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Module PDB
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module PDB</h1><p class="nomargin-top"></p>
<p>Parsing and writing of Protein Data Bank (PDB) files</p>
<p>This module provides classes that represent PDB (Protein Data Bank)
files and configurations contained in PDB files. It provides access to
PDB files on two levels: low-level (line by line) and high-level (chains,
residues, and atoms).</p>
<p>Caution: The PDB file format has been heavily abused, and it is
probably impossible to write code that can deal with all variants
correctly. This modules tries to read the widest possible range of PDB
files, but gives priority to a correct interpretation of the PDB format
as defined by the Brookhaven National Laboratory.</p>
<p>A special problem are atom names. The PDB file format specifies that
the first two letters contain the right-justified chemical element name.
A later modification allowed the initial space in hydrogen names to be
replaced by a digit. Many programs ignore all this and treat the name as
an arbitrary left-justified four-character name. This makes it difficult
to extract the chemical element accurately; most programs write the
'"CA"' for C_alpha in such a way that it actually stands for a
calcium atom. For this reason a special element field has been added
later, but only few files use it. In the absence of an element field, the
code in this module attempts to guess the element using all information
available.</p>
<p>The low-level routines in this module do not try to deal with the atom
name problem; they return and expect four-character atom names including
spaces in the correct positions. The high-level routines use atom names
without leading or trailing spaces, but provide and use the element field
whenever possible. For output, they use the element field to place the
atom name correctly, and for input, they construct the element field
content from the atom name if no explicit element field is found in the
file.</p>
<p>Except where indicated, numerical values use the same units and
conventions as specified in the PDB format description.</p>
<p>Example:</p>
<pre class="literalblock">
>>>conf = Structure('example.pdb')
>>>print conf
>>>for residue in conf.residues:
>>> for atom in residue:
>>> print atom
</pre>
<!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></a>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Scientific.IO.PDB.AminoAcidResidue-class.html" class="summary-name">AminoAcidResidue</a><br />
Amino acid residue in a PDB file
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.Atom-class.html" class="summary-name">Atom</a><br />
Atom in a PDB structure
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.Chain-class.html" class="summary-name">Chain</a><br />
Chain of PDB residues
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Scientific.IO.PDB.Group-class.html" class="summary-name">Group</a><br />
Atom group (residue or molecule) in a PDB file
</td>
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.HetAtom-class.html" class="summary-name">HetAtom</a><br />
HetAtom in a PDB structure
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.Molecule-class.html" class="summary-name">Molecule</a><br />
Molecule in a PDB file
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.NucleotideChain-class.html" class="summary-name">NucleotideChain</a><br />
Nucleotide chain in a PDB file
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.NucleotideResidue-class.html" class="summary-name">NucleotideResidue</a><br />
Nucleotide residue in a PDB file
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Scientific.IO.PDB.PDBFile-class.html" class="summary-name">PDBFile</a><br />
<a name="index-PDB"></a><i class="indexterm">PDB</i> file with
access at the record level
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.PeptideChain-class.html" class="summary-name">PeptideChain</a><br />
Peptide chain in a PDB file
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.Residue-class.html" class="summary-name">Residue</a>
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.ResidueNumber-class.html" class="summary-name">ResidueNumber</a><br />
PDB residue number
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<span class="summary-type"> </span>
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<a href="Scientific.IO.PDB.Structure-class.html" class="summary-name">Structure</a><br />
A high-level representation of the contents of a PDB file
</td>
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<!-- ==================== FUNCTIONS ==================== -->
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<td><span class="summary-sig"><a href="Scientific.IO.PDB-module.html#defineAminoAcidResidue" class="summary-sig-name">defineAminoAcidResidue</a>(<span class="summary-sig-arg">symbol</span>)</span><br />
Make the parser recognize a particular residue type as an amino acid
residue</td>
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</td>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB-module.html#defineNucleicAcidResidue" class="summary-sig-name">defineNucleicAcidResidue</a>(<span class="summary-sig-arg">symbol</span>)</span><br />
Make the parser recognize a particular residue type as an nucleic
acid residue</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
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<!-- ==================== VARIABLES ==================== -->
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Scientific.IO.PDB-module.html#amino_acids" class="summary-name">amino_acids</a> = <code title="['ALA',
'ARG',
'ASN',
'ASP',
'CYS',
'CYX',
'GLN',
'GLU',
..."><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">ARG</code><code class="variable-quote">'</code><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><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">CYS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">CYX</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GLN</code><code class="variable-quote">'</code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Scientific.IO.PDB-module.html#nucleic_acids" class="summary-name">nucleic_acids</a> = <code title="['A',
'C',
'G',
'I',
'T',
'U',
'+A',
'+C',
..."><code class="variable-group">[</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">C</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">G</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">I</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">T</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">U</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">+C</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">+G</code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
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cellspacing="0" width="100%" bgcolor="white">
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<span class="table-header">Function Details</span></td>
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<a name="defineAminoAcidResidue"></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">defineAminoAcidResidue</span>(<span class="sig-arg">symbol</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Make the parser recognize a particular residue type as an amino acid
residue</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>symbol</code></strong> (<code>str</code>) - the three-letter code for an amino acid</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="defineNucleicAcidResidue"></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">defineNucleicAcidResidue</span>(<span class="sig-arg">symbol</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Make the parser recognize a particular residue type as an nucleic acid
residue</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>symbol</code></strong> (<code>str</code>) - the one-letter code for a nucleic acid</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<span class="table-header">Variables Details</span></td>
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</table>
<a name="amino_acids"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">amino_acids</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">ARG</code><code class="variable-quote">'</code><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>
<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">CYS</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">CYX</code><code class="variable-quote">'</code><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>
<code class="variable-quote">'</code><code class="variable-string">GLU</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>
</div>
<a name="nucleic_acids"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">nucleic_acids</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">A</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">C</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">G</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">I</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">T</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">U</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">+C</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>
</div>
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