<?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.Vector'.Vector</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.Vector%27-module.html">Module Vector'</a> :: Class Vector </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.Vector%27.Vector-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class Vector</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector">source code</a></span></p> <pre class="base-tree"> object --+ | <strong class="uidshort">Vector</strong> </pre> <hr /> <p>3D vector</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 name="__add__"></a><span class="summary-sig-name">__add__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">other</span>)</span><br /> Return Vector+other Vector or scalar</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__add__">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="__div__"></a><span class="summary-sig-name">__div__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">x</span>)</span><br /> Return Vector(coords/a)</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__div__">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="__getitem__"></a><span class="summary-sig-name">__getitem__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">i</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__getitem__">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.Vector%27.Vector-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">x</span>, <span class="summary-sig-arg">y</span>=<span class="summary-sig-default">None</span>, <span class="summary-sig-arg">z</span>=<span class="summary-sig-default">None</span>)</span><br /> x.__init__(...) initializes x; see help(type(x)) for signature</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__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="__mul__"></a><span class="summary-sig-name">__mul__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">other</span>)</span><br /> Return Vector.Vector (dot product)</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__mul__">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="__neg__"></a><span class="summary-sig-name">__neg__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return Vector(-x, -y, -z)</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__neg__">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="__pow__"></a><span class="summary-sig-name">__pow__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">other</span>)</span><br /> Return VectorxVector (cross product) or Vectorxscalar</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__pow__">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.Vector%27.Vector-class.html#__repr__" class="summary-sig-name">__repr__</a>(<span class="summary-sig-arg">self</span>)</span><br /> repr(x)</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__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 name="__setitem__"></a><span class="summary-sig-name">__setitem__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">i</span>, <span class="summary-sig-arg">value</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__setitem__">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="__sub__"></a><span class="summary-sig-name">__sub__</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">other</span>)</span><br /> Return Vector-other Vector or scalar</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__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="angle"></a><span class="summary-sig-name">angle</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">other</span>)</span><br /> Return angle between two vectors</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.angle">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="copy"></a><span class="summary-sig-name">copy</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return a deep copy of the Vector</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.copy">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_array"></a><span class="summary-sig-name">get_array</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return (a copy of) the array of coordinates</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.get_array">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="left_multiply"></a><span class="summary-sig-name">left_multiply</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">matrix</span>)</span><br /> Return Vector=Matrix x Vector</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.left_multiply">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="norm"></a><span class="summary-sig-name">norm</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return vector norm</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.norm">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="normalize"></a><span class="summary-sig-name">normalize</span>(<span class="summary-sig-arg">self</span>)</span><br /> Normalize the Vector</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.normalize">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="normalized"></a><span class="summary-sig-name">normalized</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return a normalized copy of the Vector</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.normalized">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="normsq"></a><span class="summary-sig-name">normsq</span>(<span class="summary-sig-arg">self</span>)</span><br /> Return square of vector norm</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.normsq">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="right_multiply"></a><span class="summary-sig-name">right_multiply</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">matrix</span>)</span><br /> Return Vector=Vector x Matrix</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.right_multiply">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>: <code>__delattr__</code>, <code>__format__</code>, <code>__getattribute__</code>, <code>__hash__</code>, <code>__new__</code>, <code>__reduce__</code>, <code>__reduce_ex__</code>, <code>__setattr__</code>, <code>__sizeof__</code>, <code>__str__</code>, <code>__subclasshook__</code> </p> </td> </tr> </table> <!-- ==================== PROPERTIES ==================== --> <a name="section-Properties"></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">Properties</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Properties" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>: <code>__class__</code> </p> </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">x</span>, <span class="sig-arg">y</span>=<span class="sig-default">None</span>, <span class="sig-arg">z</span>=<span class="sig-default">None</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__init__">source code</a></span> </td> </tr></table> <p>x.__init__(...) initializes x; see help(type(x)) for signature</p> <dl class="fields"> <dt>Overrides: object.__init__ <dd><em class="note">(inherited documentation)</em></dd> </dt> </dl> </td></tr></table> </div> <a name="__repr__"></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">__repr__</span>(<span class="sig-arg">self</span>)</span> <br /><em class="fname">(Representation operator)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.Vector%27-pysrc.html#Vector.__repr__">source code</a></span> </td> </tr></table> <p>repr(x)</p> <dl class="fields"> <dt>Overrides: object.__repr__ <dd><em class="note">(inherited documentation)</em></dd> </dt> </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 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