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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.definitions</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>.definitions</strong></big></big> (15 May 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/definitions.py">/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/definitions.py</a></font></td></tr></table>
<p><tt>Definitions for PDB2PQR<br>
<br>
This file contains classes associated with Amino Acid and Rotamer<br>
definitions as used by PDB2PQR.<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.</tt></p>
<p>
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<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="copy.html">copy</a><br>
<a href="getopt.html">getopt</a><br>
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<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.definitions.html#Definition">Definition</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.definitions.html#Patch">Patch</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.structures.html#Atom">src.structures.Atom</a>(<a href="src.pdb.html#ATOM">src.pdb.ATOM</a>)
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.definitions.html#DefinitionAtom">DefinitionAtom</a>
</font></dt></dl>
</dd>
<dt><font face="helvetica, arial"><a href="src.structures.html#Residue">src.structures.Residue</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.definitions.html#DefinitionResidue">DefinitionResidue</a>
</font></dt></dl>
</dd>
<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.definitions.html#DefinitionHandler">DefinitionHandler</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="Definition">class <strong>Definition</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Definition">Definition</a> class<br>
<br>
The <a href="#Definition">Definition</a> class contains the structured definitions found<br>
in the files and several mappings for easy access to the information.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Definition-__init__"><strong>__init__</strong></a>(self)</dt><dd><tt>Create a new <a href="#Definition">Definition</a> Object</tt></dd></dl>
<dl><dt><a name="Definition-addPatch"><strong>addPatch</strong></a>(self, patch, refname, newname)</dt><dd><tt>Add a patch to a definition residue.<br>
<br>
Parameters<br>
patch: The patch object to add (<a href="#Patch">Patch</a>)<br>
refname: The name of the object to add the patch to (string)<br>
newname: The name of the new (patched) object (string)</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="DefinitionAtom">class <strong>DefinitionAtom</strong></a>(<a href="src.structures.html#Atom">src.structures.Atom</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt>A trimmed down version of the <a href="src.structures.html#Atom">Atom</a> class<br> </tt></td></tr>
<tr><td> </td>
<td width="100%"><dl><dt>Method resolution order:</dt>
<dd><a href="src.definitions.html#DefinitionAtom">DefinitionAtom</a></dd>
<dd><a href="src.structures.html#Atom">src.structures.Atom</a></dd>
<dd><a href="src.pdb.html#ATOM">src.pdb.ATOM</a></dd>
<dd><a href="src.pdb.html#BaseRecord">src.pdb.BaseRecord</a></dd>
<dd><a href="__builtin__.html#object">__builtin__.object</a></dd>
</dl>
<hr>
Methods defined here:<br>
<dl><dt><a name="DefinitionAtom-__init__"><strong>__init__</strong></a>(self, name<font color="#909090">=None</font>, x<font color="#909090">=None</font>, y<font color="#909090">=None</font>, z<font color="#909090">=None</font>)</dt><dd><tt>Initialize the class</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>A basic string representation for debugging</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-isBackbone"><strong>isBackbone</strong></a>(self)</dt><dd><tt>Return true if atom name is in backbone, otherwise false<br>
<br>
Returns<br>
state: 1 if true, 0 if false</tt></dd></dl>
<hr>
Methods inherited from <a href="src.structures.html#Atom">src.structures.Atom</a>:<br>
<dl><dt><a name="DefinitionAtom-addBond"><strong>addBond</strong></a>(self, bondedatom)</dt><dd><tt>Add a bond to the list of bonds<br>
<br>
Parameters:<br>
bondedatom: The atom to bond to (<a href="src.structures.html#Atom">Atom</a>)</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get a member of the <a href="src.structures.html#Atom">Atom</a> class<br>
<br>
Parameters<br>
name: The name of the member (string)<br>
Possible Values<br>
type: The type of <a href="src.structures.html#Atom">Atom</a> (either ATOM or HETATM)<br>
serial: <a href="src.structures.html#Atom">Atom</a> serial number<br>
name: <a href="src.structures.html#Atom">Atom</a> name<br>
altLoc: Alternate location<br>
resName: <a href="src.structures.html#Residue">Residue</a> name<br>
chainID: Chain identifier<br>
resSeq: <a href="src.structures.html#Residue">Residue</a> sequence number<br>
iCode: Code for insertion of residues<br>
x: Orthogonal coordinates for X in Angstroms.<br>
y: Orthogonal coordinates for Y in Angstroms.<br>
z: Orthogonal coordinates for Z in Angstroms.<br>
occupancy: Occupancy<br>
tempFactor: Temperature Factor<br>
segID: Segment identifier<br>
element: Element symbol<br>
charge: Charge on the atom<br>
bonds: The bonds associated with the atom<br>
interbonds: The intrabonds associated with the atom<br>
extrabonds: The extrabonds assocaited with the atom<br>
residue: The parent residue of the atom<br>
radius: The radius of the atom<br>
ffcharge: The forcefield charge on the atom<br>
hdonor: Whether the atom is a hydrogen donor<br>
hacceptor: Whether the atom is a hydrogen acceptor<br>
Returns<br>
item: The value of the member</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-getCommonStringRep"><strong>getCommonStringRep</strong></a>(self, chainflag<font color="#909090">=False</font>)</dt><dd><tt>Returns a string of the common column of the new atom type. <br>
Uses the ATOM string output but changes the first field <br>
to either by ATOM or HETATM as necessary.<br>
<br>
This is used to create the output for pqr and pdb files! No touchy!<br>
<br>
Returns<br>
outstr: String with ATOM/HETATM field set appropriately</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-getCoords"><strong>getCoords</strong></a>(self)</dt><dd><tt>Return the x,y,z coordinates of the atom in list form<br>
<br>
Returns<br>
List of the coordinates (list)</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-getPDBString"><strong>getPDBString</strong></a>(self)</dt><dd><tt>Returns a string of the new atom type. Uses the ATOM string<br>
output but changes the first field to either by ATOM or<br>
HETATM as necessary.<br>
<br>
This is for the pdb representation of the atom. The propka30 module <br>
depends on this being correct. No touchy!<br>
<br>
Returns<br>
str: String with ATOM/HETATM field set appropriately</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-getPQRString"><strong>getPQRString</strong></a>(self, chainflag<font color="#909090">=False</font>)</dt><dd><tt>Returns a string of the new atom type. Uses the ATOM string<br>
output but changes the first field to either by ATOM or<br>
HETATM as necessary.<br>
<br>
This is used to create the output for pqr files! No touchy!<br>
<br>
Returns<br>
str: String with ATOM/HETATM field set appropriately</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-hasReference"><strong>hasReference</strong></a>(self)</dt><dd><tt>Determine if the atom object has a reference object or not.<br>
All known atoms should have reference objects.<br>
<br>
Returns<br>
True if atom has a reference object, False otherwise.</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-isHydrogen"><strong>isHydrogen</strong></a>(self)</dt><dd><tt>Is this atom a Hydrogen atom?<br>
<br>
Returns<br>
value: 1 if <a href="src.structures.html#Atom">Atom</a> is a Hydrogen, 0 otherwise</tt></dd></dl>
<dl><dt><a name="DefinitionAtom-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set a member of the <a href="src.structures.html#Atom">Atom</a> class<br>
<br>
Parameters<br>
name: The name of the member (string)<br>
value: The value to set the member to<br>
Possible Values<br>
type: The type of <a href="src.structures.html#Atom">Atom</a> (either ATOM or HETATM)<br>
serial: <a href="src.structures.html#Atom">Atom</a> serial number<br>
name: <a href="src.structures.html#Atom">Atom</a> name<br>
altLoc: Alternate location<br>
resName: <a href="src.structures.html#Residue">Residue</a> name<br>
chainID: Chain identifier<br>
resSeq: <a href="src.structures.html#Residue">Residue</a> sequence number<br>
iCode: Code for insertion of residues<br>
x: Orthogonal coordinates for X in Angstroms.<br>
y: Orthogonal coordinates for Y in Angstroms.<br>
z: Orthogonal coordinates for Z in Angstroms.<br>
occupancy: Occupancy<br>
tempFactor: Temperature Factor<br>
segID: Segment identifier<br>
element: Element symbol<br>
charge: Charge on the atom<br>
residue: The parent residue of the atom<br>
radius: The radius of the atom<br>
ffcharge: The forcefield charge on the atom<br>
hdonor: Whether the atom is a hydrogen donor<br>
hacceptor: Whether the atom is a hydrogen acceptor</tt></dd></dl>
<hr>
Data descriptors inherited from <a href="src.pdb.html#BaseRecord">src.pdb.BaseRecord</a>:<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> <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="DefinitionHandler">class <strong>DefinitionHandler</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="DefinitionHandler-__init__"><strong>__init__</strong></a>(self)</dt></dl>
<dl><dt><a name="DefinitionHandler-characters"><strong>characters</strong></a>(self, text)</dt></dl>
<dl><dt><a name="DefinitionHandler-endElement"><strong>endElement</strong></a>(self, name)</dt></dl>
<dl><dt><a name="DefinitionHandler-startElement"><strong>startElement</strong></a>(self, name, attributes)</dt></dl>
<hr>
Methods inherited from <a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>:<br>
<dl><dt><a name="DefinitionHandler-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="DefinitionHandler-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="DefinitionHandler-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="DefinitionHandler-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="DefinitionHandler-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="DefinitionHandler-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="DefinitionHandler-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="DefinitionHandler-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="DefinitionHandler-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="DefinitionHandler-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="DefinitionResidue">class <strong>DefinitionResidue</strong></a>(<a href="src.structures.html#Residue">src.structures.Residue</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#DefinitionResidue">DefinitionResidue</a> class<br>
<br>
The <a href="#DefinitionResidue">DefinitionResidue</a> class extends the <a href="src.structures.html#Residue">Residue</a> class to allow for a<br>
trimmed down initializing function.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="DefinitionResidue-__init__"><strong>__init__</strong></a>(self)</dt><dd><tt>Initialize the class using a few parameters<br>
<br>
Parameters:<br>
name: The abbreviated amino acid name of the <a href="#DefinitionResidue">DefinitionResidue</a></tt></dd></dl>
<dl><dt><a name="DefinitionResidue-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>A basic string representation for debugging</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-addDihedral"><strong>addDihedral</strong></a>(self, atom)</dt><dd><tt>Add the atom to the list of dihedral bonds<br>
<br>
Parameters:<br>
atom: The atom to be added</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-getNearestBonds"><strong>getNearestBonds</strong></a>(self, atomname)</dt><dd><tt>Parameters<br>
number: The number of bonds to get<br>
Returns<br>
bonds: A list of atomnames that are within three bonds of<br>
the atom and present in residue (list)</tt></dd></dl>
<hr>
Methods inherited from <a href="src.structures.html#Residue">src.structures.Residue</a>:<br>
<dl><dt><a name="DefinitionResidue-addAtom"><strong>addAtom</strong></a>(self, atom)</dt><dd><tt>Add the atom object to the residue.<br>
<br>
Parameters<br>
atom: The object to be added (ATOM)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-addMissing"><strong>addMissing</strong></a>(self, value)</dt><dd><tt>Add the value to the list of missing atoms<br>
<br>
Parameters<br>
value: The name of the missing atom (string)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-createAtom"><strong>createAtom</strong></a>(self, name, newcoords, type)</dt><dd><tt>Add a new atom object to the residue. Uses an atom<br>
currently in the residue to seed the new atom<br>
object, then replaces the coordinates and name accordingly.<br>
<br>
Parameters<br>
name: The name of the new atom (string)<br>
newcoords: The x,y,z coordinates of the new atom (list)<br>
type: The type of atom, ATOM or HETATM</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-get"><strong>get</strong></a>(self, name)</dt><dd><tt>Get a member of the <a href="src.structures.html#Residue">Residue</a> class<br>
<br>
Parameters<br>
name: The name of the member (string)<br>
Possible Values<br>
atoms: The atoms in the residue<br>
name: The name of the residue<br>
chainID: The chainID associated with the residue<br>
resSeq: The sequence number of the residue<br>
icode: The iCode of the residue<br>
SSbonded: 1 if the residue has a SS bond, 0 otherwise<br>
SSbondpartner: The residue of the bond partner<br>
type: The type associated with this residue<br>
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise<br>
isCterm: 1 if the residue is the C-Terminus, 0 otherwise<br>
missing: List of missing atoms of the residue<br>
Returns<br>
item: The value of the member</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-getAtom"><strong>getAtom</strong></a>(self, name)</dt><dd><tt>Retrieve an atom from the mapping<br>
<br>
Parameters<br>
resname: The name of the residue to retrieve (string)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-getAtoms"><strong>getAtoms</strong></a>(self)</dt></dl>
<dl><dt><a name="DefinitionResidue-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get the total charge of the residue. In order to get rid<br>
of floating point rounding error, do the string<br>
transformation.<br>
<br>
Returns:<br>
charge: The charge of the residue (float)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-hasAtom"><strong>hasAtom</strong></a>(self, name)</dt></dl>
<dl><dt><a name="DefinitionResidue-letterCode"><strong>letterCode</strong></a>(self)</dt></dl>
<dl><dt><a name="DefinitionResidue-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get the number of atoms for the residue<br>
<br>
Returns<br>
Number of atoms in the residue (int)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-removeAtom"><strong>removeAtom</strong></a>(self, atomname)</dt><dd><tt>Remove an atom from the residue object.<br>
<br>
Parameters<br>
atomname: The name of the atom to be removed (string)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-renameAtom"><strong>renameAtom</strong></a>(self, oldname, newname)</dt><dd><tt>Rename an atom to a new name<br>
<br>
Parameters<br>
oldname: The old atom name (string)<br>
newname: The new atom name (string)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-renameResidue"><strong>renameResidue</strong></a>(self, name)</dt><dd><tt>Rename a given residue<br>
<br>
Parameters<br>
name: The new name of the residue</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-reorder"><strong>reorder</strong></a>(self)</dt><dd><tt>Reorder the atoms to start with N, CA, C, O if they exist</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-rotateTetrahedral"><strong>rotateTetrahedral</strong></a>(self, atom1, atom2, angle)</dt><dd><tt>Rotate about the atom1-atom2 bond by a given angle<br>
All atoms connected to atom2 will rotate.<br>
<br>
Parameters:<br>
atom1: The first atom of the bond to rotate about (atom)<br>
atom2: The second atom of the bond to rotate about (atom)<br>
angle: The number of degrees to rotate (float)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-set"><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set a member of the <a href="src.structures.html#Residue">Residue</a> class to a specific value <br>
<br>
Parameters<br>
name: The name of the object to set (string)<br>
value: The object to append<br>
Possible Values<br>
atoms: The atoms in the residue<br>
name: The name of the residue<br>
chain: The chainID associated with the residue<br>
resSeq: The sequence number of the residue<br>
icode: The iCode of the residue<br>
SSbonded: 1 if the residue has a SS bond, 0 otherwise<br>
SSbondpartner: The residue of the bond partner<br>
type: The type associated with this residue<br>
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise<br>
isCterm: 1 if the residue is the C-Terminus, 0 otherwise<br>
isDirty: 1 if the residue is not missing atoms,<br>
0 otherwise<br>
Notes<br>
resSeq points to the residue.setResSeq function<br>
Returns<br>
item: The value of the member</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-setChainID"><strong>setChainID</strong></a>(self, value)</dt><dd><tt>Set the chainID field to a certain value</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-setDonorsAndAcceptors"><strong>setDonorsAndAcceptors</strong></a>(self)</dt><dd><tt>Set the donors and acceptors within the residue</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-setResSeq"><strong>setResSeq</strong></a>(self, value)</dt><dd><tt>Set the atom field resSeq to a certain value and<br>
change the residue's information. The icode field is no longer<br>
useful.<br>
<br>
Parameters<br>
value: The new value of resSeq (int)</tt></dd></dl>
<dl><dt><a name="DefinitionResidue-update_terminus_status"><strong>update_terminus_status</strong></a>(self)</dt><dd><tt>Update the isNterms and isCterm flags</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="Patch">class <strong>Patch</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Patch">Patch</a> the definitionResidue class<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Patch-__init__"><strong>__init__</strong></a>(self)</dt><dd><tt>Initialize the <a href="#Patch">Patch</a> object.</tt></dd></dl>
<dl><dt><a name="Patch-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>A basic string representation for debugging</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>AAPATH</strong> = 'dat/AA.xml'<br>
<strong>AAS</strong> = ['ALA', 'ARG', 'ASH', 'ASN', 'ASP', 'CYS', 'CYM', 'GLN', 'GLU', 'GLH', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU', ...]<br>
<strong>BACKBONE</strong> = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']<br>
<strong>BONDED_SS_LIMIT</strong> = 2.5<br>
<strong>BUMP_DIST</strong> = 2.0<br>
<strong>BUMP_HDIST</strong> = 1.5<br>
<strong>BUMP_HEAVY_SIZE</strong> = 1.0<br>
<strong>BUMP_HYDROGEN_SIZE</strong> = 0.5<br>
<strong>CELL_SIZE</strong> = 2<br>
<strong>DIHEDRAL</strong> = 57.2958<br>
<strong>INSTALLDIR</strong> = '/Users/d3y382/pdb2pqr/'<br>
<strong>NAPATH</strong> = 'dat/NA.xml'<br>
<strong>NAS</strong> = ['A', 'A5', 'A3', 'C', 'C5', 'C3', 'G', 'G5', 'G3', 'T', 'T5', 'T3', 'U', 'U5', 'U3', 'RA', 'RG', 'RC', 'RU', 'DA', ...]<br>
<strong>PATCHPATH</strong> = 'dat/PATCHES.xml'<br>
<strong>PEPTIDE_DIST</strong> = 1.7<br>
<strong>REPAIR_LIMIT</strong> = 10<br>
<strong>SMALL</strong> = 1e-07<br>
<strong>TMPDIR</strong> = 'tmp/'<br>
<strong>__author__</strong> = 'Jens Erik Nielsen, Todd Dolinsky, Yong Huang'<br>
<strong>__date__</strong> = '15 May 2008'<br>
<strong>lineParsers</strong> = {'ANISOU': <class 'src.pdb.ANISOU'>, 'ATOM': <class 'src.pdb.ATOM'>, 'AUTHOR': <class 'src.pdb.AUTHOR'>, 'CAVEAT': <class 'src.pdb.CAVEAT'>, 'CISPEP': <class 'src.pdb.CISPEP'>, 'COMPND': <class 'src.pdb.COMPND'>, 'CONECT': <class 'src.pdb.CONECT'>, 'CRYST1': <class 'src.pdb.CRYST1'>, 'DBREF': <class 'src.pdb.DBREF'>, 'END': <class 'src.pdb.END'>, ...}</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%">Jens Erik Nielsen, Todd Dolinsky, Yong Huang</td></tr></table>
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