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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.utilities</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>.utilities</strong></big></big> (6 November 2007)</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/utilities.py">/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/utilities.py</a></font></td></tr></table>
<p><tt>Utilities for PDB2PQR Suite<br>
<br>
This module provides various utilities for the PDB2PQR suite to be<br>
imported into other Python scripts.<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="math.html">math</a><br>
</td><td width="25%" valign=top><a href="os.html">os</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="__builtin__.html#object">__builtin__.object</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.utilities.html#ExtraOptions">ExtraOptions</a>
</font></dt></dl>
</dd>
</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="ExtraOptions">class <strong>ExtraOptions</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
<tr><td bgcolor="#ffc8d8"><tt> </tt></td><td> </td>
<td width="100%">Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</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="-add"><strong>add</strong></a>(coords1, coords2)</dt><dd><tt>Add one 3-dimensional point to another<br>
<br>
Parameters<br>
coords1: coordinates of form [x,y,z]<br>
coords2: coordinates of form [x,y,z]<br>
Returns<br>
list: List of coordinates equal to coords2 + coords1 (list)</tt></dd></dl>
<dl><dt><a name="-analyzeConnectivity"><strong>analyzeConnectivity</strong></a>(map, key)</dt><dd><tt>Analyze the connectivity of a given map using the key value.<br>
<br>
Parameters<br>
map: The map to analyze (dict)<br>
key: The key value (variable)<br>
Returns<br>
list: A list of connected values to the key (list)</tt></dd></dl>
<dl><dt><a name="-appendToLogFile"><strong>appendToLogFile</strong></a>(jobName, fileName, logInput)</dt></dl>
<dl><dt><a name="-createPropkaOptions"><strong>createPropkaOptions</strong></a>(pH, verbose<font color="#909090">=False</font>, reference<font color="#909090">='neutral'</font>)</dt><dd><tt>Create a propka options <a href="__builtin__.html#object">object</a> for running propka.</tt></dd></dl>
<dl><dt><a name="-cross"><strong>cross</strong></a>(coords1, coords2)</dt><dd><tt>Find the cross product of two 3-dimensional points<br>
<br>
Parameters<br>
coords1: coordinates of form [x,y,z]<br>
coords2: coordinates of form [x,y,z]<br>
Returns<br>
list: Cross product coords2 and coords1 (list)</tt></dd></dl>
<dl><dt><a name="-distance"><strong>distance</strong></a>(coords1, coords2)</dt><dd><tt>Calculate the distance between two coordinates, as denoted by<br>
<br>
dist = sqrt((x2- x1)^2 + (y2 - y1)^2 + (z2 - z1)^2))<br>
<br>
Parameters<br>
coords1: Coordinates of form [x,y,z]<br>
coords2: Coordinates of form [x,y,z]<br>
Returns<br>
dist: Distance between the two coordinates (float)</tt></dd></dl>
<dl><dt><a name="-dot"><strong>dot</strong></a>(coords1, coords2)</dt><dd><tt>Find the dot product of two 3-dimensional points<br>
<br>
Parameters<br>
coords1: coordinates of form [x,y,z]<br>
coords2: coordinates of form [x,y,z]<br>
Returns<br>
value: Dot product coords2 and coords1 (float)</tt></dd></dl>
<dl><dt><a name="-factorial"><strong>factorial</strong></a>(n)</dt><dd><tt>Returns the factorial of the given number n</tt></dd></dl>
<dl><dt><a name="-getAngle"><strong>getAngle</strong></a>(coords1, coords2, coords3)</dt><dd><tt>Get the angle between three coordinates<br>
<br>
Parameters<br>
coords1: The first coordinate set (atom)<br>
coords2: The second (vertex) coordinate set (atom)<br>
coords3: The third coordinate set (atom)<br>
Returns<br>
angle: The angle between the atoms (float)</tt></dd></dl>
<dl><dt><a name="-getDatFile"><strong>getDatFile</strong></a>(name)</dt><dd><tt>Grab a data file. If the file cannot be found in the<br>
given directory, try the current system path.<br>
<br>
Parameters<br>
name: The name of the file to get (string)<br>
Returns<br>
path: The path to the file (string)</tt></dd></dl>
<dl><dt><a name="-getDihedral"><strong>getDihedral</strong></a>(coords1, coords2, coords3, coords4)</dt><dd><tt>Calculate the angle using the four atoms<br>
<br>
Parameters<br>
coords1: First of four coordinates of form [x,y,z]<br>
coords2: Second of four<br>
coords3: Third of four<br>
coords4: Fourth of four<br>
Returns<br>
value: Size of the angle (float)</tt></dd></dl>
<dl><dt><a name="-getEventTrackingString"><strong>getEventTrackingString</strong></a>(category, action, label, value<font color="#909090">=None</font>)</dt></dl>
<dl><dt><a name="-getFFfile"><strong>getFFfile</strong></a>(name)</dt><dd><tt>Grab the forcefield file. May or may not residue in the dat/<br>
directory.</tt></dd></dl>
<dl><dt><a name="-getNamesFile"><strong>getNamesFile</strong></a>(name)</dt><dd><tt>Grab the *.names file that contains the XML mapping.<br>
<br>
Parameters<br>
name: The name of the forcefield (string)<br>
Returns<br>
path: The path to the file (string)</tt></dd></dl>
<dl><dt><a name="-getPDBFile"><strong>getPDBFile</strong></a>(path)</dt><dd><tt>Obtain a PDB file. First check the path given on the command<br>
line - if that file is not available, obtain the file from the<br>
PDB webserver at <a href="http://www.rcsb.org/pdb/">http://www.rcsb.org/pdb/</a> .<br>
<br>
Parameters<br>
path: Name of PDB file to obtain (string)<br>
<br>
Returns<br>
file: File <a href="__builtin__.html#object">object</a> containing PDB file (file <a href="__builtin__.html#object">object</a>)</tt></dd></dl>
<dl><dt><a name="-getPQRBaseFileName"><strong>getPQRBaseFileName</strong></a>(filename)</dt></dl>
<dl><dt><a name="-getTrackingScriptString"><strong>getTrackingScriptString</strong></a>(jobid<font color="#909090">=None</font>)</dt><dd><tt>For injecting tracking script into a web page.<br>
<br>
jobid -> current jobid. Adds "jobid" custom variable to events and page views on this page.</tt></dd></dl>
<dl><dt><a name="-normalize"><strong>normalize</strong></a>(coords)</dt><dd><tt>Normalize a set of coordinates<br>
<br>
Parameters<br>
coords: coordinates of form [x,y,z]<br>
Returns<br>
list: normalized coordinates (list)</tt></dd></dl>
<dl><dt><a name="-resetLogFile"><strong>resetLogFile</strong></a>(jobName, fileName)</dt><dd><tt>For clearing out old log files if needed.<br>
Used mainly for removing apbs_end_time if apbs is rerun.</tt></dd></dl>
<dl><dt><a name="-shortestPath"><strong>shortestPath</strong></a>(graph, start, end, path<font color="#909090">=[]</font>)</dt><dd><tt>Uses recursion to find the shortest path from one node to<br>
another in an unweighted graph. Adapted from<br>
<a href="http://www.python.org/doc/essays/graphs.html">http://www.python.org/doc/essays/graphs.html</a> .<br>
<br>
Parameters:<br>
graph: A mapping of the graph to analyze, of the form<br>
{0: [1,2], 1:[3,4], ...} . Each key has a list<br>
of edges.<br>
start: The ID of the key to start the analysis from<br>
end: The ID of the key to end the analysis<br>
path: Optional argument used during the recursive step<br>
to keep the current path up to that point<br>
<br>
Returns:<br>
(variable): Returns a list of the shortest path (list)<br>
Returns None if start and end are not<br>
connected</tt></dd></dl>
<dl><dt><a name="-sortDictByValue"><strong>sortDictByValue</strong></a>(inputdict)</dt><dd><tt>Sort a dictionary by its values<br>
<br>
Parameters<br>
inputdict: The dictionary to sort (inputdict)<br>
Returns<br>
items: The dictionary sorted by value (list)</tt></dd></dl>
<dl><dt><a name="-startLogFile"><strong>startLogFile</strong></a>(jobName, fileName, logInput)</dt></dl>
<dl><dt><a name="-subtract"><strong>subtract</strong></a>(coords1, coords2)</dt><dd><tt>Subtract one 3-dimensional point from another<br>
<br>
Parameters<br>
coords1: coordinates of form [x,y,z]<br>
coords2: coordinates of form [x,y,z]<br>
Returns<br>
list: List of coordinates equal to coords1 - coords2 (list)</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>DIHEDRAL</strong> = 57.2958<br>
<strong>INSTALLDIR</strong> = '/Users/d3y382/pdb2pqr/'<br>
<strong>SMALL</strong> = 1e-07<br>
<strong>TMPDIR</strong> = 'tmp/'<br>
<strong>__author__</strong> = 'Todd Dolinsky, Yong Huang'<br>
<strong>__date__</strong> = '6 November 2007'</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%">Todd Dolinsky, Yong Huang</td></tr></table>
</body></html>
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