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<a href="Bio-module.html">Package Bio</a> ::
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Module DSSP'
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module DSSP'</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.DSSP%27-pysrc.html">source code</a></span></p>
<p>Use the DSSP program to calculate secondary structure and
accessibility. You need to have a working version of DSSP (and a license,
free for academic use) in order to use this. For DSSP, see <a
href="http://www.cmbi.kun.nl/gv/dssp/"
target="_top">http://www.cmbi.kun.nl/gv/dssp/</a>.</p>
<p>The DSSP codes for secondary structure used here are:</p>
<ul>
<li>
H Alpha helix (4-12)
</li>
<li>
B Isolated beta-bridge residue
</li>
<li>
E Strand
</li>
<li>
G 3-10 helix
</li>
<li>
I pi helix
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<li>
T Turn
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<li>
S Bend
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- None
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<a href="Bio.PDB.DSSP%27.DSSP-class.html" class="summary-name">DSSP</a><br />
Run DSSP on a pdb file, and provide a handle to the DSSP secondary
structure and accessibility.
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<span class="summary-type">{}</span>
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<td><span class="summary-sig"><a href="Bio.PDB.DSSP%27-module.html#dssp_dict_from_pdb_file" class="summary-sig-name">dssp_dict_from_pdb_file</a>(<span class="summary-sig-arg">in_file</span>,
<span class="summary-sig-arg">DSSP</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">dssp</code><code class="variable-quote">'</code></span>)</span><br />
Create a DSSP dictionary from a PDB file.</td>
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<span class="codelink"><a href="Bio.PDB.DSSP%27-pysrc.html#dssp_dict_from_pdb_file">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.DSSP%27-module.html#make_dssp_dict" class="summary-sig-name">make_dssp_dict</a>(<span class="summary-sig-arg">filename</span>)</span><br />
Return a DSSP dictionary that maps (chainid, resid) to aa, ss and
accessibility, from a DSSP file.</td>
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<span class="codelink"><a href="Bio.PDB.DSSP%27-pysrc.html#make_dssp_dict">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PDB.DSSP%27-module.html#ss_to_index" class="summary-sig-name">ss_to_index</a>(<span class="summary-sig-arg">ss</span>)</span><br />
Secondary structure symbol to index.</td>
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<span class="codelink"><a href="Bio.PDB.DSSP%27-pysrc.html#ss_to_index">source code</a></span>
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<span class="summary-type"> </span>
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<a href="Bio.PDB.DSSP%27-module.html#MAX_ACC" class="summary-name">MAX_ACC</a> = <code title="{'ALA': 106.0,
'ARG': 248.0,
'ASN': 157.0,
'ASP': 163.0,
'CYS': 135.0,
'GLN': 198.0,
'GLU': 194.0,
'GLY': 84.0,
..."><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">: </code>106.0<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ARG</code><code class="variable-quote">'</code><code class="variable-op">: </code>248.0<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ASN</code><code class="variable-quote">'</code><code class="variable-op">: </code>157.0<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">: </code>16<code class="variable-ellipsis">...</code></code>
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<span class="summary-type"> </span>
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<a name="PDBException"></a><span class="summary-name">PDBException</span> = <code title="'PDBException'"><code class="variable-quote">'</code><code class="variable-string">PDBException</code><code class="variable-quote">'</code></code>
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<a name="_dssp_cys"></a><span class="summary-name">_dssp_cys</span> = <code title="re.compile(r'[a-z]')">re.compile(r'<code class="re-group">[</code>a<code class="re-op">-</code>z<code class="re-group">]</code>')</code>
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<span class="summary-type"> </span>
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<a href="Bio.PDB.DSSP%27-module.html#standard_aa_names" class="summary-name">standard_aa_names</a> = <code title="['ALA',
'CYS',
'ASP',
'GLU',
'PHE',
'GLY',
'HIS',
'ILE',
..."><code class="variable-group">[</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">CYS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PHE</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">,</code><code class="variable-ellipsis">...</code></code>
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<a href="Bio.PDB.DSSP%27-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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<a name="dssp_dict_from_pdb_file"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">dssp_dict_from_pdb_file</span>(<span class="sig-arg">in_file</span>,
<span class="sig-arg">DSSP</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">dssp</code><code class="variable-quote">'</code></span>)</span>
</h3>
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><span class="codelink"><a href="Bio.PDB.DSSP%27-pysrc.html#dssp_dict_from_pdb_file">source code</a></span>
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<p>Create a DSSP dictionary from a PDB file.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>dssp_dict=dssp_dict_from_pdb_file(<span class="py-string">"1fat.pdb"</span>)
<span class="py-prompt">>>> </span>aa, ss, acc=dssp_dict[(<span class="py-string">'A'</span>, 1)]</pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>in_file</code></strong> (string) - pdb file</li>
<li><strong class="pname"><code>DSSP</code></strong> (string) - DSSP executable (argument to os.system)</li>
</ul></dd>
<dt>Returns: {}</dt>
<dd>a dictionary that maps (chainid, resid) to amino acid type,
secondary structure code and accessibility.</dd>
</dl>
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<a name="make_dssp_dict"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">make_dssp_dict</span>(<span class="sig-arg">filename</span>)</span>
</h3>
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><span class="codelink"><a href="Bio.PDB.DSSP%27-pysrc.html#make_dssp_dict">source code</a></span>
</td>
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<p>Return a DSSP dictionary that maps (chainid, resid) to aa, ss and
accessibility, from a DSSP file.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>filename</code></strong> (string) - the DSSP output file</li>
</ul></dd>
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">ss_to_index</span>(<span class="sig-arg">ss</span>)</span>
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><span class="codelink"><a href="Bio.PDB.DSSP%27-pysrc.html#ss_to_index">source code</a></span>
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<p>Secondary structure symbol to index. H=0 E=1 C=2</p>
<dl class="fields">
</dl>
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<h3 class="epydoc">MAX_ACC</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">ALA</code><code class="variable-quote">'</code><code class="variable-op">: </code>106.0<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ARG</code><code class="variable-quote">'</code><code class="variable-op">: </code>248.0<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ASN</code><code class="variable-quote">'</code><code class="variable-op">: </code>157.0<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">: </code>163.0<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">CYS</code><code class="variable-quote">'</code><code class="variable-op">: </code>135.0<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLN</code><code class="variable-quote">'</code><code class="variable-op">: </code>198.0<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">: </code>194.0<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">: </code>84.0<code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
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<h3 class="epydoc">standard_aa_names</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">[</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">CYS</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ASP</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLU</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">PHE</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">GLY</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">HIS</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">ILE</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
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<a name="to_one_letter_code"></a>
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<h3 class="epydoc">to_one_letter_code</h3>
<dl class="fields">
</dl>
<dl class="fields">
<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>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
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