<?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.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer</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.SVDSuperimposer-module.html">Package SVDSuperimposer</a> :: <a href="Bio.SVDSuperimposer.SVDSuperimposer%27-module.html">Module SVDSuperimposer'</a> :: Class SVDSuperimposer </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.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class SVDSuperimposer</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer">source code</a></span></p> <p>SVDSuperimposer finds the best rotation and translation to put two point sets on top of each other (minimizing the RMSD). This is eg. useful to superimpose crystal structures.</p> <p>SVD stands for Singular Value Decomposition, which is used to calculate the superposition.</p> <p>Reference:</p> <p>Matrix computations, 2nd ed. Golub, G. & Van Loan, CF., The Johns Hopkins University Press, Baltimore, 1989</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="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <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="_clear"></a><span class="summary-sig-name">_clear</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer._clear">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <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="_rms"></a><span class="summary-sig-name">_rms</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">coords1</span>, <span class="summary-sig-arg">coords2</span>)</span><br /> Return rms deviations between coords1 and coords2.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer._rms">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_init_rms"></a><span class="summary-sig-name">get_init_rms</span>(<span class="summary-sig-arg">self</span>)</span><br /> Root mean square deviation of untransformed coordinates.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer.get_init_rms">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_rms"></a><span class="summary-sig-name">get_rms</span>(<span class="summary-sig-arg">self</span>)</span><br /> Root mean square deviation of superimposed coordinates.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer.get_rms">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_rotran"></a><span class="summary-sig-name">get_rotran</span>(<span class="summary-sig-arg">self</span>)</span><br /> Right multiplying rotation matrix and translation.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer.get_rotran">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_transformed"></a><span class="summary-sig-name">get_transformed</span>(<span class="summary-sig-arg">self</span>)</span><br /> Get the transformed coordinate set.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer.get_transformed">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="run"></a><span class="summary-sig-name">run</span>(<span class="summary-sig-arg">self</span>)</span><br /> Superimpose the coordinate sets.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer.run">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.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#set" class="summary-sig-name">set</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">reference_coords</span>, <span class="summary-sig-arg">coords</span>)</span><br /> Set the coordinates to be superimposed.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer.set">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="set"></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</span>(<span class="sig-arg">self</span>, <span class="sig-arg">reference_coords</span>, <span class="sig-arg">coords</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-pysrc.html#SVDSuperimposer.set">source code</a></span> </td> </tr></table> <p>Set the coordinates to be superimposed. coords will be put on top of reference_coords.</p> <p>o reference_coords: an NxDIM array o coords: an NxDIM array</p> <p>DIM is the dimension of the points, N is the number of points to be superimposed.</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" 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