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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.PDBList%27-module.html">Module PDBList'</a> ::
Class PDBList
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class PDBList</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList">source code</a></span></p>
<p>This class provides quick access to the structure lists on the PDB
server or its mirrors. The structure lists contain four-letter PDB codes,
indicating that structures are new, have been modified or are obsolete.
The lists are released on a weekly basis.</p>
<p>It also provides a function to retrieve PDB files from the server. To
use it properly, prepare a directory /pdb or the like, where PDB files
are stored.</p>
<p>If You want to use this module from inside a proxy, add the proxy
variable to Your environment, e.g. in Unix export
HTTP_PROXY='http://realproxy.charite.de:888' (This can also be added to
~/.bashrc)</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">server</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">ftp://ftp.rcsb.org</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">pdb</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">/home/mandrake/rpm/BUILD/biopython-1.47</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">obsolete_pdb</span>=<span class="summary-sig-default">None</span>)</span><br />
Initialize the class with the default server or a custom one.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.__init__">source code</a></span>
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<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.PDB.PDBList%27.PDBList-class.html#download_entire_pdb" class="summary-sig-name">download_entire_pdb</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">listfile</span>=<span class="summary-sig-default">None</span>)</span><br />
Retrieves all PDB entries not present in the local PDB copy.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.download_entire_pdb">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.PDBList%27.PDBList-class.html#download_obsolete_entries" class="summary-sig-name">download_obsolete_entries</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">listfile</span>=<span class="summary-sig-default">None</span>)</span><br />
Retrieves all obsolete PDB entries not present in the local obsolete
PDB copy.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.download_obsolete_entries">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.PDBList%27.PDBList-class.html#get_all_entries" class="summary-sig-name">get_all_entries</a>(<span class="summary-sig-arg">self</span>)</span><br />
Retrieves a big file containing all the PDB entries and some
annotation to them.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_all_entries">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.PDBList%27.PDBList-class.html#get_all_obsolete" class="summary-sig-name">get_all_obsolete</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns a list of all obsolete entries ever in the PDB.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_all_obsolete">source code</a></span>
</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="Bio.PDB.PDBList%27.PDBList-class.html#get_recent_changes" class="summary-sig-name">get_recent_changes</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns three lists of the newest weekly files (added,mod,obsolete).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_recent_changes">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="get_seqres_file"></a><span class="summary-sig-name">get_seqres_file</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">savefile</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">pdb_seqres.txt</code><code class="variable-quote">'</code></span>)</span><br />
Retrieves a (big) file containing all the sequences of PDB entries
and writes it to a file.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_seqres_file">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.PDBList%27.PDBList-class.html#get_status_list" class="summary-sig-name">get_status_list</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">url</span>)</span><br />
Retrieves a list of pdb codes in the weekly pdb status file
from the given URL.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_status_list">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">string</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.PDB.PDBList%27.PDBList-class.html#retrieve_pdb_file" class="summary-sig-name">retrieve_pdb_file</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">pdb_code</span>,
<span class="summary-sig-arg">obsolete</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">compression</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.Z</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">uncompress</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">gunzip</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">pdir</span>=<span class="summary-sig-default">None</span>)</span><br />
Retrieves a PDB structure file from the PDB server and stores it in a
local file tree.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.retrieve_pdb_file">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"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.PDB.PDBList%27.PDBList-class.html#update_pdb" class="summary-sig-name">update_pdb</a>(<span class="summary-sig-arg">self</span>)</span><br />
I guess this is the 'most wanted' function from this module.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.update_pdb">source code</a></span>
</td>
</tr>
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</td>
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<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></a>
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<td align="left"><span class="table-header">Class Variables</span></td>
<td align="right" valign="top"
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class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.PDB.PDBList%27.PDBList-class.html#PDB_REF" class="summary-name">PDB_REF</a> = <code title="'''
The Protein Data Bank: a computer-based archival file for macromol\
ecular structures.
F.C.Bernstein, T.F.Koetzle, G.J.B.Williams, E.F.Meyer Jr, M.D.Bric\
e, J.R.Rodgers, O.Kennard, T.Shimanouchi, M.Tasumi
J. Mol. Biol. 112 pp. 535-542 (1977)
http://www.pdb.org/.
'''"><code class="variable-quote">'</code><code class="variable-string">\n The Protein Data Bank: a computer-based archi</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 name="alternative_download_url"></a><span class="summary-name">alternative_download_url</span> = <code title="'http://www.rcsb.org/pdb/files/'"><code class="variable-quote">'</code><code class="variable-string">http://www.rcsb.org/pdb/files/</code><code class="variable-quote">'</code></code>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
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<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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</td>
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<a name="download_entire_pdb"></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">download_entire_pdb</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">listfile</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.download_entire_pdb">source code</a></span>
</td>
</tr></table>
<p>Retrieves all PDB entries not present in the local PDB copy. Writes a
list file containing all PDB codes (optional, if listfile is given).</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="download_obsolete_entries"></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">download_obsolete_entries</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">listfile</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.download_obsolete_entries">source code</a></span>
</td>
</tr></table>
<p>Retrieves all obsolete PDB entries not present in the local obsolete
PDB copy. Writes a list file containing all PDB codes (optional, if
listfile is given).</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_all_entries"></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">get_all_entries</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_all_entries">source code</a></span>
</td>
</tr></table>
<p>Retrieves a big file containing all the PDB entries and some
annotation to them. Returns a list of PDB codes in the index file.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_all_obsolete"></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">get_all_obsolete</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_all_obsolete">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Returns a list of all obsolete entries ever in the PDB.
Returns a list of all obsolete pdb codes that have ever been
in the PDB.
Gets and parses the file from the PDB server in the format
(the first pdb_code column is the one used).
LIST OF OBSOLETE COORDINATE ENTRIES AND SUCCESSORS
OBSLTE 30-SEP-03 1Q1D 1QZR
OBSLTE 26-SEP-03 1DYV 1UN2
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_recent_changes"></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">get_recent_changes</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_recent_changes">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Returns three lists of the newest weekly files (added,mod,obsolete).
Reads the directories with changed entries from the PDB server and
returns a tuple of three URL's to the files of new, modified and
obsolete entries from the most recent list. The directory with the
largest numerical name is used.
Returns None if something goes wrong.
Contents of the data/status dir (20031013 would be used);
drwxrwxr-x 2 1002 sysadmin 512 Oct 6 18:28 20031006
drwxrwxr-x 2 1002 sysadmin 512 Oct 14 02:14 20031013
-rw-r--r-- 1 1002 sysadmin 1327 Mar 12 2001 README
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_status_list"></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">get_status_list</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">url</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.get_status_list">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Retrieves a list of pdb codes in the weekly pdb status file
from the given URL. Used by get_recent_files.
Typical contents of the list files parsed by this method;
-rw-r--r-- 1 rcsb rcsb 330156 Oct 14 2003 pdb1cyq.ent
-rw-r--r-- 1 rcsb rcsb 333639 Oct 14 2003 pdb1cz0.ent
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="retrieve_pdb_file"></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">retrieve_pdb_file</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">pdb_code</span>,
<span class="sig-arg">obsolete</span>=<span class="sig-default">0</span>,
<span class="sig-arg">compression</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">.Z</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">uncompress</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">gunzip</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">pdir</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.retrieve_pdb_file">source code</a></span>
</td>
</tr></table>
<p>Retrieves a PDB structure file from the PDB server and stores it in a
local file tree. The PDB structure is returned as a single string. If
obsolete is 1, the file will be by default saved in a special file tree.
The compression should be '.Z' or '.gz'. 'uncompress' is the command
called to uncompress the files.</p>
<dl class="fields">
<dt>Parameters:</dt>
<dd><ul class="nomargin-top">
<li><strong class="pname"><code>pdir</code></strong> (string) - put the file in this directory (default: create a PDB-style
directory tree)</li>
</ul></dd>
<dt>Returns: string</dt>
<dd>filename</dd>
</dl>
</td></tr></table>
</div>
<a name="update_pdb"></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">update_pdb</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PDB.PDBList%27-pysrc.html#PDBList.update_pdb">source code</a></span>
</td>
</tr></table>
<p>I guess this is the 'most wanted' function from this module. It gets
the weekly lists of new and modified pdb entries and automatically
downloads the according PDB files. You can call this module as a weekly
cronjob.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== CLASS VARIABLE DETAILS ==================== -->
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-quote">'''</code><code class="variable-string"></code>
<code class="variable-string"> The Protein Data Bank: a computer-based archival file for macromol</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">ecular structures.</code>
<code class="variable-string"> F.C.Bernstein, T.F.Koetzle, G.J.B.Williams, E.F.Meyer Jr, M.D.Bric</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">e, J.R.Rodgers, O.Kennard, T.Shimanouchi, M.Tasumi</code>
<code class="variable-string"> J. Mol. Biol. 112 pp. 535-542 (1977)</code>
<code class="variable-string"> http://www.pdb.org/.</code>
<code class="variable-string"> </code><code class="variable-quote">'''</code>
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