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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.forcefield</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>.forcefield</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/forcefield.py">/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/forcefield.py</a></font></td></tr></table>
<p><tt><a href="#Forcefield">Forcefield</a>.py<br>
<br>
This module takes a pdblist as input and replaces the occupancy and<br>
tempfactor fields with charge and radius fields, with values as defined<br>
by a particular forcefield. The forcefield structure is modeled off of<br>
the structures.py file, where each forcefield is considered a chain of<br>
residues of atoms.<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>
<a href="math.html">math</a><br>
</td><td width="25%" valign=top><a href="os.html">os</a><br>
<a href="re.html">re</a><br>
</td><td width="25%" valign=top><a href="xml.sax.html">xml.sax</a><br>
<a href="string.html">string</a><br>
</td><td width="25%" valign=top><a href="sys.html">sys</a><br>
</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.forcefield.html#Forcefield">Forcefield</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.forcefield.html#ForcefieldAtom">ForcefieldAtom</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.forcefield.html#ForcefieldResidue">ForcefieldResidue</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.forcefield.html#ForcefieldHandler">ForcefieldHandler</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="Forcefield">class <strong>Forcefield</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Forcefield">Forcefield</a> class<br>
<br>
The forcefield class contains definitions for a given forcefield.<br>
Each forcefield object contains a dictionary of residues, with each<br>
residue containing a dictionary of atoms. Dictionaries are used<br>
instead of lists as the ordering is not important. The forcefield<br>
definition files are unedited, directly from the forcefield - all<br>
transformations are done within.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Forcefield-__init__"><strong>__init__</strong></a>(self, ff, definition, userff, usernames<font color="#909090">=None</font>)</dt><dd><tt>Initialize the class by parsing the definition file<br>
<br>
Parameters<br>
ff: The name of the forcefield (string) can be None.<br>
definition: The definition objects<br>
userff: A link to the file for CGI based user-defined<br>
forcefields</tt></dd></dl>
<dl><dt><a name="Forcefield-getAmberParams"><strong>getAmberParams</strong></a>(self, residue, name)</dt><dd><tt>Get the forcefield definitions from the Amber database<br>
<br>
Parameters<br>
residue: The residue (residue)<br>
name: The atom name (string)<br>
Returns<br>
resname: The name of the amber residue<br>
atomname: The name of the amber atom</tt></dd></dl>
<dl><dt><a name="Forcefield-getCharmmParams"><strong>getCharmmParams</strong></a>(self, residue, name)</dt><dd><tt>Get the forcefield definitions from the Charmm database<br>
<br>
Parameters<br>
residue: The residue (residue)<br>
name: The atom name (string)<br>
Returns<br>
resname: The name of the Charmm residue<br>
atomname: The name of the Charmm atom</tt></dd></dl>
<dl><dt><a name="Forcefield-getGroup"><strong>getGroup</strong></a>(self, resname, atomname)</dt><dd><tt>Get the group/type associated with the input<br>
fields. If not found, return a null string.<br>
<br>
Parameters:<br>
resname: The residue name (string)<br>
atomname: The atom name (string)</tt></dd></dl>
<dl><dt><a name="Forcefield-getNames"><strong>getNames</strong></a>(self, resname, atomname)</dt><dd><tt>Get the actual names associated with the input fields.<br>
The names passed in point to <a href="#ForcefieldResidue">ForcefieldResidue</a> and<br>
<a href="#ForcefieldAtom">ForcefieldAtom</a> objects which may have different names;<br>
grab these names and return.<br>
<br>
Parameters<br>
resname: The residue name (string)<br>
atomname: The atom name (string)<br>
Returns<br>
rname: The forcefield's name for this residue (string)<br>
aname: The forcefield's name for this atom (string)</tt></dd></dl>
<dl><dt><a name="Forcefield-getParams"><strong>getParams</strong></a>(self, resname, atomname)</dt><dd><tt>Get the parameters associated with the input fields.<br>
The residue itself is needed instead of simply its name<br>
because the forcefield may use a different residue name<br>
than the standard amino acid name.<br>
<br>
Parameters<br>
resname: The residue name (string)<br>
atomname: The atom name (string)<br>
Returns<br>
charge: The charge on the atom (float)<br>
radius: The radius of the atom (float)</tt></dd></dl>
<dl><dt><a name="Forcefield-getParams1"><strong>getParams1</strong></a>(self, residue, name)</dt><dd><tt>Get the parameters associated with the input fields.<br>
The residue itself is needed instead of simply its name<br>
because the forcefield may use a different residue name<br>
than the standard amino acid name.<br>
<br>
Parameters<br>
residue: The residue (residue)<br>
name: The atom name (string)<br>
Returns<br>
charge: The charge on the atom (float)<br>
radius: The radius of the atom (float)</tt></dd></dl>
<dl><dt><a name="Forcefield-getParseParams"><strong>getParseParams</strong></a>(self, residue, name)</dt><dd><tt>Get the forcefield definitions from the Parse database<br>
<br>
Parameters<br>
residue: The residue (residue)<br>
name: The atom name (string)<br>
Returns<br>
resname: The name of the amber residue<br>
atomname: The name of the amber atom</tt></dd></dl>
<dl><dt><a name="Forcefield-getResidue"><strong>getResidue</strong></a>(self, resname)</dt><dd><tt>Return the residue object with the given resname<br>
<br>
Parameters<br>
resname: The name of the residue (string)<br>
Returns<br>
residue: The residue object (<a href="#ForcefieldResidue">ForcefieldResidue</a>)</tt></dd></dl>
<dl><dt><a name="Forcefield-hasResidue"><strong>hasResidue</strong></a>(self, resname)</dt><dd><tt>Check if the residue name is in the map or not.<br>
<br>
Parameters<br>
resname: The name to search for (string)<br>
<br>
Returns<br>
1 if the resname is in the map, 0 otherwise.</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="ForcefieldAtom">class <strong>ForcefieldAtom</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#ForcefieldAtom">ForcefieldAtom</a> class<br>
<br>
The <a href="#ForcefieldAtom">ForcefieldAtom</a> object contains fields that are related to the<br>
forcefield at the atom level<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="ForcefieldAtom-__init__"><strong>__init__</strong></a>(self, name, charge, radius, resname, group<font color="#909090">=''</font>)</dt><dd><tt>Initialize the object<br>
<br>
Parameters<br>
name: The atom name (string)<br>
charge: The charge on the atom (float)<br>
radius: The radius of the atom (float)<br>
resname: The residue name (string)<br>
group: The group name (string)</tt></dd></dl>
<dl><dt><a name="ForcefieldAtom-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>String representation of the forcefield atom.</tt></dd></dl>
<dl><dt><a name="ForcefieldAtom-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get a member of the <a href="#ForcefieldAtom">ForcefieldAtom</a> class<br>
<br>
Parameters<br>
name: The name of the member (string)<br>
Possible Values<br>
name: The atom name (string)<br>
charge: The charge on the atom (float)<br>
radius: The radius of the atom (float)<br>
epsilon: The epsilon assocaited with the atom (float)<br>
Returns<br>
item: The value of the member</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="ForcefieldHandler">class <strong>ForcefieldHandler</strong></a>(<a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>)</font></td></tr>
<tr><td bgcolor="#ffc8d8"><tt> </tt></td><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="ForcefieldHandler-__init__"><strong>__init__</strong></a>(self, map, reference)</dt></dl>
<dl><dt><a name="ForcefieldHandler-characters"><strong>characters</strong></a>(self, text)</dt><dd><tt>Store the information in the object for future use/<br>
<br>
Parameters<br>
text: The text value between the XML tags</tt></dd></dl>
<dl><dt><a name="ForcefieldHandler-endElement"><strong>endElement</strong></a>(self, name)</dt><dd><tt>At the end of the element, act on the stored information.<br>
<br>
Parameters<br>
name: The name of the element (string)</tt></dd></dl>
<dl><dt><a name="ForcefieldHandler-findMatchingNames"><strong>findMatchingNames</strong></a>(self, regname, map)</dt><dd><tt>Find a list of strings that match the given regular<br>
expression.<br>
<br>
Parameters<br>
regname: The regular expression (string)<br>
map: The dictionary to search (dict)<br>
<br>
Returns<br>
list: A list of regular expression objects that match<br>
the regular expression.</tt></dd></dl>
<dl><dt><a name="ForcefieldHandler-startElement"><strong>startElement</strong></a>(self, name, attributes)</dt><dd><tt>Override the startElement function to keep track of the current<br>
element.</tt></dd></dl>
<dl><dt><a name="ForcefieldHandler-updateMap"><strong>updateMap</strong></a>(self, toname, fromname, map)</dt><dd><tt>Update the given map by adding a pointer from a new<br>
name to an object.<br>
<br>
Parameters<br>
toname: The new name for the object (string)<br>
fromname: The old name for the object (string)<br>
map: A dictionary of items (dict)</tt></dd></dl>
<hr>
Methods inherited from <a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>:<br>
<dl><dt><a name="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldHandler-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="ForcefieldResidue">class <strong>ForcefieldResidue</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#ForcefieldResidue">ForcefieldResidue</a> class<br>
<br>
The ForceFieldResidue class contains a mapping of all atoms within<br>
the residue for easy searching.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="ForcefieldResidue-__init__"><strong>__init__</strong></a>(self, name)</dt><dd><tt>Initialize the ForceFieldResidue object<br>
<br>
Parameters<br>
name: The name of the residue (string)</tt></dd></dl>
<dl><dt><a name="ForcefieldResidue-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Add an atom to the <a href="#ForcefieldResidue">ForcefieldResidue</a><br>
<br>
Parameters<br>
atom: The atom to be added (atom)</tt></dd></dl>
<dl><dt><a name="ForcefieldResidue-getAtom"><strong>getAtom</strong></a>(self, atomname)</dt><dd><tt>Return the atom object with the given atomname<br>
<br>
Parameters<br>
resname: The name of the atom (string)<br>
Returns<br>
residue: The atom object (<a href="#ForcefieldAtom">ForcefieldAtom</a>)</tt></dd></dl>
<dl><dt><a name="ForcefieldResidue-getAtoms"><strong>getAtoms</strong></a>(self)</dt><dd><tt>Return the list of atoms in this residue.</tt></dd></dl>
<dl><dt><a name="ForcefieldResidue-hasAtom"><strong>hasAtom</strong></a>(self, atomname)</dt><dd><tt>Check to see if the atomname is in the current residue.<br>
<br>
Parameters<br>
atomname: The name of the atom to search for<br>
Returns<br>
1 if the atom is present in the residue, 0 otherwise</tt></dd></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>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>
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