<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Bio.PDB.Atom.Atom</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
<a href="Bio.PDB.Atom-module.html">Module Atom</a> ::
Class Atom
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.PDB.Atom.Atom-class.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Atom</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom">source code</a></span></p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Instance Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-InstanceMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">coord</span>,
<span class="summary-sig-arg">bfactor</span>,
<span class="summary-sig-arg">occupancy</span>,
<span class="summary-sig-arg">altloc</span>,
<span class="summary-sig-arg">fullname</span>,
<span class="summary-sig-arg">serial_number</span>)</span><br />
Atom object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.__init__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="__repr__"></a><span class="summary-sig-name">__repr__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Print Atom object as <Atom atom_name>.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.__repr__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#__sub__" class="summary-sig-name">__sub__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Calculate distance between two atoms.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.__sub__">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="set_serial_number"></a><span class="summary-sig-name">set_serial_number</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">n</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_serial_number">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="set_bfactor"></a><span class="summary-sig-name">set_bfactor</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">bfactor</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_bfactor">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="set_coord"></a><span class="summary-sig-name">set_coord</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">coord</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_coord">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="set_altloc"></a><span class="summary-sig-name">set_altloc</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">altloc</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_altloc">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="set_occupancy"></a><span class="summary-sig-name">set_occupancy</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">occupancy</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_occupancy">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#set_sigatm" class="summary-sig-name">set_sigatm</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sigatm_array</span>)</span><br />
Set standard deviation of atomic parameters.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_sigatm">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#set_siguij" class="summary-sig-name">set_siguij</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">siguij_array</span>)</span><br />
Set standard deviations of anisotropic temperature factors.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_siguij">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#set_anisou" class="summary-sig-name">set_anisou</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">anisou_array</span>)</span><br />
Set anisotropic B factor.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_anisou">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#flag_disorder" class="summary-sig-name">flag_disorder</a>(<span class="summary-sig-arg">self</span>)</span><br />
Set the disordered flag to 1.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.flag_disorder">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="is_disordered"></a><span class="summary-sig-name">is_disordered</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the disordered flag (1 if disordered, 0 otherwise).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.is_disordered">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#set_parent" class="summary-sig-name">set_parent</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">parent</span>)</span><br />
Set the parent residue.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_parent">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="detach_parent"></a><span class="summary-sig-name">detach_parent</span>(<span class="summary-sig-arg">self</span>)</span><br />
Remove reference to parent.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.detach_parent">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_sigatm"></a><span class="summary-sig-name">get_sigatm</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return standard deviation of atomic parameters.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_sigatm">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_siguij"></a><span class="summary-sig-name">get_siguij</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return standard deviations of anisotropic temperature factors.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_siguij">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_anisou"></a><span class="summary-sig-name">get_anisou</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return anisotropic B factor.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_anisou">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_parent"></a><span class="summary-sig-name">get_parent</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return parent residue.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_parent">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_serial_number"></a><span class="summary-sig-name">get_serial_number</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_serial_number">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_name"></a><span class="summary-sig-name">get_name</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return atom name.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_name">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_id"></a><span class="summary-sig-name">get_id</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the id of the atom (which is its atom name).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_id">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#get_full_id" class="summary-sig-name">get_full_id</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the full id of the atom.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_full_id">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_coord"></a><span class="summary-sig-name">get_coord</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return atomic coordinates.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_coord">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_bfactor"></a><span class="summary-sig-name">get_bfactor</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return B factor.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_bfactor">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_occupancy"></a><span class="summary-sig-name">get_occupancy</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return occupancy.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_occupancy">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_fullname"></a><span class="summary-sig-name">get_fullname</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the atom name, including leading and trailing spaces.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_fullname">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_altloc"></a><span class="summary-sig-name">get_altloc</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return alternative location specifier.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_altloc">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="get_level"></a><span class="summary-sig-name">get_level</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_level">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#transform" class="summary-sig-name">transform</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">rot</span>,
<span class="summary-sig-arg">tran</span>)</span><br />
Apply rotation and translation to the atomic coordinates.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.transform">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">Vector</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.Atom.Atom-class.html#get_vector" class="summary-sig-name">get_vector</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return coordinates as Vector.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_vector">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">coord</span>,
<span class="sig-arg">bfactor</span>,
<span class="sig-arg">occupancy</span>,
<span class="sig-arg">altloc</span>,
<span class="sig-arg">fullname</span>,
<span class="sig-arg">serial_number</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.__init__">source code</a></span>
</td>
</tr></table>
<p>Atom object.</p>
<p>The Atom object stores atom name (both with and without spaces),
coordinates, B factor, occupancy, alternative location specifier and
(optionally) anisotropic B factor and standard deviations of B factor and
positions.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>name</code></strong> (string) - atom name (eg. "CA"). Note that spaces are normally
stripped.</li>
<li><strong class="pname"><code>coord</code></strong> (Numeric array (Float0, size 3)) - atomic coordinates (x,y,z)</li>
<li><strong class="pname"><code>bfactor</code></strong> (number) - isotropic B factor</li>
<li><strong class="pname"><code>occupancy</code></strong> (number) - occupancy (0.0-1.0)</li>
<li><strong class="pname"><code>altloc</code></strong> (string) - alternative location specifier for disordered atoms</li>
<li><strong class="pname"><code>fullname</code></strong> (string) - full atom name, including spaces, e.g. " CA ". Normally
these spaces are stripped from the atom name.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="__sub__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__sub__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">other</span>)</span>
<br /><em class="fname">(Subtraction operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.__sub__">source code</a></span>
</td>
</tr></table>
<p>Calculate distance between two atoms.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>distance=atom1-atom2</pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>other</code></strong> (<a href="Bio.PDB.Atom.Atom-class.html" class="link">Atom</a>) - the other atom</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="set_sigatm"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">set_sigatm</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">sigatm_array</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_sigatm">source code</a></span>
</td>
</tr></table>
<p>Set standard deviation of atomic parameters.</p>
<p>The standard deviation of atomic parameters consists of 3 positional,
1 B factor and 1 occupancy standard deviation.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>sigatm_array</code></strong> (Numeric array (length 5)) - standard deviations of atomic parameters.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="set_siguij"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">set_siguij</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">siguij_array</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_siguij">source code</a></span>
</td>
</tr></table>
<p>Set standard deviations of anisotropic temperature factors.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>siguij_array</code></strong> (Numeric array (length 6)) - standard deviations of anisotropic temperature factors.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="set_anisou"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">set_anisou</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">anisou_array</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_anisou">source code</a></span>
</td>
</tr></table>
<p>Set anisotropic B factor.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>anisou_array</code></strong> (Numeric array (length 6)) - anisotropic B factor.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="flag_disorder"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">flag_disorder</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.flag_disorder">source code</a></span>
</td>
</tr></table>
<p>Set the disordered flag to 1.</p>
<p>The disordered flag indicates whether the atom is disordered or
not.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="set_parent"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">set_parent</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">parent</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.set_parent">source code</a></span>
</td>
</tr></table>
<p>Set the parent residue.</p>
<p>Arguments: o parent - Residue object</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_full_id"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">get_full_id</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_full_id">source code</a></span>
</td>
</tr></table>
<p>Return the full id of the atom.</p>
<p>The full id of an atom is the tuple (structure id, model id, chain id,
residue id, atom name, altloc).</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="transform"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">transform</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">rot</span>,
<span class="sig-arg">tran</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.transform">source code</a></span>
</td>
</tr></table>
<p>Apply rotation and translation to the atomic coordinates.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>rotation=rotmat(pi, Vector(1,0,0))
<span class="py-prompt">>>> </span>translation=array((0,0,1), <span class="py-string">'f'</span>)
<span class="py-prompt">>>> </span>atom.transform(rotation, translation)</pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>rot</code></strong> (3x3 Numeric array) - A right multiplying rotation matrix</li>
<li><strong class="pname"><code>tran</code></strong> (size 3 Numeric array) - the translation vector</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="get_vector"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">get_vector</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.Atom-pysrc.html#Atom.get_vector">source code</a></span>
</td>
</tr></table>
<p>Return coordinates as Vector.</p>
<dl class="fields">
<dt>Returns: Vector</dt>
<dd>coordinates as 3D vector</dd>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:36 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
