<?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.ResidueDepth'</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> :: Module ResidueDepth' </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.ResidueDepth%27-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module ResidueDepth'</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html">source code</a></span></p> <pre class="literalblock"> Calculation of residue depth (using Michel Sanner's MSMS program for the surface calculation). Residue depth is the average distance of the atoms of a residue from the solvent accessible surface. Residue Depth: rd=ResidueDepth(model, pdb_file) print rd[(chain_id, res_id)] Direct MSMS interface: Typical use: surface=get_surface("1FAT.pdb") Surface is a Numeric array with all the surface vertices. Distance to surface: dist=min_dist(coord, surface) where coord is the coord of an atom within the volume bound by the surface (ie. atom depth). To calculate the residue depth (average atom depth of the atoms in a residue): rd=residue_depth(residue, surface) </pre> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></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">Classes</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Classes" 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"> <a href="Bio.PDB.ResidueDepth%27.ResidueDepth-class.html" class="summary-name">ResidueDepth</a><br /> Calculate residue and CA depth for all residues. </td> </tr> </table> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></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">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" class="privatelink" onclick="toggle_private();" >hide private</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="_read_vertex_array"></a><span class="summary-sig-name">_read_vertex_array</span>(<span class="summary-sig-arg">filename</span>)</span><br /> Read the vertex list into a Numeric array.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html#_read_vertex_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="ca_depth"></a><span class="summary-sig-name">ca_depth</span>(<span class="summary-sig-arg">residue</span>, <span class="summary-sig-arg">surface</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html#ca_depth">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.ResidueDepth%27-module.html#get_surface" class="summary-sig-name">get_surface</a>(<span class="summary-sig-arg">pdb_file</span>, <span class="summary-sig-arg">PDB_TO_XYZR</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">pdb_to_xyzr</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">MSMS</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">msms</code><code class="variable-quote">'</code></span>)</span><br /> Return a Numeric array that represents the vertex list of the molecular surface.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html#get_surface">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="min_dist"></a><span class="summary-sig-name">min_dist</span>(<span class="summary-sig-arg">coord</span>, <span class="summary-sig-arg">surface</span>)</span><br /> Return minimum distance between coord and surface.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html#min_dist">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.ResidueDepth%27-module.html#residue_depth" class="summary-sig-name">residue_depth</a>(<span class="summary-sig-arg">residue</span>, <span class="summary-sig-arg">surface</span>)</span><br /> Return average distance to surface for all atoms in a residue, ie.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html#residue_depth">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== VARIABLES ==================== --> <a name="section-Variables"></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">Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Variables" 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"> <a name="sqrt"></a><span class="summary-name">sqrt</span> = <code title="<ufunc 'sqrt'>"><ufunc 'sqrt'></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.PDB.ResidueDepth%27-module.html#standard_aa_names" class="summary-name">standard_aa_names</a> = <code title="['ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY', 'HIS', 'ILE', ..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">CYS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PHE</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">,</code><code class="variable-ellipsis">...</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.PDB.ResidueDepth%27-module.html#to_one_letter_code" class="summary-name">to_one_letter_code</a> = <code title="{'2AS': 'D', '3AH': 'H', '5HP': 'E', 'ACL': 'R', 'AGM': 'R', 'AIB': 'A', 'ALA': 'A', 'ALM': 'A', ..."><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">2AS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">3AH</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">H</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">5HP</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ACL</code><code class="variable-ellipsis">...</code></code> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></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">Function Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-FunctionDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="get_surface"></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_surface</span>(<span class="sig-arg">pdb_file</span>, <span class="sig-arg">PDB_TO_XYZR</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">pdb_to_xyzr</code><code class="variable-quote">'</code></span>, <span class="sig-arg">MSMS</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">msms</code><code class="variable-quote">'</code></span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html#get_surface">source code</a></span> </td> </tr></table> <p>Return a Numeric array that represents the vertex list of the molecular surface.</p> <p>PDB_TO_XYZR --- pdb_to_xyzr executable (arg. to os.system) MSMS --- msms executable (arg. to os.system)</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="residue_depth"></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">residue_depth</span>(<span class="sig-arg">residue</span>, <span class="sig-arg">surface</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PDB.ResidueDepth%27-pysrc.html#residue_depth">source code</a></span> </td> </tr></table> <p>Return average distance to surface for all atoms in a residue, ie. the residue depth.</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== VARIABLES DETAILS ==================== --> <a name="section-VariablesDetails"></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">Variables Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-VariablesDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="standard_aa_names"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">standard_aa_names</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">CYS</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">PHE</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">HIS</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">ILE</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-ellipsis">...</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="to_one_letter_code"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">to_one_letter_code</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">2AS</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">3AH</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">H</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">5HP</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">ACL</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">R</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">AGM</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">R</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">AIB</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">ALM</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-ellipsis">...</code> </pre></td></tr></table> </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> 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