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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.FragmentMapper%27-module.html">Module FragmentMapper'</a> ::
Class Fragment
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Fragment</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Fragment</strong>
</pre>
<hr />
<p>Represent a polypeptide C-alpha fragment.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.FragmentMapper%27.Fragment-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">length</span>,
<span class="summary-sig-arg">fid</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.FragmentMapper%27-pysrc.html#Fragment.__init__">source code</a></span>
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<span class="summary-type">int</span>
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<td><span class="summary-sig"><a href="Bio.PDB.FragmentMapper%27.Fragment-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
length of fragment</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.__len__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.FragmentMapper%27.Fragment-class.html#__repr__" class="summary-sig-name">__repr__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns <Fragment length=L id=ID> where L=length of fragment
and ID the identifier (rank in the library).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.__repr__">source code</a></span>
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<span class="summary-type">float</span>
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<td><span class="summary-sig"><a href="Bio.PDB.FragmentMapper%27.Fragment-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 />
Return rmsd between two fragments.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.__sub__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.FragmentMapper%27.Fragment-class.html#add_residue" class="summary-sig-name">add_residue</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">resname</span>,
<span class="summary-sig-arg">ca_coord</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.add_residue">source code</a></span>
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<span class="summary-type">Numeric (Nx3) array</span>
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<td><span class="summary-sig"><a href="Bio.PDB.FragmentMapper%27.Fragment-class.html#get_coords" class="summary-sig-name">get_coords</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
the CA coords in the fragment</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.get_coords">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">int</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.PDB.FragmentMapper%27.Fragment-class.html#get_id" class="summary-sig-name">get_id</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
id for the fragment</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.get_id">source code</a></span>
</td>
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<span class="summary-type">[string, string,...]</span>
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<td><span class="summary-sig"><a href="Bio.PDB.FragmentMapper%27.Fragment-class.html#get_resname_list" class="summary-sig-name">get_resname_list</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns:
the residue names</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.get_resname_list">source code</a></span>
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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>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
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<!-- ==================== PROPERTIES ==================== -->
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<td align="left"><span class="table-header">Properties</span></td>
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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">length</span>,
<span class="sig-arg">fid</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.__init__">source code</a></span>
</td>
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<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>length</code></strong> (int) - length of the fragment</li>
<li><strong class="pname"><code>fid</code></strong> (int) - id for the fragment</li>
</ul></dd>
<dt>Overrides:
object.__init__
</dt>
</dl>
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<a name="__len__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.__len__">source code</a></span>
</td>
</tr></table>
<dl class="fields">
<dt>Returns: int</dt>
<dd>length of fragment</dd>
</dl>
</td></tr></table>
</div>
<a name="__repr__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<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.FragmentMapper%27-pysrc.html#Fragment.__repr__">source code</a></span>
</td>
</tr></table>
<p>Returns <Fragment length=L id=ID> where L=length of fragment and
ID the identifier (rank in the library).</p>
<dl class="fields">
<dt>Overrides:
object.__repr__
</dt>
</dl>
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<a name="__sub__"></a>
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<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.FragmentMapper%27-pysrc.html#Fragment.__sub__">source code</a></span>
</td>
</tr></table>
<p>Return rmsd between two fragments.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>rmsd=fragment1-fragment2</pre>
<dl class="fields">
<dt>Returns: float</dt>
<dd>rmsd between fragments</dd>
</dl>
</td></tr></table>
</div>
<a name="add_residue"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">add_residue</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">resname</span>,
<span class="sig-arg">ca_coord</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.add_residue">source code</a></span>
</td>
</tr></table>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>resname</code></strong> (string) - residue name (eg. GLY).</li>
<li><strong class="pname"><code>ca_coord</code></strong> (Numeric array with length 3) - the c-alpha coorinates of the residues</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="get_coords"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_coords</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.get_coords">source code</a></span>
</td>
</tr></table>
<dl class="fields">
<dt>Returns: Numeric (Nx3) array</dt>
<dd>the CA coords in the fragment</dd>
</dl>
</td></tr></table>
</div>
<a name="get_id"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_id</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.get_id">source code</a></span>
</td>
</tr></table>
<dl class="fields">
<dt>Returns: int</dt>
<dd>id for the fragment</dd>
</dl>
</td></tr></table>
</div>
<a name="get_resname_list"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_resname_list</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.FragmentMapper%27-pysrc.html#Fragment.get_resname_list">source code</a></span>
</td>
</tr></table>
<dl class="fields">
<dt>Returns: [string, string,...]</dt>
<dd>the residue names</dd>
</dl>
</td></tr></table>
</div>
<br />
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