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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.AbstractPropertyMap-module.html">Module AbstractPropertyMap</a> ::
Class AbstractPropertyMap
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class AbstractPropertyMap</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">AbstractPropertyMap</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.PDB.HSExposure.ExposureCN-class.html">HSExposure.ExposureCN</a></li><li class="private">, <a href="Bio.PDB.HSExposure._AbstractHSExposure-class.html" onclick="show_private();">HSExposure._AbstractHSExposure</a></li><li>, <a href="Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap-class.html">AbstractAtomPropertyMap</a></li><li>, <a href="Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap-class.html">AbstractResiduePropertyMap</a></li><li>, <a href="Bio.PDB.ResidueDepth%27.ResidueDepth-class.html">ResidueDepth'.ResidueDepth</a></li> </ul>
</dd></dl>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">property_dict</span>,
<span class="summary-sig-arg">property_keys</span>,
<span class="summary-sig-arg">property_list</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
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<span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="_translate_id"></a><span class="summary-sig-name">_translate_id</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">entity_id</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap._translate_id">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.AbstractPropertyMap.AbstractPropertyMap-class.html#__contains__" class="summary-sig-name">__contains__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
True if the mapping has a property for this residue.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__contains__">source code</a></span>
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<span class="summary-type">anything (can be a tuple)</span>
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<td><span class="summary-sig"><a href="Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">key</span>)</span><br />
Return property for a residue.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__getitem__">source code</a></span>
</td>
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<span class="summary-type">int</span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return number of residues for which the property is available.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__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.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key" class="summary-sig-name">has_key</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">id</span>)</span><br />
True if the mapping has a property for this residue.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.has_key">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">[(chain_id, res_id), (chain_id, res_id),...]</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys" class="summary-sig-name">keys</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the list of residues.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.keys">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over the (entity, property) list.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__iter__">source code</a></span>
</td>
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<td colspan="2" class="summary">
<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>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
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<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
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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>
</p>
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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">property_dict</span>,
<span class="sig-arg">property_keys</span>,
<span class="sig-arg">property_list</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__init__">source code</a></span>
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<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__contains__"></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">__contains__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>)</span>
<br /><em class="fname">(In operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__contains__">source code</a></span>
</td>
</tr></table>
<p>True if the mapping has a property for this residue.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">if</span> (chain_id, res_id) <span class="py-keyword">in</span> apmap:
<span class="py-more">... </span> res, prop = apmap[(chain_id, res_id)]</pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>chain_id</code></strong> (char) - chain id</li>
<li><strong class="pname"><code>res_id</code></strong> (char) - residue id</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="__getitem__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">key</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__getitem__">source code</a></span>
</td>
</tr></table>
<p>Return property for a residue.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>chain_id</code></strong> (char) - chain id</li>
<li><strong class="pname"><code>res_id</code></strong> (int or (char, int, char)) - residue id</li>
</ul></dd>
<dt>Returns: anything (can be a tuple)</dt>
<dd>some residue property</dd>
</dl>
</td></tr></table>
</div>
<a name="__len__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<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.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__len__">source code</a></span>
</td>
</tr></table>
<p>Return number of residues for which the property is available.</p>
<dl class="fields">
<dt>Returns: int</dt>
<dd>number of residues</dd>
</dl>
</td></tr></table>
</div>
<a name="has_key"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">has_key</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">id</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.has_key">source code</a></span>
</td>
</tr></table>
<p>True if the mapping has a property for this residue.</p>
<p>(Obsolete; use "id in mapping" instead.)</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">if</span> apmap.has_key((chain_id, res_id)):
<span class="py-more">... </span> res, prop = apmap[(chain_id, res_id)]</pre>
<p>Is equivalent to:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">if</span> (chain_id, res_id) <span class="py-keyword">in</span> apmap:
<span class="py-more">... </span> res, prop = apmap[(chain_id, res_id)]</pre>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>chain_id</code></strong> (char) - chain id</li>
<li><strong class="pname"><code>res_id</code></strong> (char) - residue id</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="keys"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">keys</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.keys">source code</a></span>
</td>
</tr></table>
<p>Return the list of residues.</p>
<dl class="fields">
<dt>Returns: [(chain_id, res_id), (chain_id, res_id),...]</dt>
<dd>list of residues for which the property was calculated</dd>
</dl>
</td></tr></table>
</div>
<a name="__iter__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__iter__</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.AbstractPropertyMap-pysrc.html#AbstractPropertyMap.__iter__">source code</a></span>
</td>
</tr></table>
<p>Iterate over the (entity, property) list. Handy alternative to the
dictionary-like access.</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">for</span> (res, property) <span class="py-keyword">in</span> iter(map):
<span class="py-more">... </span> <span class="py-keyword">print</span> res, property</pre>
<dl class="fields">
<dt>Returns:</dt>
<dd>iterator</dd>
</dl>
</td></tr></table>
</div>
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