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Module PDBList'
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<h1 class="epydoc">Source Code for <a href="Bio.PDB.PDBList%27-module.html">Module Bio.PDB.PDBList'</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># PDBList.py</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># A tool for tracking changes in the PDB Protein Structure Database.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Version 2.0</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># (c) 2003 Kristian Rother</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This work was supported by the German Ministry of Education</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># and Research (BMBF). Project http://www.bcbio.de</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Contact the author</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># homepage : http://www.rubor.de/bioinf</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># email : krother@genesilico.pl</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This Code is released under the conditions of the Biopython license.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># It may be distributed freely with respect to the original author.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Any maintainer of the BioPython code may change this notice</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># when appropriate.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Last modified on Fri, Oct 24th 2006, Warszawa</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Removed 'write' options from retrieve_pdb_file method: it is not used.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Also added a 'dir' options (pdb file is put in this directory if given),</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># and an 'exist' option (test if the file is already there). This method</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># now returns the name of the downloaded uncompressed file.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># -Thomas, 1/06/04</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Including bugfixes from Sunjoong Lee (9/2006)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-0', '__doc__', 'link-0');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-docstring">"Access the PDB over the internet (for example to download structures)."</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt><tt class="py-op">,</tt><tt class="py-name">string</tt><tt class="py-op">,</tt><tt class="py-name">re</tt><tt class="py-op">,</tt><tt class="py-name">os</tt><tt class="py-op">,</tt><tt class="py-name">sys</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="PDBList"></a><div id="PDBList-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="PDBList-toggle" onclick="return toggle('PDBList');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html">PDBList</a><tt class="py-op">:</tt> </tt>
</div><div id="PDBList-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PDBList-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> This class provides quick access to the structure lists on the</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> PDB server or its mirrors. The structure lists contain</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> four-letter PDB codes, indicating that structures are</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> new, have been modified or are obsolete. The lists are released</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> on a weekly basis.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> It also provides a function to retrieve PDB files from the server.</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> To use it properly, prepare a directory /pdb or the like,</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> where PDB files are stored.</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> If You want to use this module from inside a proxy, add</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> the proxy variable to Your environment, e.g. in Unix</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> export HTTP_PROXY='http://realproxy.charite.de:888' </tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> (This can also be added to ~/.bashrc)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt id="link-1" class="py-name" targets="Variable Bio.PDB.PDBList'.PDBList.PDB_REF=Bio.PDB.PDBList%27.PDBList-class.html#PDB_REF"><a title="Bio.PDB.PDBList'.PDBList.PDB_REF" class="py-name" href="#" onclick="return doclink('link-1', 'PDB_REF', 'link-1');">PDB_REF</a></tt><tt class="py-op">=</tt><tt class="py-string">"""</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-string"> The Protein Data Bank: a computer-based archival file for macromolecular structures.</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-string"> F.C.Bernstein, T.F.Koetzle, G.J.B.Williams, E.F.Meyer Jr, M.D.Brice, J.R.Rodgers, O.Kennard, T.Shimanouchi, M.Tasumi</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-string"> J. Mol. Biol. 112 pp. 535-542 (1977)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-string"> http://www.pdb.org/.</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-string"> """</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt id="link-2" class="py-name" targets="Variable Bio.PDB.PDBList'.PDBList.alternative_download_url=Bio.PDB.PDBList%27.PDBList-class.html#alternative_download_url"><a title="Bio.PDB.PDBList'.PDBList.alternative_download_url" class="py-name" href="#" onclick="return doclink('link-2', 'alternative_download_url', 'link-2');">alternative_download_url</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"http://www.rcsb.org/pdb/files/"</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-comment"># just append PDB code to this, and then it works.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PDBList.__init__"></a><div id="PDBList.__init__-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="PDBList.__init__-toggle" onclick="return toggle('PDBList.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">server</tt><tt class="py-op">=</tt><tt class="py-string">'ftp://ftp.rcsb.org'</tt><tt class="py-op">,</tt> <tt class="py-param">pdb</tt><tt class="py-op">=</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-param">obsolete_pdb</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.__init__-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the class with the default server or a custom one."""</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-comment"># remote pdb server</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_server</tt> <tt class="py-op">=</tt> <tt class="py-name">server</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-comment"># local pdb file tree</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">local_pdb</tt> <tt class="py-op">=</tt> <tt id="link-3" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.pdb()=Bio.FSSP.FSSPAlignDict-class.html#pdb,Module Bio.dbdefs.pdb=Bio.dbdefs.pdb-module.html,Variable Bio.dbdefs.pdb.pdb=Bio.dbdefs.pdb-module.html#pdb"><a title="Bio.FSSP.FSSPAlignDict.pdb
Bio.dbdefs.pdb
Bio.dbdefs.pdb.pdb" class="py-name" href="#" onclick="return doclink('link-3', 'pdb', 'link-3');">pdb</a></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-comment"># local file tree for obsolete pdb files</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">obsolete_pdb</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">obsolete_pdb</tt> <tt class="py-op">=</tt> <tt class="py-name">obsolete_pdb</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">obsolete_pdb</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">local_pdb</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'obsolete'</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">access</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">obsolete_pdb</tt><tt class="py-op">,</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">F_OK</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">makedirs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">obsolete_pdb</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-comment"># variables for command-line options</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">overwrite</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flat_tree</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt>
<a name="PDBList.get_status_list"></a><div id="PDBList.get_status_list-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="PDBList.get_status_list-toggle" onclick="return toggle('PDBList.get_status_list');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#get_status_list">get_status_list</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">url</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.get_status_list-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.get_status_list-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieves a list of pdb codes in the weekly pdb status file</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> from the given URL. Used by get_recent_files.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> Typical contents of the list files parsed by this method;</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring">-rw-r--r-- 1 rcsb rcsb 330156 Oct 14 2003 pdb1cyq.ent</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring">-rw-r--r-- 1 rcsb rcsb 333639 Oct 14 2003 pdb1cz0.ent</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">url</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">url</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">url</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readlines()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readlines,Method Bio.File.SGMLHandle.readlines()=Bio.File.SGMLHandle-class.html#readlines,Method Bio.File.UndoHandle.readlines()=Bio.File.UndoHandle-class.html#readlines,Method Bio.SGMLExtractor.SGMLExtractorHandle.readlines()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readlines"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-4', 'readlines', 'link-4');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt id="link-5" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-5', 'list', 'link-5');">list</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-comment"># added by S. Lee</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-6" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-6', 'list', 'link-5');">list</a></tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-7', 'map', 'link-7');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-8" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-8', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-9" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-9', 'x', 'link-8');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> \ </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt id="link-10" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-10', 'filter', 'link-10');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-11" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-11', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-12" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-12', 'x', 'link-8');">x</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'.ent'</tt><tt class="py-op">,</tt> \ </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-13', 'map', 'link-7');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-14" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-14', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-15" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-15', 'x', 'link-8');">x</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-16', 'split', 'link-16');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-17" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-17', 'list', 'link-5');">list</a></tt> </tt>
</div><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="PDBList.get_recent_changes"></a><div id="PDBList.get_recent_changes-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="PDBList.get_recent_changes-toggle" onclick="return toggle('PDBList.get_recent_changes');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#get_recent_changes">get_recent_changes</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.get_recent_changes-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.get_recent_changes-expanded"><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns three lists of the newest weekly files (added,mod,obsolete).</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> Reads the directories with changed entries from the PDB server and</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> returns a tuple of three URL's to the files of new, modified and</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> obsolete entries from the most recent list. The directory with the</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> largest numerical name is used.</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> Returns None if something goes wrong.</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> Contents of the data/status dir (20031013 would be used);</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring">drwxrwxr-x 2 1002 sysadmin 512 Oct 6 18:28 20031006</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring">drwxrwxr-x 2 1002 sysadmin 512 Oct 14 02:14 20031013</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring">-rw-r--r-- 1 1002 sysadmin 1327 Mar 12 2001 README</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">url</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_server</tt><tt class="py-op">+</tt><tt class="py-string">'/pub/pdb/data/status/'</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">url</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-18', 'readlines', 'link-4');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-comment"># added by S.Lee</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">recent</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-19', 'filter', 'link-10');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-20" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-20', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-21" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-21', 'x', 'link-8');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">isdigit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-22', 'map', 'link-7');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-23" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-23', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-24" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-24', 'x', 'link-8');">x</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-25', 'split', 'link-16');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">path</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_server</tt><tt class="py-op">+</tt><tt class="py-string">'/pub/pdb/data/status/%s/'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">recent</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-comment"># retrieve the lists</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">added</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.PDB.PDBList'.PDBList.get_status_list()=Bio.PDB.PDBList%27.PDBList-class.html#get_status_list"><a title="Bio.PDB.PDBList'.PDBList.get_status_list" class="py-name" href="#" onclick="return doclink('link-26', 'get_status_list', 'link-26');">get_status_list</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">+</tt><tt class="py-string">'added.pdb'</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">modified</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.PDBList'.PDBList.get_status_list" class="py-name" href="#" onclick="return doclink('link-27', 'get_status_list', 'link-26');">get_status_list</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">+</tt><tt class="py-string">'modified.pdb'</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">obsolete</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.PDB.PDBList'.PDBList.get_status_list" class="py-name" href="#" onclick="return doclink('link-28', 'get_status_list', 'link-26');">get_status_list</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">+</tt><tt class="py-string">'obsolete.pdb'</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">added</tt><tt class="py-op">,</tt><tt class="py-name">modified</tt><tt class="py-op">,</tt><tt class="py-name">obsolete</tt><tt class="py-op">]</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
<a name="PDBList.get_all_entries"></a><div id="PDBList.get_all_entries-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="PDBList.get_all_entries-toggle" onclick="return toggle('PDBList.get_all_entries');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#get_all_entries">get_all_entries</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.get_all_entries-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.get_all_entries-expanded"><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieves a big file containing all the </tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> PDB entries and some annotation to them. </tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list of PDB codes in the index file.</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"retrieving index file. Takes about 5 MB."</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">url</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_server</tt><tt class="py-op">+</tt><tt class="py-string">'/pub/pdb/derived_data/index/entries.idx'</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-comment"># extract four-letter-codes</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-29', 'map', 'link-7');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-30" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-30', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-31" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-31', 'x', 'link-8');">x</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> \ </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt id="link-32" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-32', 'filter', 'link-10');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-33" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-33', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-34" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-34', 'x', 'link-8');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-name">url</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-35', 'readlines', 'link-4');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">entries</tt> </tt>
</div><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> </tt>
<a name="PDBList.get_all_obsolete"></a><div id="PDBList.get_all_obsolete-def"><a name="L160"></a><tt class="py-lineno">160</tt> <a class="py-toggle" href="#" id="PDBList.get_all_obsolete-toggle" onclick="return toggle('PDBList.get_all_obsolete');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#get_all_obsolete">get_all_obsolete</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.get_all_obsolete-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.get_all_obsolete-expanded"><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a list of all obsolete entries ever in the PDB.</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list of all obsolete pdb codes that have ever been</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> in the PDB.</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> Gets and parses the file from the PDB server in the format</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> (the first pdb_code column is the one used).</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> LIST OF OBSOLETE COORDINATE ENTRIES AND SUCCESSORS</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring">OBSLTE 30-SEP-03 1Q1D 1QZR</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring">OBSLTE 26-SEP-03 1DYV 1UN2 </tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">url</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_server</tt><tt class="py-op">+</tt><tt class="py-string">'/pub/pdb/data/status/obsolete.dat'</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-comment"># extract pdb codes</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">obsolete</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-36', 'map', 'link-7');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-37" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-37', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-38', 'x', 'link-8');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">21</tt><tt class="py-op">:</tt><tt class="py-number">25</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt id="link-39" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-39', 'filter', 'link-10');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-40" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-40', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-41" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-41', 'x', 'link-8');">x</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'OBSLTE'</tt><tt class="py-op">,</tt> <tt class="py-name">url</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-42', 'readlines', 'link-4');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">obsolete</tt> </tt>
</div><a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
<a name="PDBList.retrieve_pdb_file"></a><div id="PDBList.retrieve_pdb_file-def"><a name="L181"></a><tt class="py-lineno">181</tt> <a class="py-toggle" href="#" id="PDBList.retrieve_pdb_file-toggle" onclick="return toggle('PDBList.retrieve_pdb_file');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#retrieve_pdb_file">retrieve_pdb_file</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">pdb_code</tt><tt class="py-op">,</tt> <tt class="py-param">obsolete</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">compression</tt><tt class="py-op">=</tt><tt class="py-string">'.Z'</tt><tt class="py-op">,</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-param">uncompress</tt><tt class="py-op">=</tt><tt class="py-string">"gunzip"</tt><tt class="py-op">,</tt> <tt class="py-param">pdir</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.retrieve_pdb_file-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.retrieve_pdb_file-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieves a PDB structure file from the PDB server and</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"> stores it in a local file tree.</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> The PDB structure is returned as a single string.</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> If obsolete is 1, the file will be by default saved in a special file tree.</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> The compression should be '.Z' or '.gz'. 'uncompress' is</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> the command called to uncompress the files.</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> @param pdir: put the file in this directory (default: create a PDB-style directory tree) </tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> @type pdir: string</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> @return: filename</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: string</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-comment"># get the structure</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">code</tt><tt class="py-op">=</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-string">"pdb%s.ent%s"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">code</tt><tt class="py-op">,</tt><tt id="link-43" class="py-name" targets="Module Bio.Mindy.compression=Bio.Mindy.compression-module.html"><a title="Bio.Mindy.compression" class="py-name" href="#" onclick="return doclink('link-43', 'compression', 'link-43');">compression</a></tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">obsolete</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">url</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_server</tt><tt class="py-op">+</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-string">'/pub/pdb/data/structures/divided/pdb/%s/pdb%s.ent%s'</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">code</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">code</tt><tt class="py-op">,</tt><tt id="link-44" class="py-name"><a title="Bio.Mindy.compression" class="py-name" href="#" onclick="return doclink('link-44', 'compression', 'link-43');">compression</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">url</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_server</tt><tt class="py-op">+</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-string">'/pub/pdb/data/structures/obsolete/pdb/%s/pdb%s.ent%s'</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">code</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">code</tt><tt class="py-op">,</tt><tt id="link-45" class="py-name"><a title="Bio.Mindy.compression" class="py-name" href="#" onclick="return doclink('link-45', 'compression', 'link-43');">compression</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-comment"># in which dir to put the pdb file?</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">pdir</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flat_tree</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">obsolete</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">path</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">local_pdb</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">path</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">obsolete_pdb</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-comment"># Put in PDB style directory tree</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">obsolete</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">path</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">local_pdb</tt><tt class="py-op">+</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">+</tt><tt class="py-name">code</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">path</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">obsolete_pdb</tt><tt class="py-op">+</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">+</tt><tt class="py-name">code</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-comment"># Put in specified directory</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">path</tt><tt class="py-op">=</tt><tt class="py-name">pdir</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">access</tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">,</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">F_OK</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">makedirs</tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">path</tt><tt class="py-op">+</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">+</tt><tt class="py-name">filename</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-comment"># the final uncompressed file</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">final_file</tt><tt class="py-op">=</tt><tt class="py-name">path</tt><tt class="py-op">+</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">+</tt><tt class="py-string">"pdb%s.ent"</tt> <tt class="py-op">%</tt> <tt class="py-name">code</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-comment"># check whether the file exists</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">overwrite</tt><tt class="py-op">:</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.biblio.Biblio.exists()=Bio.biblio.Biblio-class.html#exists,Method Bio.biblio.BiblioCollection.exists()=Bio.biblio.BiblioCollection-class.html#exists"><a title="Bio.biblio.Biblio.exists
Bio.biblio.BiblioCollection.exists" class="py-name" href="#" onclick="return doclink('link-46', 'exists', 'link-46');">exists</a></tt><tt class="py-op">(</tt><tt class="py-name">final_file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"file exists, not retrieved"</tt><tt class="py-op">,</tt><tt class="py-name">final_file</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">final_file</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-comment"># Retrieve the file</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">'retrieving'</tt><tt class="py-op">,</tt><tt class="py-name">url</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">=</tt><tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">url</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-47', 'read', 'link-47');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt id="link-48" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-48', 'open', 'link-48');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt><tt class="py-string">'wb'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-49', 'write', 'link-49');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-comment"># uncompress the file</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">system</tt><tt class="py-op">(</tt><tt class="py-string">"%s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">uncompress</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">final_file</tt> </tt>
</div><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> </tt>
<a name="PDBList.update_pdb"></a><div id="PDBList.update_pdb-def"><a name="L249"></a><tt class="py-lineno">249</tt> <a class="py-toggle" href="#" id="PDBList.update_pdb-toggle" onclick="return toggle('PDBList.update_pdb');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#update_pdb">update_pdb</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.update_pdb-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.update_pdb-expanded"><a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> I guess this is the 'most wanted' function from this module.</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-docstring"> It gets the weekly lists of new and modified pdb entries and</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-docstring"> automatically downloads the according PDB files.</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"> You can call this module as a weekly cronjob.</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">changes</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.PDB.PDBList'.PDBList.get_recent_changes()=Bio.PDB.PDBList%27.PDBList-class.html#get_recent_changes"><a title="Bio.PDB.PDBList'.PDBList.get_recent_changes" class="py-name" href="#" onclick="return doclink('link-50', 'get_recent_changes', 'link-50');">get_recent_changes</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">new</tt> <tt class="py-op">=</tt> <tt class="py-name">changes</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">modified</tt> <tt class="py-op">=</tt> <tt class="py-name">changes</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">obsolete</tt> <tt class="py-op">=</tt> <tt class="py-name">changes</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pdb_code</tt> <tt class="py-keyword">in</tt> <tt class="py-name">new</tt><tt class="py-op">+</tt><tt class="py-name">modified</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'retrieving %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.PDB.PDBList'.PDBList.retrieve_pdb_file()=Bio.PDB.PDBList%27.PDBList-class.html#retrieve_pdb_file"><a title="Bio.PDB.PDBList'.PDBList.retrieve_pdb_file" class="py-name" href="#" onclick="return doclink('link-51', 'retrieve_pdb_file', 'link-51');">retrieve_pdb_file</a></tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'error %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-comment"># you can insert here some more log notes that</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># something has gone wrong. </tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-comment"># move the obsolete files to a special folder</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">pdb_code</tt> <tt class="py-keyword">in</tt> <tt class="py-name">obsolete</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flat_tree</tt><tt class="py-op">:</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">old_file</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">local_pdb</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'pdb%s.ent'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">new_file</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">obsolete_pdb</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'pdb%s.ent'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">old_file</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">local_pdb</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">pdb_code</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'pdb%s.ent'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">new_file</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">obsolete_pdb</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">pdb_code</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'pdb%s.ent'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">cmd</tt><tt class="py-op">(</tt><tt class="py-string">'mv %s %s'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">old_file</tt><tt class="py-op">,</tt><tt class="py-name">new_file</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> </tt>
<a name="PDBList.download_entire_pdb"></a><div id="PDBList.download_entire_pdb-def"><a name="L281"></a><tt class="py-lineno">281</tt> <a class="py-toggle" href="#" id="PDBList.download_entire_pdb-toggle" onclick="return toggle('PDBList.download_entire_pdb');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#download_entire_pdb">download_entire_pdb</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">listfile</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.download_entire_pdb-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.download_entire_pdb-expanded"><a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieves all PDB entries not present in the local PDB copy.</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-docstring"> Writes a list file containing all PDB codes (optional, if listfile is given).</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method Bio.PDB.PDBList'.PDBList.get_all_entries()=Bio.PDB.PDBList%27.PDBList-class.html#get_all_entries"><a title="Bio.PDB.PDBList'.PDBList.get_all_entries" class="py-name" href="#" onclick="return doclink('link-52', 'get_all_entries', 'link-52');">get_all_entries</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pdb_code</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entries</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.PDB.PDBList'.PDBList.retrieve_pdb_file" class="py-name" href="#" onclick="return doclink('link-53', 'retrieve_pdb_file', 'link-51');">retrieve_pdb_file</a></tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-comment"># write the list</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">listfile</tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-54', 'open', 'link-48');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">listfile</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">writelines</tt><tt class="py-op">(</tt><tt id="link-55" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-55', 'map', 'link-7');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-56" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-56', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-57" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-57', 'x', 'link-8');">x</a></tt><tt class="py-op">+</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt><tt class="py-name">entries</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> </tt>
<a name="PDBList.download_obsolete_entries"></a><div id="PDBList.download_obsolete_entries-def"><a name="L293"></a><tt class="py-lineno">293</tt> <a class="py-toggle" href="#" id="PDBList.download_obsolete_entries-toggle" onclick="return toggle('PDBList.download_obsolete_entries');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#download_obsolete_entries">download_obsolete_entries</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">listfile</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.download_obsolete_entries-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.download_obsolete_entries-expanded"><a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieves all obsolete PDB entries not present in the local obsolete PDB copy.</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> Writes a list file containing all PDB codes (optional, if listfile is given).</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method Bio.PDB.PDBList'.PDBList.get_all_obsolete()=Bio.PDB.PDBList%27.PDBList-class.html#get_all_obsolete"><a title="Bio.PDB.PDBList'.PDBList.get_all_obsolete" class="py-name" href="#" onclick="return doclink('link-58', 'get_all_obsolete', 'link-58');">get_all_obsolete</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pdb_code</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entries</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.PDB.PDBList'.PDBList.retrieve_pdb_file" class="py-name" href="#" onclick="return doclink('link-59', 'retrieve_pdb_file', 'link-51');">retrieve_pdb_file</a></tt><tt class="py-op">(</tt><tt class="py-name">pdb_code</tt><tt class="py-op">,</tt><tt class="py-name">obsolete</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-comment"># write the list</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">listfile</tt><tt class="py-op">:</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt id="link-60" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-60', 'open', 'link-48');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">listfile</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">writelines</tt><tt class="py-op">(</tt><tt id="link-61" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-61', 'map', 'link-7');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-62" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-62', 'x', 'link-8');">x</a></tt><tt class="py-op">:</tt> <tt id="link-63" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-63', 'x', 'link-8');">x</a></tt><tt class="py-op">+</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt><tt class="py-name">entries</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># this is actually easter egg code not used by any of the methods</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># maybe someone will find it useful.</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt>
<a name="PDBList.get_seqres_file"></a><div id="PDBList.get_seqres_file-def"><a name="L311"></a><tt class="py-lineno">311</tt> <a class="py-toggle" href="#" id="PDBList.get_seqres_file-toggle" onclick="return toggle('PDBList.get_seqres_file');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PDB.PDBList'.PDBList-class.html#get_seqres_file">get_seqres_file</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">savefile</tt><tt class="py-op">=</tt><tt class="py-string">'pdb_seqres.txt'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PDBList.get_seqres_file-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PDBList.get_seqres_file-expanded"><a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieves a (big) file containing all the sequences </tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-docstring"> of PDB entries and writes it to a file."""</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"retrieving sequence file. Takes about 15 MB."</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">url</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdb_server</tt><tt class="py-op">+</tt><tt class="py-string">'/pub/pdb/derived_data/pdb_seqres.txt'</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">url</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-64', 'readlines', 'link-4');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt id="link-65" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-65', 'open', 'link-48');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">savefile</tt><tt class="py-op">,</tt><tt class="py-string">'w'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">writelines</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">doc</tt> <tt class="py-op">=</tt> <tt class="py-string">"""PDBList.py</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-string"> (c) Kristian Rother 2003, Contributed to BioPython</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-string"> Usage:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-string"> PDBList.py update <pdb_path> [options] - write weekly PDB updates to</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-string"> local pdb tree.</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-string"> PDBList.py all <pdb_path> [options] - write all PDB entries to</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"><tt class="py-string"> local pdb tree.</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-string"> PDBList.py obsol <pdb_path> [options] - write all obsolete PDB</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-string"> entries to local pdb tree.</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-string"> PDBList.py <PDB-ID> <pdb_path> [options] - retrieve single structure</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-string"> Options:</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt class="py-string"> -d A single directory will be used as <pdb_path>, not a tree.</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt class="py-string"> -o Overwrite existing structure files.</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-string"> """</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">doc</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-name">pdb_path</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">pl</tt> <tt class="py-op">=</tt> <tt id="link-66" class="py-name" targets="Class Bio.PDB.PDBList'.PDBList=Bio.PDB.PDBList%27.PDBList-class.html"><a title="Bio.PDB.PDBList'.PDBList" class="py-name" href="#" onclick="return doclink('link-66', 'PDBList', 'link-66');">PDBList</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.pdb
Bio.dbdefs.pdb
Bio.dbdefs.pdb.pdb" class="py-name" href="#" onclick="return doclink('link-67', 'pdb', 'link-3');">pdb</a></tt><tt class="py-op">=</tt><tt class="py-name">pdb_path</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-op">==</tt> <tt class="py-string">'-d'</tt><tt class="py-op">:</tt> <tt class="py-name">pl</tt><tt class="py-op">.</tt><tt class="py-name">flat_tree</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">option</tt> <tt class="py-op">==</tt> <tt class="py-string">'-o'</tt><tt class="py-op">:</tt> <tt class="py-name">pl</tt><tt class="py-op">.</tt><tt class="py-name">overwrite</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">pdb_path</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">pl</tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Bio.PDB.PDBList'.PDBList" class="py-name" href="#" onclick="return doclink('link-68', 'PDBList', 'link-66');">PDBList</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-name">pl</tt><tt class="py-op">.</tt><tt class="py-name">flat_tree</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'update'</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-comment"># update PDB</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">"updating local PDB at "</tt><tt class="py-op">+</tt><tt class="py-name">pdb_path</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-name">pl</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method Bio.PDB.PDBList'.PDBList.update_pdb()=Bio.PDB.PDBList%27.PDBList-class.html#update_pdb"><a title="Bio.PDB.PDBList'.PDBList.update_pdb" class="py-name" href="#" onclick="return doclink('link-69', 'update_pdb', 'link-69');">update_pdb</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'all'</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-comment"># get the entire PDB</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">pl</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method Bio.PDB.PDBList'.PDBList.download_entire_pdb()=Bio.PDB.PDBList%27.PDBList-class.html#download_entire_pdb"><a title="Bio.PDB.PDBList'.PDBList.download_entire_pdb" class="py-name" href="#" onclick="return doclink('link-70', 'download_entire_pdb', 'link-70');">download_entire_pdb</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'obsol'</tt><tt class="py-op">:</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-comment"># get all obsolete entries</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">pl</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Method Bio.PDB.PDBList'.PDBList.download_obsolete_entries()=Bio.PDB.PDBList%27.PDBList-class.html#download_obsolete_entries"><a title="Bio.PDB.PDBList'.PDBList.download_obsolete_entries" class="py-name" href="#" onclick="return doclink('link-71', 'download_obsolete_entries', 'link-71');">download_obsolete_entries</a></tt><tt class="py-op">(</tt><tt class="py-name">pdb_path</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-72', 'search', 'link-72');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">'^\d...$'</tt><tt class="py-op">,</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-comment"># get single PDB entry</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">pl</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.PDB.PDBList'.PDBList.retrieve_pdb_file" class="py-name" href="#" onclick="return doclink('link-73', 'retrieve_pdb_file', 'link-51');">retrieve_pdb_file</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">pdir</tt><tt class="py-op">=</tt><tt class="py-name">pdb_path</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> </tt><script type="text/javascript">
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