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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.StructureBuilder-module.html">Module StructureBuilder</a> ::
Class StructureBuilder
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class StructureBuilder</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder">source code</a></span></p>
<p>Deals with contructing the Structure object. The StructureBuilder
class is used by the PDBParser classes to translate a file to a Structure
object.</p>
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<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>
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<td><span class="summary-sig"><a name="_is_completely_disordered"></a><span class="summary-sig-name">_is_completely_disordered</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">residue</span>)</span><br />
Return 1 if all atoms in the residue have a non blanc altloc.</td>
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder._is_completely_disordered">source code</a></span>
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<td><span class="summary-sig"><a name="set_header"></a><span class="summary-sig-name">set_header</span>(<span class="summary-sig-arg">self</span>,
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.set_header">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#set_line_counter" class="summary-sig-name">set_line_counter</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">line_counter</span>)</span><br />
The line counter keeps track of the line in the PDB file that is
being parsed.</td>
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<td><span class="summary-sig"><a href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_structure" class="summary-sig-name">init_structure</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">structure_id</span>)</span><br />
Initiate a new Structure object with given id.</td>
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_structure">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_model" class="summary-sig-name">init_model</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">model_id</span>)</span><br />
Initiate a new Model object with given id.</td>
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_model">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_chain" class="summary-sig-name">init_chain</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">chain_id</span>)</span><br />
Initiate a new Chain object with given id.</td>
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_chain">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_seg" class="summary-sig-name">init_seg</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">segid</span>)</span><br />
Flag a change in segid.</td>
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_seg">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_residue" class="summary-sig-name">init_residue</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">resname</span>,
<span class="summary-sig-arg">field</span>,
<span class="summary-sig-arg">resseq</span>,
<span class="summary-sig-arg">icode</span>)</span><br />
Initiate a new Residue object.</td>
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_residue">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.StructureBuilder.StructureBuilder-class.html#init_atom" class="summary-sig-name">init_atom</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">coord</span>,
<span class="summary-sig-arg">b_factor</span>,
<span class="summary-sig-arg">occupancy</span>,
<span class="summary-sig-arg">altloc</span>,
<span class="summary-sig-arg">fullname</span>,
<span class="summary-sig-arg">serial_number</span>=<span class="summary-sig-default">None</span>)</span><br />
Initiate a new Atom object.</td>
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_atom">source code</a></span>
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<td><span class="summary-sig"><a name="set_anisou"></a><span class="summary-sig-name">set_anisou</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">anisou_array</span>)</span><br />
Set anisotropic B factor of current Atom.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.set_anisou">source code</a></span>
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<td><span class="summary-sig"><a name="set_siguij"></a><span class="summary-sig-name">set_siguij</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">siguij_array</span>)</span><br />
Set standard deviation of anisotropic B factor of current Atom.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.set_siguij">source code</a></span>
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<td><span class="summary-sig"><a name="set_sigatm"></a><span class="summary-sig-name">set_sigatm</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sigatm_array</span>)</span><br />
Set standard deviation of atom position of current Atom.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.set_sigatm">source code</a></span>
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<td><span class="summary-sig"><a name="get_structure"></a><span class="summary-sig-name">get_structure</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return the structure.</td>
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<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.get_structure">source code</a></span>
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<td><span class="summary-sig"><a name="set_symmetry"></a><span class="summary-sig-name">set_symmetry</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">spacegroup</span>,
<span class="summary-sig-arg">cell</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.set_symmetry">source code</a></span>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">set_line_counter</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">line_counter</span>)</span>
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<p>The line counter keeps track of the line in the PDB file that is being
parsed.</p>
<p>Arguments: o line_counter - int</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">init_structure</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">structure_id</span>)</span>
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><span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_structure">source code</a></span>
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<p>Initiate a new Structure object with given id.</p>
<p>Arguments: o id - string</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">init_model</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">model_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_model">source code</a></span>
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<p>Initiate a new Model object with given id.</p>
<p>Arguments: o id - int</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">init_chain</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">chain_id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_chain">source code</a></span>
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<p>Initiate a new Chain object with given id.</p>
<p>Arguments: o chain_id - string</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">init_seg</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">segid</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_seg">source code</a></span>
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<p>Flag a change in segid.</p>
<p>Arguments: o segid - string</p>
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</dl>
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<a name="init_residue"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">init_residue</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">resname</span>,
<span class="sig-arg">field</span>,
<span class="sig-arg">resseq</span>,
<span class="sig-arg">icode</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_residue">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blanc.
o resseq - int, sequence identifier
o icode - string, insertion code
</pre>
<dl class="fields">
</dl>
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<a name="init_atom"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">init_atom</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">coord</span>,
<span class="sig-arg">b_factor</span>,
<span class="sig-arg">occupancy</span>,
<span class="sig-arg">altloc</span>,
<span class="sig-arg">fullname</span>,
<span class="sig-arg">serial_number</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.StructureBuilder-pysrc.html#StructureBuilder.init_atom">source code</a></span>
</td>
</tr></table>
<p>Initiate a new Atom object.</p>
<p>Arguments: o name - string, atom name, e.g. CA, spaces should be
stripped o coord - Numeric array (Float0, size 3), atomic coordinates o
b_factor - float, B factor o occupancy - float o altloc - string,
alternative location specifier o fullname - string, atom name including
spaces, e.g. " CA "</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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