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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SCOP-module.html">Package SCOP</a> ::
Module Raf
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<h1 class="epydoc">Module Raf</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html">source code</a></span></p>
<pre class="literalblock">
ASTRAL RAF (Rapid Access Format) Sequence Maps.
The ASTRAL RAF Sequence Maps record the relationship between the PDB SEQRES
records (representing the sequence of the molecule used in an experiment) to
the ATOM records (representing the atoms experimentally observed).
This data is derived from the Protein Data Bank CIF files. Known errors in the
CIF files are corrected manually, with the original PDB file serving as the
final arbiter in case of discrepancies.
Residues are referenced by residue ID. This consists of a the PDB residue
sequence number (upto 4 digits) and an optional PDB insertion code (an
ascii alphabetic character, a-z, A-Z). e.g. "1", "10A", "1010b", "-1"
See "ASTRAL RAF Sequence Maps":http://astral.stanford.edu/raf.html
to_one_letter_code -- A mapping from the 3-letter amino acid codes found
in PDB files to 1-letter codes. The 3-letter codes
include chemically modified residues.
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<span class="summary-type"> </span>
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<a href="Bio.SCOP.Raf.SeqMapIndex-class.html" class="summary-name">SeqMapIndex</a><br />
An RAF file index.
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<span class="summary-type"> </span>
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<a href="Bio.SCOP.Raf.SeqMap-class.html" class="summary-name">SeqMap</a><br />
An ASTRAL RAF (Rapid Access Format) Sequence Map.
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<a href="Bio.SCOP.Raf.Res-class.html" class="summary-name">Res</a><br />
A single residue mapping from a RAF record.
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<a href="Bio.SCOP.Raf.Iterator-class.html" class="summary-name">Iterator</a><br />
Iterates over a RAF file.
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<td><span class="summary-sig"><a href="Bio.SCOP.Raf-module.html#normalize_letters" class="summary-sig-name">normalize_letters</a>(<span class="summary-sig-arg">one_letter_code</span>)</span><br />
Convert RAF one-letter amino acid codes into IUPAC standard codes.</td>
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<span class="codelink"><a href="Bio.SCOP.Raf-pysrc.html#normalize_letters">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SCOP.Raf-module.html#parse" class="summary-sig-name">parse</a>(<span class="summary-sig-arg">handle</span>)</span><br />
Iterates over a RAF file, returning a SeqMap object for each line
in the file.</td>
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<span class="summary-type"> </span>
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<a href="Bio.SCOP.Raf-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>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">normalize_letters</span>(<span class="sig-arg">one_letter_code</span>)</span>
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<p>Convert RAF one-letter amino acid codes into IUPAC standard codes.</p>
<p>Letters are uppercased, and "." ("Unknown") is
converted to "X".</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">parse</span>(<span class="sig-arg">handle</span>)</span>
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<pre class="literalblock">
Iterates over a RAF file, returning a SeqMap object for each line
in the file.
Arguments:
handle -- file-like object.
</pre>
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<h3 class="epydoc">to_one_letter_code</h3>
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<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>
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