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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SCOP-module.html">Package SCOP</a> ::
<a href="Bio.SCOP.Raf-module.html">Module Raf</a> ::
Class SeqMap
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SeqMap</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap">source code</a></span></p>
<p>An ASTRAL RAF (Rapid Access Format) Sequence Map.</p>
<p>This is a list like object; You can find the location of particular
residues with index(), slice this SeqMap into fragments, and glue
fragments back together with extend().</p>
<p>pdbid -- The PDB 4 character ID</p>
<p>pdb_datestamp -- From the PDB file</p>
<p>version -- The RAF format version. e.g. 0.01</p>
<p>flags -- RAF flags. (See release notes for more information.)</p>
<p>res -- A list of Res objects, one for each residue in this sequence
map</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 class="summary-sig-arg">line</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="_process"></a><span class="summary-sig-name">_process</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">line</span>)</span><br />
Parses a RAF record into a SeqMap object.</td>
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<td><span class="summary-sig"><a name="index"></a><span class="summary-sig-name">index</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">resid</span>,
<span class="summary-sig-arg">chainid</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">_</code><code class="variable-quote">'</code></span>)</span></td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.index">source code</a></span>
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<td><span class="summary-sig"><a name="__getslice__"></a><span class="summary-sig-name">__getslice__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">i</span>,
<span class="summary-sig-arg">j</span>)</span></td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.__getslice__">source code</a></span>
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<td><span class="summary-sig"><a name="append"></a><span class="summary-sig-name">append</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">res</span>)</span><br />
Append another Res object onto the list of residue mappings.</td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.append">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SCOP.Raf.SeqMap-class.html#extend" class="summary-sig-name">extend</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Append another SeqMap onto the end of self.</td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.extend">source code</a></span>
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<td><span class="summary-sig"><a name="__iadd__"></a><span class="summary-sig-name">__iadd__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span></td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.__iadd__">source code</a></span>
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<td><span class="summary-sig"><a name="__add__"></a><span class="summary-sig-name">__add__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span></td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.__add__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SCOP.Raf.SeqMap-class.html#getAtoms" class="summary-sig-name">getAtoms</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">pdb_handle</span>,
<span class="summary-sig-arg">out_handle</span>)</span><br />
Extract all relevant ATOM and HETATOM records from a PDB file.</td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.getAtoms">source code</a></span>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">extend</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">other</span>)</span>
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<p>Append another SeqMap onto the end of self.</p>
<p>Both SeqMaps must have the same PDB ID, PDB datestamp and RAF version.
The RAF flags are erased if they are inconsistent. This may happen when
fragments are taken from different chains.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">getAtoms</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">pdb_handle</span>,
<span class="sig-arg">out_handle</span>)</span>
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</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#SeqMap.getAtoms">source code</a></span>
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<p>Extract all relevant ATOM and HETATOM records from a PDB file.</p>
<p>The PDB file is scanned for ATOM and HETATOM records. If the chain ID,
residue ID (seqNum and iCode), and residue type match a residue in this
sequence map, then the record is echoed to the output handle.</p>
<p>This is typically used to find the coordinates of a domain, or other
residue subset.</p>
<p>pdb_handle -- A handle to the relevant PDB file.</p>
<p>out_handle -- All output is written to this file like object.</p>
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