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<a href="Scientific-module.html">Package Scientific</a> ::
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Class PDBFile
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class PDBFile</h1><p class="nomargin-top"></p>
<p><a name="index-PDB"></a><i class="indexterm">PDB</i> file with access
at the record level</p>
<p>The low-level file access is handled by the module <a
href="Scientific.IO.TextFile-module.html"
class="link">Scientific.IO.TextFile</a>, therefore compressed files and
URLs (for reading) can be used as well.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
<a name="section-InstanceMethods"></a>
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<td><span class="summary-sig"><a name="__del__"></a><span class="summary-sig-name">__del__</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.PDBFile-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">file_or_filename</span>,
<span class="summary-sig-arg">mode</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">r</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">subformat</span>=<span class="summary-sig-default">None</span>)</span></td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.PDBFile-class.html#close" class="summary-sig-name">close</a>(<span class="summary-sig-arg">self</span>)</span><br />
Close the file.</td>
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</td>
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</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.PDBFile-class.html#nextChain" class="summary-sig-name">nextChain</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">chain_id</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">segment_id</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span><br />
Signal the beginning of a new chain.</td>
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</td>
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</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.PDBFile-class.html#nextResidue" class="summary-sig-name">nextResidue</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">number</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">terminus</span>=<span class="summary-sig-default">None</span>)</span><br />
Signal the beginning of a new residue, starting with the next call to
<a href="Scientific.IO.PDB.PDBFile-class.html#writeAtom"
class="link">writeAtom</a>.</td>
<td align="right" valign="top">
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"><code>tuple</code></span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.PDBFile-class.html#readLine" class="summary-sig-name">readLine</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the contents of the next non-blank line (= record) The return
value is a tuple whose first element (a string) contains the record
type.</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="terminateChain"></a><span class="summary-sig-name">terminateChain</span>(<span class="summary-sig-arg">self</span>)</span><br />
Signal the end of a chain.</td>
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</td>
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</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.PDBFile-class.html#writeAtom" class="summary-sig-name">writeAtom</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">position</span>,
<span class="summary-sig-arg">occupancy</span>=<span class="summary-sig-default">0.0</span>,
<span class="summary-sig-arg">temperature_factor</span>=<span class="summary-sig-default">0.0</span>,
<span class="summary-sig-arg">element</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span><br />
Write an ATOM or HETATM record using the information supplied.</td>
<td align="right" valign="top">
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Scientific.IO.PDB.PDBFile-class.html#writeComment" class="summary-sig-name">writeComment</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">text</span>)</span><br />
Write text into one or several comment lines.</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Scientific.IO.PDB.PDBFile-class.html#writeLine" class="summary-sig-name">writeLine</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">type</span>,
<span class="summary-sig-arg">data</span>)</span><br />
Write a line using record type and data dictionary in the same format
as returned by readLine().</td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<td align="left" colspan="2" class="table-header">
<span class="table-header">Method Details</span></td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">file_or_filename</span>,
<span class="sig-arg">mode</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">r</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">subformat</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>file_or_filename</code></strong> (<code>str</code> or <code>file</code>) - the name of the PDB file, or a file object</li>
<li><strong class="pname"><code>mode</code></strong> (<code>str</code>) - the file access mode, 'r' (read) or 'w' (write)</li>
<li><strong class="pname"><code>subformat</code></strong> (<code>str</code> or <code>NoneType</code>) - indicates a specific dialect of the PDB format. Subformats are
defined in <code
class="link">Scientific.IO.PDBExportFilters</code>; they are used
only when writing.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="close"></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">close</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Close the file. This method <b>must</b> be called for write mode
because otherwise the file will be incomplete.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="nextChain"></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">nextChain</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">chain_id</span>=<span class="sig-default">None</span>,
<span class="sig-arg">segment_id</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Signal the beginning of a new chain.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>chain_id</code></strong> (<code>str</code> or <code>NoneType</code>) - a chain identifier. If <code>None</code>, consecutive letters
from the alphabet are used.</li>
<li><strong class="pname"><code>segment_id</code></strong> (<code>str</code>) - a chain identifier</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="nextResidue"></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">nextResidue</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">number</span>=<span class="sig-default">None</span>,
<span class="sig-arg">terminus</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Signal the beginning of a new residue, starting with the next call to
<a href="Scientific.IO.PDB.PDBFile-class.html#writeAtom"
class="link">writeAtom</a>.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>name</code></strong> (<code>str</code>) - the residue name</li>
<li><strong class="pname"><code>number</code></strong> (<code>int</code> or <code>NoneType</code>) - the residue number. If <code>None</code>, the residues will be
numbered sequentially, starting from 1.</li>
<li><strong class="pname"><code>terminus</code></strong> - <code>None</code>, "C", or "N". This
information is passed to export filters that can use this
information in order to use different atom or residue names in
terminal residues.</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="readLine"></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">readLine</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Return the contents of the next non-blank line (= record) The return
value is a tuple whose first element (a string) contains the record type.
For supported record types (HEADER, CRYST1, SCALEn, MTRIXn, ATOM, HETATM,
ANISOU, TERM, MODEL, CONECT), the items from the remaining fields are put
into a dictionary which is returned as the second tuple element. Most
dictionary elements are strings or numbers; atom positions are returned
as a vector, and anisotropic temperature factors are returned as a rank-2
tensor, already multiplied by 1.e-4. White space is stripped from all
strings except for atom names, whose correct interpretation can depend on
an initial space. For unsupported record types, the second tuple element
is a string containing the remaining part of the record.</p>
<dl class="fields">
<dt>Returns: <code>tuple</code></dt>
<dd>the contents of one PDB record</dd>
</dl>
</td></tr></table>
</div>
<a name="writeAtom"></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">writeAtom</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>,
<span class="sig-arg">position</span>,
<span class="sig-arg">occupancy</span>=<span class="sig-default">0.0</span>,
<span class="sig-arg">temperature_factor</span>=<span class="sig-default">0.0</span>,
<span class="sig-arg">element</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Write an ATOM or HETATM record using the information supplied. The
residue and chain information is taken from the last calls to the methods
<a href="Scientific.IO.PDB.PDBFile-class.html#nextResidue"
class="link">nextResidue</a> and <a
href="Scientific.IO.PDB.PDBFile-class.html#nextChain"
class="link">nextChain</a>.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>name</code></strong> (<code>str</code>) - the atom name</li>
<li><strong class="pname"><code>position</code></strong> (<a href="Scientific.Geometry.Vector-class.html"
class="link">Scientific.Geometry.Vector</a>) - the atom position</li>
<li><strong class="pname"><code>occupancy</code></strong> (<code>float</code>) - the occupancy</li>
<li><strong class="pname"><code>temperature_factor</code></strong> (<code>float</code>) - the temperature factor (B-factor)</li>
<li><strong class="pname"><code>element</code></strong> (<code>str</code>) - the chemical element</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="writeComment"></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">writeComment</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">text</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Write text into one or several comment lines. Each line of the text is
prefixed with 'REMARK' and written to the file.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>text</code></strong> (<code>str</code>) - the comment contents</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
<a name="writeLine"></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">writeLine</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">type</span>,
<span class="sig-arg">data</span>)</span>
</h3>
</td><td align="right" valign="top"
>
</td>
</tr></table>
<p>Write a line using record type and data dictionary in the same format
as returned by readLine(). Default values are provided for non-essential
information, so the data dictionary need not contain all entries.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>type</code></strong> (<code>str</code>) - PDB record type</li>
<li><strong class="pname"><code>data</code></strong> (<code>tuple</code>) - PDB record data</li>
</ul></dd>
</dl>
</td></tr></table>
</div>
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