1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.server</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>.server</strong></big></big> (4 August 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/server.py">/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/server.py</a></font></td></tr></table>
<p><tt>CGI Server for PDB2PQR<br>
<br>
This module contains the various functions necessary to run PDB2PQR<br>
from a web server.<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="os.html">os</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><a href="time.html">time</a><br>
</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="-cleanTmpdir"><strong>cleanTmpdir</strong></a>()</dt><dd><tt>Clean up the temp directory for CGI. If the size of the directory<br>
is greater than LIMIT, delete the older half of the files. Since<br>
the files are stored by system time of creation, this is an<br>
easier task.</tt></dd></dl>
<dl><dt><a name="-createError"><strong>createError</strong></a>(name, details)</dt><dd><tt>Create an error results page for CGI-based runs<br>
<br>
Parameters<br>
name: The result file root name, based on local time (string)<br>
details: The details of the error (string)</tt></dd></dl>
<dl><dt><a name="-createResults"><strong>createResults</strong></a>(header, input, name, time, missedligands<font color="#909090">=[]</font>)</dt><dd><tt>Create the results web page for CGI-based runs<br>
<br>
Parameters<br>
header: The header of the PQR file (string)<br>
input: A flag whether an input file has been created (int)<br>
tmpdir: The resulting file directory (string)<br>
name: The result file root name, based on local time (string)<br>
time: The time taken to run the script (float)<br>
missedligands: A list of ligand names whose parameters could<br>
not be assigned. Optional. (list)</tt></dd></dl>
<dl><dt><a name="-setID"><strong>setID</strong></a>(time)</dt><dd><tt>Given a floating point time.time(), generate an ID.<br>
Use the tenths of a second to differentiate.<br>
<br>
Parameters<br>
time: The current time.time() (float)<br>
Returns<br>
id : The file id (string)</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>APBS_LOCATION</strong> = ''<br>
<strong>APBS_OPAL_URL</strong> = ''<br>
<strong>HAVE_APBS</strong> = False<br>
<strong>HAVE_PDB2PQR_OPAL</strong> = False<br>
<strong>INSTALLDIR</strong> = '/Users/d3y382/pdb2pqr/'<br>
<strong>LIMIT</strong> = 500.0<br>
<strong>LOADPATH</strong> = '/proc/loadavg'<br>
<strong>LOGPATH</strong> = '/Users/d3y382/pdb2pqr//tmp//usage.txt'<br>
<strong>MAXATOMS</strong> = 10000<br>
<strong>PDB2PQR_OPAL_URL</strong> = ''<br>
<strong>PDB2PQR_VERSION</strong> = 'master'<br>
<strong>REFRESHTIME</strong> = 20<br>
<strong>SRCPATH</strong> = '/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/'<br>
<strong>STYLESHEET</strong> = 'http://PT24098/pdb2pqr/pdb2pqr.css'<br>
<strong>TMPDIR</strong> = 'tmp/'<br>
<strong>WEBNAME</strong> = 'index.html'<br>
<strong>WEBSITE</strong> = 'http://PT24098/pdb2pqr/'<br>
<strong>__author__</strong> = 'Todd Dolinsky, Samir Unni, Yong Huang'<br>
<strong>__date__</strong> = '4 August 2008'</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, Samir Unni, Yong Huang</td></tr></table>
</body></html>
|
