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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module src.protein</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>.protein</strong></big></big> (13 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/protein.py">/Users/d3y382/workspaces/apbs-pdb2pqr/pdb2pqr/src/protein.py</a></font></td></tr></table>
<p><tt>Routines for PDB2PQR<br>
<br>
This module contains the protein object used in PDB2PQR and associated<br>
methods<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>
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* 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>
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND <br>
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----------------------------</tt></p>
<p>
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<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>
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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.protein.html#Protein">Protein</a>
</font></dt></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="Protein">class <strong>Protein</strong></a></font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Protein">Protein</a> class<br>
<br>
The protein class represents the parsed PDB, and provides a<br>
hierarchy of information - each <a href="#Protein">Protein</a> contains a list of Chain<br>
objects as provided in the PDB file. Each Chain then contains its<br>
associated list of Residue objects, and each Residue contains a list<br>
of Atom objects, completing the hierarchy.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Protein-__init__"><strong>__init__</strong></a>(self, pdblist, definition)</dt><dd><tt>Initialize using parsed PDB file<br>
<br>
Parameters<br>
pdblist: List of Classes of PDB lines as created</tt></dd></dl>
<dl><dt><a name="Protein-createHTMLTypeMap"><strong>createHTMLTypeMap</strong></a>(self, definition, outfilename)</dt><dd><tt>Create an HTML typemap file at the desired location. If a<br>
type cannot be found for an atom a blank is listed.<br>
<br>
Parameters<br>
definition: The definition objects.<br>
outfilename: The name of the file to write (string)</tt></dd></dl>
<dl><dt><a name="Protein-createResidue"><strong>createResidue</strong></a>(self, residue, resname)</dt><dd><tt>Create a residue object. If the resname is a known residue<br>
type, try to make that specific object, otherwise just make<br>
a standard residue object.<br>
<br>
Parameters<br>
residue: A list of atoms (list)<br>
resname: The name of the residue (string)<br>
<br>
Returns:<br>
residue: The residue object (Residue)</tt></dd></dl>
<dl><dt><a name="Protein-getAtoms"><strong>getAtoms</strong></a>(self)</dt><dd><tt>Return all Atom objects in list format<br>
<br>
Returns<br>
atomlist: List of Atom objects in the protein (list)</tt></dd></dl>
<dl><dt><a name="Protein-getChains"><strong>getChains</strong></a>(self)</dt><dd><tt>Get the chains object<br>
<br>
Returns<br>
chains: The list of chains in the protein (chain)</tt></dd></dl>
<dl><dt><a name="Protein-getCharge"><strong>getCharge</strong></a>(self)</dt><dd><tt>Get the total charge on the protein<br>
NOTE: Since the misslist is used to identify incorrect<br>
charge assignments, this routine does not list the<br>
3 and 5 termini of nucleic acid chains as having<br>
non-integer charge even though they are (correctly)<br>
non-integer.<br>
Returns:<br>
misslist: List of residues with non-integer<br>
charges (list)<br>
charge: The total charge on the protein (float)</tt></dd></dl>
<dl><dt><a name="Protein-getResidues"><strong>getResidues</strong></a>(self)</dt><dd><tt>Return the list of residues in the entire protein</tt></dd></dl>
<dl><dt><a name="Protein-getSummary"><strong>getSummary</strong></a>(self)</dt></dl>
<dl><dt><a name="Protein-numAtoms"><strong>numAtoms</strong></a>(self)</dt><dd><tt>Get the number of atoms for the entire protein(including<br>
multiple chains)</tt></dd></dl>
<dl><dt><a name="Protein-numResidues"><strong>numResidues</strong></a>(self)</dt><dd><tt>Get the number of residues for the entire protein (including<br>
multiple chains)<br>
<br>
Returns<br>
count: Number of residues in the protein (int)</tt></dd></dl>
<dl><dt><a name="Protein-printAtoms"><strong>printAtoms</strong></a>(self, atomlist, chainflag<font color="#909090">=False</font>, pdbfile<font color="#909090">=False</font>)</dt><dd><tt>Get the text for the entire protein<br>
Parameters<br>
atomlist: The list of atoms to include (list)<br>
chainflag: Flag whether to print chainid or not -<br>
Defaults to False<br>
Returns<br>
text: The list of (stringed) atoms (list)</tt></dd></dl>
<dl><dt><a name="Protein-reSerialize"><strong>reSerialize</strong></a>(self)</dt><dd><tt>Generate new serial numbers for atoms in the protein</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>BACKBONE</strong> = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN']<br>
<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> = '13 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%">Todd Dolinsky, Yong Huang</td></tr></table>
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