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  <div class="section" id="module-isambard.ampal.pdb_parser">
<span id="isambard-ampal-pdb-parser-module"></span><h1>isambard.ampal.pdb_parser module<a class="headerlink" href="#module-isambard.ampal.pdb_parser" title="Permalink to this headline">¶</a></h1>
<p>Contains code for parsing PDB files.</p>
<dl class="class">
<dt id="isambard.ampal.pdb_parser.PDBColFormat">
<em class="property">class </em><code class="descname">PDBColFormat</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PDBColFormat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PDBColFormat" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">sqlalchemy.ext.declarative.api.Base</span></code></p>
<p>Database handler for <cite>ampal_database.py</cite>.</p>
<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PDBColFormat.atom_col">
<code class="descname">atom_col</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PDBColFormat.atom_col" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PDBColFormat.atom_name">
<code class="descname">atom_name</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PDBColFormat.atom_name" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PDBColFormat.id">
<code class="descname">id</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PDBColFormat.id" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

</dd></dl>

<dl class="class">
<dt id="isambard.ampal.pdb_parser.PdbParser">
<em class="property">class </em><code class="descname">PdbParser</code><span class="sig-paren">(</span><em>pdb</em>, <em>path=True</em>, <em>pdb_id=''</em>, <em>ignore_end=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/2/library/functions.html#object" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">object</span></code></a></p>
<p>Parses a PDB file and produces and AMPAL Assembly.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>pdb</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) &#8211; Either a path to a PDB file or a string containing PDB
format structural data.</li>
<li><strong>path</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a><em>, </em><em>optional</em>) &#8211; If <cite>true</cite>, flags <cite>pdb</cite> as a path and not a PDB string.</li>
<li><strong>pdb_id</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a><em>, </em><em>optional</em>) &#8211; Identifier for the <cite>Assembly</cite>.</li>
<li><strong>ignore_end</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a><em>, </em><em>optional</em>) &#8211; If <cite>false</cite>, parsing of the file will stop when an &#8220;END&#8221;
record is encountered.</li>
</ul>
</td>
</tr>
</tbody>
</table>
<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PdbParser.proc_functions">
<code class="descname">proc_functions</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.proc_functions" title="Permalink to this definition">¶</a></dt>
<dd><p><em>dict</em> &#8211; Keys are PDB labels i.e. &#8220;ATOM&#8221; or &#8220;END&#8221;, values are the
function that processes that specific line.</p>
</dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PdbParser.id">
<code class="descname">id</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.id" title="Permalink to this definition">¶</a></dt>
<dd><p><em>str</em> &#8211; Identifier for the <cite>Assembly</cite>.</p>
</dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PdbParser.pdb_lines">
<code class="descname">pdb_lines</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.pdb_lines" title="Permalink to this definition">¶</a></dt>
<dd><p><em>[str]</em> &#8211; Input PDB split into line.</p>
</dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PdbParser.new_labels">
<code class="descname">new_labels</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.new_labels" title="Permalink to this definition">¶</a></dt>
<dd><p><em>bool</em> &#8211; Indicates if new atom or residue labels have been found while
parsing the PDB file.</p>
</dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PdbParser.state">
<code class="descname">state</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.state" title="Permalink to this definition">¶</a></dt>
<dd><p><em>int</em> &#8211; Current state being appended to. This is used on multi-state
files like NMR structures.</p>
</dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PdbParser.pdb_parse_tree">
<code class="descname">pdb_parse_tree</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.pdb_parse_tree" title="Permalink to this definition">¶</a></dt>
<dd><p><em>dict</em> &#8211; This dictionary represents the parse tree of the PDB file.
Each line of the structure is broken down into a key, the
entry label, and a value, the data.</p>
</dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PdbParser.current_line">
<code class="descname">current_line</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.current_line" title="Permalink to this definition">¶</a></dt>
<dd><p><em>int</em> &#8211; The line that is currently being parsed.</p>
</dd></dl>

<dl class="attribute">
<dt id="isambard.ampal.pdb_parser.PdbParser.ignore_end">
<code class="descname">ignore_end</code><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.ignore_end" title="Permalink to this definition">¶</a></dt>
<dd><p><em>bool, optional</em> &#8211; If <cite>false</cite>, parsing of the file will stop when an &#8220;END&#8221;
record is encountered.</p>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.change_state">
<code class="descname">change_state</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.change_state"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.change_state" title="Permalink to this definition">¶</a></dt>
<dd><p>Increments current state and adds a new dict to the parse tree.</p>
</dd></dl>

<dl class="staticmethod">
<dt id="isambard.ampal.pdb_parser.PdbParser.check_for_non_canonical">
<em class="property">static </em><code class="descname">check_for_non_canonical</code><span class="sig-paren">(</span><em>residue</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.check_for_non_canonical"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.check_for_non_canonical" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks to see if the residue is non-canonical.</p>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.end">
<code class="descname">end</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.end"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.end" title="Permalink to this definition">¶</a></dt>
<dd><p>Processes an &#8220;END&#8221; record.</p>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.gen_states">
<code class="descname">gen_states</code><span class="sig-paren">(</span><em>monomer_data</em>, <em>parent</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.gen_states"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.gen_states" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates the <cite>states</cite> dictionary for a <cite>Monomer</cite>.</p>
<dl class="docutils">
<dt>monomer_data <span class="classifier-delimiter">:</span> <span class="classifier">list</span></dt>
<dd>A list of atom data parsed from the input PDB.</dd>
<dt>parent <span class="classifier-delimiter">:</span> <span class="classifier">ampal.Monomer</span></dt>
<dd><cite>Monomer</cite> used to assign <cite>ampal_parent</cite> on created
<cite>Atoms</cite>.</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.make_ampal">
<code class="descname">make_ampal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.make_ampal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.make_ampal" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates an AMPAL object from the parse tree.</p>
<p class="rubric">Notes</p>
<p>Will create an <cite>Assembly</cite> if there is a single state in the
parese tree or an <cite>AmpalContainer</cite> if there is more than one.</p>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.parse_pdb_file">
<code class="descname">parse_pdb_file</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.parse_pdb_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.parse_pdb_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Runs the PDB parser.</p>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.proc_atom">
<code class="descname">proc_atom</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.proc_atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.proc_atom" title="Permalink to this definition">¶</a></dt>
<dd><p>Processes an &#8220;ATOM&#8221; or &#8220;HETATM&#8221; record.</p>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.proc_chain">
<code class="descname">proc_chain</code><span class="sig-paren">(</span><em>chain_info</em>, <em>parent</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.proc_chain"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.proc_chain" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts a chain into a <cite>Polymer</cite> type object.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>chain_info</strong> (<em>(</em><a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#set" title="(in Python v2.7)"><em>set</em></a><em>, </em><em>OrderedDict</em><em>)</em>) &#8211; Contains a set of chain labels and atom records.</li>
<li><strong>parent</strong> (<em>ampal.Assembly</em>) &#8211; <cite>Assembly</cite> used to assign <cite>ampal_parent</cite> on created
<cite>Polymer</cite>.</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><ul class="first last simple">
<li><code class="xref py py-exc docutils literal"><span class="pre">ValueError</span></code> &#8211; Raised if multiple or unknown atom types found
within the same chain.</li>
<li><code class="xref py py-exc docutils literal"><span class="pre">AttributeError</span></code> &#8211; Raised if unknown <cite>Monomer</cite> type encountered.</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.proc_line_coordinate">
<code class="descname">proc_line_coordinate</code><span class="sig-paren">(</span><em>line</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.proc_line_coordinate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.proc_line_coordinate" title="Permalink to this definition">¶</a></dt>
<dd><p>Extracts data from columns in ATOM/HETATM record.</p>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.proc_monomer">
<code class="descname">proc_monomer</code><span class="sig-paren">(</span><em>monomer_info</em>, <em>parent</em>, <em>mon_cls=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.proc_monomer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.proc_monomer" title="Permalink to this definition">¶</a></dt>
<dd><p>Processes a records into a <cite>Monomer</cite>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>monomer_info</strong> (<em>(</em><a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#set" title="(in Python v2.7)"><em>set</em></a><em>, </em><em>OrderedDict</em><em>)</em>) &#8211; Labels and data for a monomer.</li>
<li><strong>parent</strong> (<em>ampal.Polymer</em>) &#8211; <cite>Polymer</cite> used to assign <cite>ampal_parent</cite> on created
<cite>Monomer</cite>.</li>
<li><strong>mon_cls</strong> (<cite>Monomer class or subclass</cite>, optional) &#8211; A <cite>Monomer</cite> class can be defined explicitly.</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="isambard.ampal.pdb_parser.PdbParser.proc_state">
<code class="descname">proc_state</code><span class="sig-paren">(</span><em>state_data</em>, <em>state_id</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#PdbParser.proc_state"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.PdbParser.proc_state" title="Permalink to this definition">¶</a></dt>
<dd><p>Processes a state into an <cite>Assembly</cite>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>state_data</strong> (<a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#dict" title="(in Python v2.7)"><em>dict</em></a>) &#8211; Contains information about the state, including all
the per line structural data.</li>
<li><strong>state_id</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) &#8211; ID given to <cite>Assembly</cite> that represents the state.</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

<dl class="function">
<dt id="isambard.ampal.pdb_parser.convert_pdb_to_ampal">
<code class="descname">convert_pdb_to_ampal</code><span class="sig-paren">(</span><em>pdb</em>, <em>path=True</em>, <em>pdb_id=''</em>, <em>ignore_end=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/isambard/ampal/pdb_parser.html#convert_pdb_to_ampal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#isambard.ampal.pdb_parser.convert_pdb_to_ampal" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts a PDB file into an AMPAL object.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>pdb</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) &#8211; Either a path to a PDB file or a string containing PDB
format structural data.</li>
<li><strong>path</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a><em>, </em><em>optional</em>) &#8211; If <cite>true</cite>, flags <cite>pdb</cite> as a path and not a PDB string.</li>
<li><strong>pdb_id</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a><em>, </em><em>optional</em>) &#8211; Identifier for the <cite>Assembly</cite>.</li>
<li><strong>ignore_end</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a><em>, </em><em>optional</em>) &#8211; If <cite>false</cite>, parsing of the file will stop when an &#8220;END&#8221;
record is encountered.</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>ampal</strong> &#8211; AMPAL object that contains the structural information from
the PDB file provided. If the PDB file has a single state
then an <cite>Assembly</cite> will be returned, otherwise an
<cite>AmpalContainer</cite> will be returned.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">ampal.Assembly or ampal.AmpalContainer</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

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