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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.topology</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>.topology</strong></big></big> (12 November 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/topology.py">/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/topology.py</a></font></td></tr></table>
<p><tt>Parser for TOPOLOGY.xml<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="xml.sax.html">xml.sax</a><br>
</td><td width="25%" valign=top></td><td width="25%" valign=top></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.topology.html#Topology">Topology</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyAtom">TopologyAtom</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyConformer">TopologyConformer</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyConformerAdd">TopologyConformerAdd</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyConformerRemove">TopologyConformerRemove</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyDihedral">TopologyDihedral</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyReference">TopologyReference</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyResidue">TopologyResidue</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyTautomer">TopologyTautomer</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyTitrationState">TopologyTitrationState</a>
</font></dt><dt><font face="helvetica, arial"><a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.topology.html#TopologyHandler">TopologyHandler</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="Topology">class <strong>Topology</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>Contains the structured definitions of residue reference coordinates as well as alternate titration, <br>
conformer, and tautomer states.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Topology-__init__"><strong>__init__</strong></a>(self, topologyFile)</dt><dd><tt>Initialize with the topology file reference ready for reading</tt></dd></dl>
</td></tr></table> <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="TopologyAtom">class <strong>TopologyAtom</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for atom topology information<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyAtom-__init__"><strong>__init__</strong></a>(self, parent)</dt><dd><tt>Needs to be intialized with an upper-level class that contains an atoms array (e.g., <a href="#TopologyReference">TopologyReference</a><br>
or TopologyConformerAddition)</tt></dd></dl>
<dl><dt><a name="TopologyAtom-__str__"><strong>__str__</strong></a>(self)</dt></dl>
</td></tr></table> <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="TopologyConformer">class <strong>TopologyConformer</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for topology conformer information<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyConformer-__init__"><strong>__init__</strong></a>(self, topologyTautomer)</dt><dd><tt>Initialize with a <a href="#TopologyTautomer">TopologyTautomer</a> object</tt></dd></dl>
<dl><dt><a name="TopologyConformer-__str__"><strong>__str__</strong></a>(self)</dt></dl>
</td></tr></table> <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="TopologyConformerAdd">class <strong>TopologyConformerAdd</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for adding atoms to a conformer<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyConformerAdd-__init__"><strong>__init__</strong></a>(self, topologyConformer)</dt><dd><tt>Initialize with a <a href="#TopologyConformer">TopologyConformer</a> object</tt></dd></dl>
</td></tr></table> <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="TopologyConformerRemove">class <strong>TopologyConformerRemove</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for removing atoms to a conformer<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyConformerRemove-__init__"><strong>__init__</strong></a>(self, topologyConformer)</dt><dd><tt>Initialize with a <a href="#TopologyConformer">TopologyConformer</a> object</tt></dd></dl>
</td></tr></table> <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="TopologyDihedral">class <strong>TopologyDihedral</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for dihedral topology information.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyDihedral-__init__"><strong>__init__</strong></a>(self, parent)</dt><dd><tt>Needs a parent that has a dihedral list.</tt></dd></dl>
<dl><dt><a name="TopologyDihedral-__str__"><strong>__str__</strong></a>(self)</dt></dl>
</td></tr></table> <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="TopologyHandler">class <strong>TopologyHandler</strong></a>(<a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>Handler for XML-based topology files. Assumes the following hierarchy of tags:<br>
topology<br>
-->residue<br>
|-->reference<br>
|-->titrationstate<br>
|-->tautomer<br>
|-->conformer<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyHandler-__init__"><strong>__init__</strong></a>(self)</dt></dl>
<dl><dt><a name="TopologyHandler-characters"><strong>characters</strong></a>(self, text)</dt></dl>
<dl><dt><a name="TopologyHandler-endElement"><strong>endElement</strong></a>(self, tagName)</dt></dl>
<dl><dt><a name="TopologyHandler-startElement"><strong>startElement</strong></a>(self, tagName, attributes)</dt></dl>
<hr>
Methods inherited from <a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>:<br>
<dl><dt><a name="TopologyHandler-endDocument"><strong>endDocument</strong></a>(self)</dt><dd><tt>Receive notification of the end of a document.<br>
<br>
The SAX parser will invoke this method only once, and it will<br>
be the last method invoked during the parse. The parser shall<br>
not invoke this method until it has either abandoned parsing<br>
(because of an unrecoverable error) or reached the end of<br>
input.</tt></dd></dl>
<dl><dt><a name="TopologyHandler-endElementNS"><strong>endElementNS</strong></a>(self, name, qname)</dt><dd><tt>Signals the end of an element in namespace mode.<br>
<br>
The name parameter contains the name of the element type, just<br>
as with the startElementNS event.</tt></dd></dl>
<dl><dt><a name="TopologyHandler-endPrefixMapping"><strong>endPrefixMapping</strong></a>(self, prefix)</dt><dd><tt>End the scope of a prefix-URI mapping.<br>
<br>
See startPrefixMapping for details. This event will always<br>
occur after the corresponding endElement event, but the order<br>
of endPrefixMapping events is not otherwise guaranteed.</tt></dd></dl>
<dl><dt><a name="TopologyHandler-ignorableWhitespace"><strong>ignorableWhitespace</strong></a>(self, whitespace)</dt><dd><tt>Receive notification of ignorable whitespace in element content.<br>
<br>
Validating Parsers must use this method to report each chunk<br>
of ignorable whitespace (see the W3C XML 1.0 recommendation,<br>
section 2.10): non-validating parsers may also use this method<br>
if they are capable of parsing and using content models.<br>
<br>
SAX parsers may return all contiguous whitespace in a single<br>
chunk, or they may split it into several chunks; however, all<br>
of the characters in any single event must come from the same<br>
external entity, so that the Locator provides useful<br>
information.</tt></dd></dl>
<dl><dt><a name="TopologyHandler-processingInstruction"><strong>processingInstruction</strong></a>(self, target, data)</dt><dd><tt>Receive notification of a processing instruction.<br>
<br>
The Parser will invoke this method once for each processing<br>
instruction found: note that processing instructions may occur<br>
before or after the main document element.<br>
<br>
A SAX parser should never report an XML declaration (XML 1.0,<br>
section 2.8) or a text declaration (XML 1.0, section 4.3.1)<br>
using this method.</tt></dd></dl>
<dl><dt><a name="TopologyHandler-setDocumentLocator"><strong>setDocumentLocator</strong></a>(self, locator)</dt><dd><tt>Called by the parser to give the application a locator for<br>
locating the origin of document events.<br>
<br>
SAX parsers are strongly encouraged (though not absolutely<br>
required) to supply a locator: if it does so, it must supply<br>
the locator to the application by invoking this method before<br>
invoking any of the other methods in the DocumentHandler<br>
interface.<br>
<br>
The locator allows the application to determine the end<br>
position of any document-related event, even if the parser is<br>
not reporting an error. Typically, the application will use<br>
this information for reporting its own errors (such as<br>
character content that does not match an application's<br>
business rules). The information returned by the locator is<br>
probably not sufficient for use with a search engine.<br>
<br>
Note that the locator will return correct information only<br>
during the invocation of the events in this interface. The<br>
application should not attempt to use it at any other time.</tt></dd></dl>
<dl><dt><a name="TopologyHandler-skippedEntity"><strong>skippedEntity</strong></a>(self, name)</dt><dd><tt>Receive notification of a skipped entity.<br>
<br>
The Parser will invoke this method once for each entity<br>
skipped. Non-validating processors may skip entities if they<br>
have not seen the declarations (because, for example, the<br>
entity was declared in an external DTD subset). All processors<br>
may skip external entities, depending on the values of the<br>
<a href="http://xml.org/sax/features/external-general-entities">http://xml.org/sax/features/external-general-entities</a> and the<br>
<a href="http://xml.org/sax/features/external-parameter-entities">http://xml.org/sax/features/external-parameter-entities</a><br>
properties.</tt></dd></dl>
<dl><dt><a name="TopologyHandler-startDocument"><strong>startDocument</strong></a>(self)</dt><dd><tt>Receive notification of the beginning of a document.<br>
<br>
The SAX parser will invoke this method only once, before any<br>
other methods in this interface or in DTDHandler (except for<br>
setDocumentLocator).</tt></dd></dl>
<dl><dt><a name="TopologyHandler-startElementNS"><strong>startElementNS</strong></a>(self, name, qname, attrs)</dt><dd><tt>Signals the start of an element in namespace mode.<br>
<br>
The name parameter contains the name of the element type as a<br>
(uri, localname) tuple, the qname parameter the raw XML 1.0<br>
name used in the source document, and the attrs parameter<br>
holds an instance of the Attributes class containing the<br>
attributes of the element.<br>
<br>
The uri part of the name tuple is None for elements which have<br>
no namespace.</tt></dd></dl>
<dl><dt><a name="TopologyHandler-startPrefixMapping"><strong>startPrefixMapping</strong></a>(self, prefix, uri)</dt><dd><tt>Begin the scope of a prefix-URI Namespace mapping.<br>
<br>
The information from this event is not necessary for normal<br>
Namespace processing: the SAX XML reader will automatically<br>
replace prefixes for element and attribute names when the<br>
<a href="http://xml.org/sax/features/namespaces">http://xml.org/sax/features/namespaces</a> feature is true (the<br>
default).<br>
<br>
There are cases, however, when applications need to use<br>
prefixes in character data or in attribute values, where they<br>
cannot safely be expanded automatically; the<br>
start/endPrefixMapping event supplies the information to the<br>
application to expand prefixes in those contexts itself, if<br>
necessary.<br>
<br>
Note that start/endPrefixMapping events are not guaranteed to<br>
be properly nested relative to each-other: all<br>
startPrefixMapping events will occur before the corresponding<br>
startElement event, and all endPrefixMapping events will occur<br>
after the corresponding endElement event, but their order is<br>
not guaranteed.</tt></dd></dl>
</td></tr></table> <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="TopologyReference">class <strong>TopologyReference</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for the reference structure of a residue<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyReference-__init__"><strong>__init__</strong></a>(self, topologyResidue)</dt><dd><tt>Initialize with a <a href="#TopologyResidue">TopologyResidue</a> object</tt></dd></dl>
</td></tr></table> <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="TopologyResidue">class <strong>TopologyResidue</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for residue topology information<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyResidue-__init__"><strong>__init__</strong></a>(self, topology)</dt><dd><tt>Initialize with a <a href="#Topology">Topology</a> object</tt></dd></dl>
<dl><dt><a name="TopologyResidue-__str__"><strong>__str__</strong></a>(self)</dt></dl>
</td></tr></table> <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="TopologyTautomer">class <strong>TopologyTautomer</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for topology tautomer information<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyTautomer-__init__"><strong>__init__</strong></a>(self, topologyTitrationState)</dt><dd><tt>Initialize with a <a href="#TopologyTitrationState">TopologyTitrationState</a> object</tt></dd></dl>
<dl><dt><a name="TopologyTautomer-__str__"><strong>__str__</strong></a>(self)</dt></dl>
</td></tr></table> <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="TopologyTitrationState">class <strong>TopologyTitrationState</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A class for the titration state of a residue<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyTitrationState-__init__"><strong>__init__</strong></a>(self, topologyResidue)</dt><dd><tt>Initialize with a <a href="#TopologyResidue">TopologyResidue</a> object</tt></dd></dl>
<dl><dt><a name="TopologyTitrationState-__str__"><strong>__str__</strong></a>(self)</dt></dl>
</td></tr></table></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>TOPOLOGYPATH</strong> = 'TOPOLOGY.xml'<br>
<strong>__author__</strong> = 'Nathan Baker, Yong Huang'<br>
<strong>__date__</strong> = '12 November 2008'<br>
<strong>stderr</strong> = <open file '<stderr>', mode 'w'></td></tr></table><p>
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<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%">Nathan Baker, Yong Huang</td></tr></table>
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