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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PDB-module.html">Package PDB</a> ::
<a href="Bio.PDB.PDBParser%27-module.html">Module PDBParser'</a> ::
Class PDBParser
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class PDBParser</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.PDBParser%27-pysrc.html#PDBParser">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">PDBParser</strong>
</pre>
<hr />
<p>Parse a PDB file and return a Structure object.</p>
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<td><span class="summary-sig"><a href="Bio.PDB.PDBParser%27.PDBParser-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">PERMISSIVE</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">get_header</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">structure_builder</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">QUIET</span>=<span class="summary-sig-default">False</span>)</span><br />
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object.</td>
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<td><span class="summary-sig"><a name="_get_header"></a><span class="summary-sig-name">_get_header</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">header_coords_trailer</span>)</span><br />
Get the header of the PDB file, return the rest.</td>
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<span class="codelink"><a href="Bio.PDB.PDBParser%27-pysrc.html#PDBParser._get_header">source code</a></span>
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<td><span class="summary-sig"><a name="_handle_PDB_exception"></a><span class="summary-sig-name">_handle_PDB_exception</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">message</span>,
<span class="summary-sig-arg">line_counter</span>)</span><br />
This method catches an exception that occurs in the StructureBuilder
object (if PERMISSIVE), or raises it again, this time adding the PDB
line number to the error message.</td>
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<td><span class="summary-sig"><a name="_parse"></a><span class="summary-sig-name">_parse</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">header_coords_trailer</span>)</span><br />
Parse the PDB file.</td>
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<td><span class="summary-sig"><a name="_parse_coordinates"></a><span class="summary-sig-name">_parse_coordinates</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">coords_trailer</span>)</span><br />
Parse the atomic data in the PDB file.</td>
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<td><span class="summary-sig"><a name="get_header"></a><span class="summary-sig-name">get_header</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the header.</td>
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<td><span class="summary-sig"><a href="Bio.PDB.PDBParser%27.PDBParser-class.html#get_structure" class="summary-sig-name">get_structure</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>,
<span class="summary-sig-arg">file</span>)</span><br />
Return the structure.</td>
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<td><span class="summary-sig"><a name="get_trailer"></a><span class="summary-sig-name">get_trailer</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the trailer.</td>
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<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>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
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<!-- ==================== PROPERTIES ==================== -->
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">PERMISSIVE</span>=<span class="sig-default">True</span>,
<span class="sig-arg">get_header</span>=<span class="sig-default">False</span>,
<span class="sig-arg">structure_builder</span>=<span class="sig-default">None</span>,
<span class="sig-arg">QUIET</span>=<span class="sig-default">False</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBParser%27-pysrc.html#PDBParser.__init__">source code</a></span>
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<p>The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated by the
PDBParser object itself, but if the user provides his own
StructureBuilder object, the latter is used instead.</p>
<p>Arguments:</p>
<p>o PERMISSIVE - Evaluated as a Boolean. If false, exceptions in
constructing the SMCRA data structure are fatal. If true (DEFAULT), the
exceptions are caught, but some residues or atoms will be missing. THESE
EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!.</p>
<p>o structure_builder - an optional user implemented StructureBuilder
class.</p>
<p>o QUIET - Evaluated as a Boolean. If true, warnings issued in
constructing the SMCRA data will be supressed. If false (DEFAULT), they
will be shown. These warnings might be indicative of problems in the PDB
file!</p>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
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<a name="get_structure"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_structure</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>,
<span class="sig-arg">file</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBParser%27-pysrc.html#PDBParser.get_structure">source code</a></span>
</td>
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<p>Return the structure.</p>
<p>Arguments: o id - string, the id that will be used for the structure o
file - name of the PDB file OR an open filehandle</p>
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