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<?xml version="1.0" encoding="ascii"?>
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Package csb
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<h1 class="epydoc">Source Code for <a href="csb-module.html">Package csb</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">CSB is a high-level, object-oriented library used to solve problems in the</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">field of Computational Structural Biology.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">Introduction</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">============</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">The library is composed of a set of highly branched python packages</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">(namespaces). Some of the packages are meant to be directly used by</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">the clients (core library), while others are utility modules and take</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">part in the development of the library: </tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> 1. Core class library -- object-oriented, granular, with an emphasis</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> on design and clean interfaces. A Sequence is not a string, and a</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> Structure is not a dict or list. Naming conventions matter.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> 2. Application framework -- executable console applications</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> ("protocols"), which consume objects from the core library.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> The framework ensures that each CSB application is also reusable</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> and can be instantiated as a regular python object without any</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> ugly side effects (sys.exit() and friends). See L{csb.apps} for more</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> details. </tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> 3. Test framework -- built on top of the standard unittest as a thin</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> wrapping layer. Provides some sugar like transparent management of</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> test data files, and modular test execution. L{csb.test} will give</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> you all the details. </tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">The core library is roughly composed of:</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> - bioinformatics API: L{csb.bio}, which includes stuff like</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> L{csb.bio.io}, L{csb.bio.structure}, L{csb.bio.sequence},</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> L{csb.bio.hmm}</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> - statistics API: L{csb.statistics}, L{csb.numeric}</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> - utilities - L{csb.io}, L{csb.core}</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring">Getting started</tt> </tt>
<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"> </tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring">Perhaps one of the most frequently used parts of the library is the</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring">L{csb.bio.structure} module, which provides the L{Structure}, L{Chain},</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring">L{Residue} and L{Atom} objects. You could easily build a L{Structure}</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring">from scratch, but a far more common scenario is parsing a structure from</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring">a PDB file using one of the L{AbstractStructureParser}s. All bio IO</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring">objects, including the StructureParser factory, are defined in</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring">L{csb.bio.io} and sub-packages:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> >>> from csb.bio.io.wwpdb import StructureParser</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> >>> p = StructureParser("/some/file/pdb1x80.ent")</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> >>> s = p.parse_structure()</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> >>> print(s)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> <Structure: 1x80, 2 chains></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 class="py-docstring">The last statement will return a L{csb.bio.structure.Structure} instance,</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring">which is a composite hierarchical object:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> >>> for chain_id in s.chains:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> chain = s.chains[chain_id]</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> for residue in chain.residues:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> for atom_id in residue.atoms:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> atom = residue.atoms[atom_id]</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> print(atom.vector)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring">Some of the inner objects in this hierarchy behave just like dictionaries</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring">(but are not):</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> >>> s.chains['A'] # access chain A by ID</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> <Chain A: Protein></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> >>> s['A'] # the same</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> <Chain A: Protein></tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring">Others behave like collections:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> >>> chain.residues[10] # 1-based access to the residues in the chain</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> <ProteinResidue [10]: PRO 10></tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> >>> chain[10] # 0-based, list-like access</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> <ProteinResidue [11]: GLY 11></tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring">But all entities are iterable because they inherit the C{items} iterator</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring">from L{AbstractEntity}. The above loop can be shortened:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> >>> for chain in s.items:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> for residue in chain.items:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> for atom in residue.items:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> print(atom.vector)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring">or even more:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> >>> from csb.bio.structure import Atom</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> >>> for atom in s.components(klass=Atom):</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> print(atom.vector)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring">You may also be interested in extracting a sub-chain from this structure:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> >>> s.chains['B'].subregion(3, 20) # from positions 3 to 20, inclusive</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> <Chain B: Protein></tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring">or modifying it in some way, for example, in order to append a new residue,</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring">try:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> >>> from csb.bio.structure import ProteinResidue</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> >>> from csb.bio.sequence import ProteinAlphabet</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> >>> residue = ProteinResidue(401, ProteinAlphabet.ALA)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> >>> s.chains['A'].residues.append(residue)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring">Finally, you would probably want to save your structure back to a PDB file:</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"> >>> s.to_pdb('/some/file/name.pdb') </tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring">Where to go from here</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring">=====================</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">If you want to dive into statistics, you could peek inside L{csb.statistics}</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring">and its sub-packages. For example, L{csb.statistics.pdf} contains a collection</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring">of L{probability density objects<csb.statistics.pdf.AbstractDensity>},</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring">like L{Gaussian<csb.statistics.pdf.Normal>} or L{Gamma<csb.statistics.pdf.Gamma>}.</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">But chances are you would first like to try reading some files, so you could</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring">start exploring L{csb.bio.io} right now. As we have already seen,</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring">L{csb.bio.io.wwpdb} provides PDB L{Structure<csb.bio.structure.Structure>}</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring">parsers, for example L{csb.bio.io.wwpdb.RegularStructureParser} and</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring">L{csb.bio.io.wwpdb.LegacyStructureParser}.</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring">L{csb.bio.io.fasta} is all about reading FASTA</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring">L{Sequence<csb.bio.sequence.AbstractSequence>}s and</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring">L{SequenceAlignment<csb.bio.sequence.AbstractAlignment>}s. Be sure to check out </tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring">L{csb.bio.io.fasta.SequenceParser}, L{csb.bio.io.fasta.SequenceAlignmentReader}</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring">and L{csb.bio.io.fasta.StructureAlignmentFactory}.</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring">If you are working with HHpred (L{ProfileHMM<csb.bio.hmm.ProfileHMM>}s,</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring">L{HHpredHit<csb.bio.hmm.HHpredHit>}s), then L{csb.bio.io.hhpred} is for you.</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring">This package provides L{csb.bio.io.hhpred.HHProfileParser} and</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring">L{csb.bio.io.hhpred.HHOutputParser}, which are used to read *.hhm and *.hhr</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring">files.</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring">Finally, if you want to make some nice plots with matplotlib, you may like the</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring">clean object-oriented interface of our L{Chart<csb.io.plots.Chart>}. See</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring">L{csb.io.plots} and maybe also L{csb.io.tsv} to get started.</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring">Development</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring">===========</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-docstring">When contributing code to CSB, please take into account the following:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> 1. New features or bug fixes should always be accompanied by test cases.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> Also, always run the complete test suite before committing. For more</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> details on this topic, see L{csb.test}.</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> 2. The source code of CSB must be cross-platform and cross-interpreter</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> compatible. L{csb.core} and L{csb.io} will give you all necessary</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> details on how to use the CSB compatibility layer.</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring">License</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring">=======</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">CSB is open source and distributed under OSI-approved MIT license::</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"> Copyright (c) 2012 Michael Habeck</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> Permission is hereby granted, free of charge, to any person obtaining</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> a copy of this software and associated documentation files (the</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> "Software"), to deal in the Software without restriction, including</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> without limitation the rights to use, copy, modify, merge, publish,</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> distribute, sublicense, and/or sell copies of the Software, and to</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"> permit persons to whom the Software is furnished to do so, subject to</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> the following conditions:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"> The above copyright notice and this permission notice shall be</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> included in all copies or substantial portions of the Software.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"> IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"> TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"> SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-name">__version__</tt> <tt class="py-op">=</tt> <tt class="py-string">'1.2.5.{revision}'</tt> </tt>
<a name="Version"></a><div id="Version-def"><a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <a class="py-toggle" href="#" id="Version-toggle" onclick="return toggle('Version');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="csb.Version-class.html">Version</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Version-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Version-expanded"><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"> CSB version number.</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> </tt>
<a name="Version.__init__"></a><div id="Version.__init__-def"><a name="L196"></a><tt class="py-lineno">196</tt> <a class="py-toggle" href="#" id="Version.__init__-toggle" onclick="return toggle('Version.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#__init__">__init__</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="Version.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.__init__-expanded"><a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt id="link-0" class="py-name" targets="Variable csb.bio.hmm.ProfileHMM.version=csb.bio.hmm.ProfileHMM-class.html#version"><a title="csb.bio.hmm.ProfileHMM.version" class="py-name" href="#" onclick="return doclink('link-0', 'version', 'link-0');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">__version__</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-1" class="py-name"><a title="csb.bio.hmm.ProfileHMM.version" class="py-name" href="#" onclick="return doclink('link-1', 'version', 'link-0');">version</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">3</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="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt id="link-2" class="py-name"><a title="csb.bio.hmm.ProfileHMM.version" class="py-name" href="#" onclick="return doclink('link-2', 'version', 'link-0');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_package</tt> <tt class="py-op">=</tt> <tt class="py-name">__name__</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_major</tt> <tt class="py-op">=</tt> <tt id="link-3" class="py-name"><a title="csb.bio.hmm.ProfileHMM.version" class="py-name" href="#" onclick="return doclink('link-3', 'version', 'link-0');">version</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_minor</tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name"><a title="csb.bio.hmm.ProfileHMM.version" class="py-name" href="#" onclick="return doclink('link-4', 'version', 'link-0');">version</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_micro</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="csb.bio.hmm.ProfileHMM.version" class="py-name" href="#" onclick="return doclink('link-5', 'version', 'link-0');">version</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_revision</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> </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">len</tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="csb.bio.hmm.ProfileHMM.version" class="py-name" href="#" onclick="return doclink('link-6', 'version', 'link-0');">version</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_revision</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="csb.bio.hmm.ProfileHMM.version" class="py-name" href="#" onclick="return doclink('link-7', 'version', 'link-0');">version</a></tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
</div><a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
<a name="Version.__str__"></a><div id="Version.__str__-def"><a name="L213"></a><tt class="py-lineno">213</tt> <a class="py-toggle" href="#" id="Version.__str__-toggle" onclick="return toggle('Version.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#__str__">__str__</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="Version.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.__str__-expanded"><a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Variable csb.Version.short=csb.Version-class.html#short"><a title="csb.Version.short" class="py-name" href="#" onclick="return doclink('link-8', 'short', 'link-8');">short</a></tt> </tt>
</div><a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> </tt>
<a name="Version.__repr__"></a><div id="Version.__repr__-def"><a name="L216"></a><tt class="py-lineno">216</tt> <a class="py-toggle" href="#" id="Version.__repr__-toggle" onclick="return toggle('Version.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#__repr__">__repr__</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="Version.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.__repr__-expanded"><a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'{0.package} {0.full}'</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method csb.bio.io.wwpdb.EntryID.format()=csb.bio.io.wwpdb.EntryID-class.html#format,Method csb.bio.io.wwpdb.SeqResID.format()=csb.bio.io.wwpdb.SeqResID-class.html#format,Method csb.bio.sequence.A3MAlignment.format()=csb.bio.sequence.A3MAlignment-class.html#format,Method csb.bio.sequence.AbstractAlignment.format()=csb.bio.sequence.AbstractAlignment-class.html#format"><a title="csb.bio.io.wwpdb.EntryID.format
csb.bio.io.wwpdb.SeqResID.format
csb.bio.sequence.A3MAlignment.format
csb.bio.sequence.AbstractAlignment.format" class="py-name" href="#" onclick="return doclink('link-9', 'format', 'link-9');">format</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Version.major"></a><div id="Version.major-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="Version.major-toggle" onclick="return toggle('Version.major');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#major">major</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="Version.major-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.major-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> Major version (huge, incompatible changes)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_major</tt><tt class="py-op">)</tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Version.minor"></a><div id="Version.minor-def"><a name="L228"></a><tt class="py-lineno">228</tt> <a class="py-toggle" href="#" id="Version.minor-toggle" onclick="return toggle('Version.minor');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#minor">minor</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="Version.minor-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.minor-expanded"><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"> Minor version (significant, but compatible changes)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_minor</tt><tt class="py-op">)</tt> </tt>
</div><a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Version.micro"></a><div id="Version.micro-def"><a name="L236"></a><tt class="py-lineno">236</tt> <a class="py-toggle" href="#" id="Version.micro-toggle" onclick="return toggle('Version.micro');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#micro">micro</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="Version.micro-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.micro-expanded"><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> Micro version (bug fixes and small enhancements)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_micro</tt><tt class="py-op">)</tt> </tt>
</div><a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Version.revision"></a><div id="Version.revision-def"><a name="L244"></a><tt class="py-lineno">244</tt> <a class="py-toggle" href="#" id="Version.revision-toggle" onclick="return toggle('Version.revision');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#revision">revision</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="Version.revision-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.revision-expanded"><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"> Build number (exact repository revision number)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: int</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_revision</tt><tt class="py-op">)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_revision</tt> </tt>
</div><a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Version.short"></a><div id="Version.short-def"><a name="L255"></a><tt class="py-lineno">255</tt> <a class="py-toggle" href="#" id="Version.short-toggle" onclick="return toggle('Version.short');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#short">short</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="Version.short-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.short-expanded"><a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring"> Canonical three-part version number.</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'{0.major}.{0.minor}.{0.micro}'</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="csb.bio.io.wwpdb.EntryID.format
csb.bio.io.wwpdb.SeqResID.format
csb.bio.sequence.A3MAlignment.format
csb.bio.sequence.AbstractAlignment.format" class="py-name" href="#" onclick="return doclink('link-10', 'format', 'link-9');">format</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><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-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Version.full"></a><div id="Version.full-def"><a name="L262"></a><tt class="py-lineno">262</tt> <a class="py-toggle" href="#" id="Version.full-toggle" onclick="return toggle('Version.full');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#full">full</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="Version.full-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.full-expanded"><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-docstring"> Full version, including the repository revision number.</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'{0.major}.{0.minor}.{0.micro}.{0.revision}'</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="csb.bio.io.wwpdb.EntryID.format
csb.bio.io.wwpdb.SeqResID.format
csb.bio.sequence.A3MAlignment.format
csb.bio.sequence.AbstractAlignment.format" class="py-name" href="#" onclick="return doclink('link-11', 'format', 'link-9');">format</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="Version.package"></a><div id="Version.package-def"><a name="L269"></a><tt class="py-lineno">269</tt> <a class="py-toggle" href="#" id="Version.package-toggle" onclick="return toggle('Version.package');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.Version-class.html#package">package</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="Version.package-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Version.package-expanded"><a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_package</tt> </tt>
</div></div><a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt><script type="text/javascript">
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