parseInput"><strong>parseInput</strong></a>(self, filename)</dt><dd><tt>Parse input structure file in PDB or PQR format</tt></dd></dl>
<dl><dt><a name="Psize-parseLines"><strong>parseLines</strong></a>(self, lines)</dt><dd><tt>Parse the lines</tt></dd></dl>
<dl><dt><a name="Psize-parseString"><strong>parseString</strong></a>(self, structure)</dt><dd><tt>Parse the input structure as a string in PDB or PQR format</tt></dd></dl>
<dl><dt><a name="Psize-printResults"><strong>printResults</strong></a>(self)</dt><dd><tt>Return a string with the formatted results</tt></dd></dl>
<dl><dt><a name="Psize-runPsize"><strong>runPsize</strong></a>(self, filename)</dt><dd><tt>Parse input PQR file and set parameters</tt></dd></dl>
<dl><dt><a name="Psize-setAll"><strong>setAll</strong></a>(self)</dt><dd><tt>Set up all of the things calculated individually above</tt></dd></dl>
<dl><dt><a name="Psize-setCenter"><strong>setCenter</strong></a>(self, maxlen, minlen)</dt><dd><tt>Compute molecule center</tt></dd></dl>
<dl><dt><a name="Psize-setCoarseGridDims"><strong>setCoarseGridDims</strong></a>(self, olen)</dt><dd><tt>Compute coarse mesh dimensions</tt></dd></dl>
<dl><dt><a name="Psize-setConstant"><strong>setConstant</strong></a>(self, name, value)</dt><dd><tt>Set a constant to a value; returns 0 if constant not found</tt></dd></dl>
<dl><dt><a name="Psize-setFineGridDims"><strong>setFineGridDims</strong></a>(self, olen, clen)</dt><dd><tt>Compute fine mesh dimensions</tt></dd></dl>
<dl><dt><a name="Psize-setFineGridPoints"><strong>setFineGridPoints</strong></a>(self, flen)</dt><dd><tt>Compute mesh grid points, assuming 4 levels in MG hierarchy</tt></dd></dl>
<dl><dt><a name="Psize-setFocus"><strong>setFocus</strong></a>(self, flen, np, clen)</dt><dd><tt>Calculate the number of levels of focusing required for each<br>
processor subdomain</tt></dd></dl>
<dl><dt><a name="Psize-setLength"><strong>setLength</strong></a>(self, maxlen, minlen)</dt><dd><tt>Compute molecule dimensions</tt></dd></dl>
<dl><dt><a name="Psize-setProcGrid"><strong>setProcGrid</strong></a>(self, n, nsmall)</dt><dd><tt>Calculate the number of processors required to span each <br>
dimension</tt></dd></dl>
<dl><dt><a name="Psize-setSmallest"><strong>setSmallest</strong></a>(self, n)</dt><dd><tt>Compute parallel division in case memory requirement above ceiling<br>
Find the smallest dimension and see if the number of grid points in<br>
that dimension will fit below the memory ceiling<br>
Reduce nsmall until an nsmall^3 domain will fit into memory</tt></dd></dl>
</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#eeaa77">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
<tr><td bgcolor="#eeaa77"><tt> </tt></td><td> </td>
<td width="100%"><dl><dt><a name="-log"><strong>log</strong></a>(...)</dt><dd><tt><a href="#-log">log</a>(x[, base])<br>
<br>
Return the logarithm of x to the given base.<br>
If the base not specified, returns the natural logarithm (base e) of x.</tt></dd></dl>
<dl><dt><a name="-main"><strong>main</strong></a>()</dt></dl>
<dl><dt><a name="-usage"><strong>usage</strong></a>(rc)</dt><dd><tt>Print usage information and exit with error code rc</tt></dd></dl>
</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
<tr><td bgcolor="#55aa55"><tt> </tt></td><td> </td>
<td width="100%"><strong>__author__</strong> = 'Dave Sept, Nathan Baker, Todd Dolinsky, Yong Huang'<br>
<strong>__date__</strong> = '4 June 2008'<br>
<strong>stderr</strong> = <open file '<stderr>', mode 'w'><br>
<strong>stdout</strong> = <open file '<stdout>', mode 'w'></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
<tr><td bgcolor="#7799ee"><tt> </tt></td><td> </td>
<td width="100%">Dave Sept, Nathan Baker, Todd Dolinsky, Yong Huang</td></tr></table>
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