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csb.apps.bfite-pysrc.html
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<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>csb.apps.bfite</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Home link -->
<th> <a
href="csb-module.html">Home</a> </th>
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<!-- Project homepage -->
<th class="navbar" align="right" width="100%">
<table border="0" cellpadding="0" cellspacing="0">
<tr><th class="navbar" align="center"
>CSB v1.2.5.d7fd331</th>
</tr></table></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="csb-module.html">Package csb</a> ::
<a href="csb.apps-module.html">Package apps</a> ::
Module bfite
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="csb.apps.bfite-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="csb.apps.bfite-module.html">Module csb.apps.bfite</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">Python application for robust structure superposition of an ensemble of structures.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">bfite models non-rigid displacements in protein ensembles with outlier-tolerant</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">probability distributions.</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-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package csb=csb-module.html"><a title="csb" class="py-name" href="#" onclick="return doclink('link-0', 'csb', 'link-0');">csb</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package csb.apps=csb.apps-module.html"><a title="csb.apps" class="py-name" href="#" onclick="return doclink('link-1', 'apps', 'link-1');">apps</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="csb" class="py-name" href="#" onclick="return doclink('link-2', 'csb', 'link-0');">csb</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Package csb.bio=csb.bio-module.html"><a title="csb.bio" class="py-name" href="#" onclick="return doclink('link-3', 'bio', 'link-3');">bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method csb.bio.fragments.BenchmarkAdapter.structure()=csb.bio.fragments.BenchmarkAdapter-class.html#structure,Method csb.bio.hmm.ProfileHMM.structure()=csb.bio.hmm.ProfileHMM-class.html#structure,Package csb.bio.structure=csb.bio.structure-module.html"><a title="csb.bio.fragments.BenchmarkAdapter.structure
csb.bio.hmm.ProfileHMM.structure
csb.bio.structure" class="py-name" href="#" onclick="return doclink('link-4', 'structure', 'link-4');">structure</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="csb" class="py-name" href="#" onclick="return doclink('link-5', 'csb', 'link-0');">csb</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="csb.bio" class="py-name" href="#" onclick="return doclink('link-6', 'bio', 'link-3');">bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Package csb.bio.io=csb.bio.io-module.html,Package csb.io=csb.io-module.html"><a title="csb.bio.io
csb.io" class="py-name" href="#" onclick="return doclink('link-7', 'io', 'link-7');">io</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Module csb.bio.io.wwpdb=csb.bio.io.wwpdb-module.html"><a title="csb.bio.io.wwpdb" class="py-name" href="#" onclick="return doclink('link-8', 'wwpdb', 'link-8');">wwpdb</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Class csb.bio.io.wwpdb.LegacyStructureParser=csb.bio.io.wwpdb.LegacyStructureParser-class.html"><a title="csb.bio.io.wwpdb.LegacyStructureParser" class="py-name" href="#" onclick="return doclink('link-9', 'LegacyStructureParser', 'link-9');">LegacyStructureParser</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="csb" class="py-name" href="#" onclick="return doclink('link-10', 'csb', 'link-0');">csb</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="csb.bio" class="py-name" href="#" onclick="return doclink('link-11', 'bio', 'link-3');">bio</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Package csb.bio.utils=csb.bio.utils-module.html"><a title="csb.bio.utils" class="py-name" href="#" onclick="return doclink('link-12', 'utils', 'link-12');">utils</a></tt> <tt class="py-keyword">import</tt> <tt id="link-13" class="py-name" targets="Function csb.bio.utils.average_structure()=csb.bio.utils-module.html#average_structure"><a title="csb.bio.utils.average_structure" class="py-name" href="#" onclick="return doclink('link-13', 'average_structure', 'link-13');">average_structure</a></tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name" targets="Function csb.bio.utils.fit()=csb.bio.utils-module.html#fit"><a title="csb.bio.utils.fit" class="py-name" href="#" onclick="return doclink('link-14', 'fit', 'link-14');">fit</a></tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name" targets="Function csb.bio.utils.wfit()=csb.bio.utils-module.html#wfit"><a title="csb.bio.utils.wfit" class="py-name" href="#" onclick="return doclink('link-15', 'wfit', 'link-15');">wfit</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-16" class="py-name"><a title="csb" class="py-name" href="#" onclick="return doclink('link-16', 'csb', 'link-0');">csb</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Package csb.statistics=csb.statistics-module.html,Variable csb.statistics.samplers.mc.multichain.AbstractExchangeMC.statistics=csb.statistics.samplers.mc.multichain.AbstractExchangeMC-class.html#statistics"><a title="csb.statistics
csb.statistics.samplers.mc.multichain.AbstractExchangeMC.statistics" class="py-name" href="#" onclick="return doclink('link-17', 'statistics', 'link-17');">statistics</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Module csb.statistics.scalemixture=csb.statistics.scalemixture-module.html"><a title="csb.statistics.scalemixture" class="py-name" href="#" onclick="return doclink('link-18', 'scalemixture', 'link-18');">scalemixture</a></tt> <tt class="py-keyword">import</tt> <tt id="link-19" class="py-name" targets="Class csb.statistics.scalemixture.ScaleMixture=csb.statistics.scalemixture.ScaleMixture-class.html"><a title="csb.statistics.scalemixture.ScaleMixture" class="py-name" href="#" onclick="return doclink('link-19', 'ScaleMixture', 'link-19');">ScaleMixture</a></tt><tt class="py-op">,</tt> <tt id="link-20" class="py-name" targets="Class csb.statistics.scalemixture.GammaPrior=csb.statistics.scalemixture.GammaPrior-class.html"><a title="csb.statistics.scalemixture.GammaPrior" class="py-name" href="#" onclick="return doclink('link-20', 'GammaPrior', 'link-20');">GammaPrior</a></tt> </tt>
<a name="ExitCodes"></a><div id="ExitCodes-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <a class="py-toggle" href="#" id="ExitCodes-toggle" onclick="return toggle('ExitCodes');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="csb.apps.bfite.ExitCodes-class.html">ExitCodes</a><tt class="py-op">(</tt><tt class="py-base-class">csb</tt><tt class="py-op">.</tt><tt class="py-base-class">apps</tt><tt class="py-op">.</tt><tt class="py-base-class">ExitCodes</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExitCodes-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ExitCodes-expanded"><a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt id="link-21" class="py-name" targets="Variable csb.apps.bfit.ExitCodes.IO_ERROR=csb.apps.bfit.ExitCodes-class.html#IO_ERROR,Variable csb.apps.bfite.ExitCodes.IO_ERROR=csb.apps.bfite.ExitCodes-class.html#IO_ERROR,Variable csb.apps.buildhmm.ExitCodes.IO_ERROR=csb.apps.buildhmm.ExitCodes-class.html#IO_ERROR,Variable csb.apps.csfrag.ExitCodes.IO_ERROR=csb.apps.csfrag.ExitCodes-class.html#IO_ERROR,Variable csb.apps.embd.ExitCodes.IO_ERROR=csb.apps.embd.ExitCodes-class.html#IO_ERROR,Variable csb.apps.hhfrag.ExitCodes.IO_ERROR=csb.apps.hhfrag.ExitCodes-class.html#IO_ERROR,Variable csb.apps.hhsearch.ExitCodes.IO_ERROR=csb.apps.hhsearch.ExitCodes-class.html#IO_ERROR,Variable csb.apps.precision.ExitCodes.IO_ERROR=csb.apps.precision.ExitCodes-class.html#IO_ERROR,Variable csb.apps.promix.ExitCodes.IO_ERROR=csb.apps.promix.ExitCodes-class.html#IO_ERROR"><a title="csb.apps.bfit.ExitCodes.IO_ERROR
csb.apps.bfite.ExitCodes.IO_ERROR
csb.apps.buildhmm.ExitCodes.IO_ERROR
csb.apps.csfrag.ExitCodes.IO_ERROR
csb.apps.embd.ExitCodes.IO_ERROR
csb.apps.hhfrag.ExitCodes.IO_ERROR
csb.apps.hhsearch.ExitCodes.IO_ERROR
csb.apps.precision.ExitCodes.IO_ERROR
csb.apps.promix.ExitCodes.IO_ERROR" class="py-name" href="#" onclick="return doclink('link-21', 'IO_ERROR', 'link-21');">IO_ERROR</a></tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt> </tt>
</div><a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="AppRunner"></a><div id="AppRunner-def"><a name="L19"></a><tt class="py-lineno"> 19</tt> <a class="py-toggle" href="#" id="AppRunner-toggle" onclick="return toggle('AppRunner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="csb.apps.bfite.AppRunner-class.html">AppRunner</a><tt class="py-op">(</tt><tt class="py-base-class">csb</tt><tt class="py-op">.</tt><tt class="py-base-class">apps</tt><tt class="py-op">.</tt><tt class="py-base-class">AppRunner</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AppRunner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AppRunner-expanded"><a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">property</tt> </tt>
<a name="AppRunner.target"></a><div id="AppRunner.target-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="AppRunner.target-toggle" onclick="return toggle('AppRunner.target');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.apps.bfite.AppRunner-class.html#target">target</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="AppRunner.target-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AppRunner.target-expanded"><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-22" class="py-name" targets="Class csb.apps.bfit.BFitApp=csb.apps.bfit.BFitApp-class.html,Class csb.apps.bfite.BFitApp=csb.apps.bfite.BFitApp-class.html"><a title="csb.apps.bfit.BFitApp
csb.apps.bfite.BFitApp" class="py-name" href="#" onclick="return doclink('link-22', 'BFitApp', 'link-22');">BFitApp</a></tt> </tt>
</div><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="AppRunner.command_line"></a><div id="AppRunner.command_line-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="AppRunner.command_line-toggle" onclick="return toggle('AppRunner.command_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.apps.bfite.AppRunner-class.html#command_line">command_line</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="AppRunner.command_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AppRunner.command_line-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="csb" class="py-name" href="#" onclick="return doclink('link-23', 'csb', 'link-0');">csb</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="csb.apps" class="py-name" href="#" onclick="return doclink('link-24', 'apps', 'link-1');">apps</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Class csb.apps.ArgHandler=csb.apps.ArgHandler-class.html"><a title="csb.apps.ArgHandler" class="py-name" href="#" onclick="return doclink('link-25', 'ArgHandler', 'link-25');">ArgHandler</a></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="Variable csb.apps.AppRunner.program=csb.apps.AppRunner-class.html#program,Variable csb.apps.hhsearch.HHsearch.program=csb.apps.hhsearch.HHsearch-class.html#program,Variable csb.test.Console.program=csb.test.Console-class.html#program"><a title="csb.apps.AppRunner.program
csb.apps.hhsearch.HHsearch.program
csb.test.Console.program" class="py-name" href="#" onclick="return doclink('link-26', 'program', 'link-26');">program</a></tt><tt class="py-op">,</tt> <tt class="py-name">__doc__</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-comment"># Input structures</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">cmd</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method csb.apps.ArgHandler.add_positional_argument()=csb.apps.ArgHandler-class.html#add_positional_argument"><a title="csb.apps.ArgHandler.add_positional_argument" class="py-name" href="#" onclick="return doclink('link-27', 'add_positional_argument', 'link-27');">add_positional_argument</a></tt><tt class="py-op">(</tt><tt class="py-string">'pdb'</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-string">'full path to the ensemble'</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-comment"># Optional arguments </tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">cmd</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method csb.apps.ArgHandler.add_scalar_option()=csb.apps.ArgHandler-class.html#add_scalar_option"><a title="csb.apps.ArgHandler.add_scalar_option" class="py-name" href="#" onclick="return doclink('link-28', 'add_scalar_option', 'link-28');">add_scalar_option</a></tt><tt class="py-op">(</tt><tt class="py-string">'chain'</tt><tt class="py-op">,</tt> <tt class="py-string">'c'</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-string">'Chain'</tt><tt class="py-op">,</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-string">'A'</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">cmd</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="csb.apps.ArgHandler.add_scalar_option" class="py-name" href="#" onclick="return doclink('link-29', 'add_scalar_option', 'link-28');">add_scalar_option</a></tt><tt class="py-op">(</tt><tt class="py-string">'scalemixture'</tt><tt class="py-op">,</tt> <tt class="py-string">'s'</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-string">'Scale mixture distribution'</tt><tt class="py-op">,</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-string">'student'</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">choices</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">'student'</tt><tt class="py-op">,</tt> <tt class="py-string">'k'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">cmd</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="csb.apps.ArgHandler.add_scalar_option" class="py-name" href="#" onclick="return doclink('link-30', 'add_scalar_option', 'link-28');">add_scalar_option</a></tt><tt class="py-op">(</tt><tt class="py-string">'alignment'</tt><tt class="py-op">,</tt> <tt class="py-string">'a'</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-string">'Alignment in fasta format defining equivalent positions\n'</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">'Assumes that chain1 is the first sequence of '</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">'the alignment and chain2 the second sequence'</tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">cmd</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="csb.apps.ArgHandler.add_scalar_option" class="py-name" href="#" onclick="return doclink('link-31', 'add_scalar_option', 'link-28');">add_scalar_option</a></tt><tt class="py-op">(</tt><tt class="py-string">'outfile'</tt><tt class="py-op">,</tt> <tt class="py-string">'o'</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-string">'file to which the rotated second '</tt> <tt class="py-op">+</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-string">'structure will be written'</tt><tt class="py-op">,</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-string">'bfit.pdb'</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">cmd</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="csb.apps.ArgHandler.add_scalar_option" class="py-name" href="#" onclick="return doclink('link-32', 'add_scalar_option', 'link-28');">add_scalar_option</a></tt><tt class="py-op">(</tt><tt class="py-string">'niter'</tt><tt class="py-op">,</tt> <tt class="py-string">'n'</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-string">'Number of optimization steps'</tt><tt class="py-op">,</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-number">200</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cmd</tt> </tt>
</div></div><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="BFitApp"></a><div id="BFitApp-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="BFitApp-toggle" onclick="return toggle('BFitApp');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="csb.apps.bfite.BFitApp-class.html">BFitApp</a><tt class="py-op">(</tt><tt class="py-base-class">csb</tt><tt class="py-op">.</tt><tt class="py-base-class">apps</tt><tt class="py-op">.</tt><tt class="py-base-class">Application</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BFitApp-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BFitApp-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> Python application for robust structure superposition of two protein structures</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="BFitApp.main"></a><div id="BFitApp.main-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="BFitApp.main-toggle" onclick="return toggle('BFitApp.main');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.apps.bfite.BFitApp-class.html#main">main</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="BFitApp.main-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BFitApp.main-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt id="link-33" class="py-name" targets="Variable csb.apps.ArgHandler.parser=csb.apps.ArgHandler-class.html#parser,Variable csb.apps.hhsearch.HHsearch.parser=csb.apps.hhsearch.HHsearch-class.html#parser"><a title="csb.apps.ArgHandler.parser
csb.apps.hhsearch.HHsearch.parser" class="py-name" href="#" onclick="return doclink('link-33', 'parser', 'link-33');">parser</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="csb.bio.io.wwpdb.LegacyStructureParser" class="py-name" href="#" onclick="return doclink('link-34', 'LegacyStructureParser', 'link-9');">LegacyStructureParser</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Variable csb.apps.AppRunner.args=csb.apps.AppRunner-class.html#args,Variable csb.apps.Application.args=csb.apps.Application-class.html#args"><a title="csb.apps.AppRunner.args
csb.apps.Application.args" class="py-name" href="#" onclick="return doclink('link-35', 'args', 'link-35');">args</a></tt><tt class="py-op">.</tt><tt class="py-name">pdb</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt id="link-36" class="py-name" targets="Method csb.bio.io.wwpdb.AbstractStructureParser.models()=csb.bio.io.wwpdb.AbstractStructureParser-class.html#models,Variable csb.bio.structure.Ensemble.models=csb.bio.structure.Ensemble-class.html#models"><a title="csb.bio.io.wwpdb.AbstractStructureParser.models
csb.bio.structure.Ensemble.models" class="py-name" href="#" onclick="return doclink('link-36', 'models', 'link-36');">models</a></tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="csb.apps.ArgHandler.parser
csb.apps.hhsearch.HHsearch.parser" class="py-name" href="#" onclick="return doclink('link-37', 'parser', 'link-33');">parser</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="csb.bio.io.wwpdb.AbstractStructureParser.models
csb.bio.structure.Ensemble.models" class="py-name" href="#" onclick="return doclink('link-38', 'models', 'link-36');">models</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt> <tt class="py-keyword">as</tt> <tt class="py-name">e</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Static Method csb.apps.AppRunner.exit()=csb.apps.AppRunner-class.html#exit,Static Method csb.apps.Application.exit()=csb.apps.Application-class.html#exit,Static Method csb.build.Console.exit()=csb.build.Console-class.html#exit"><a title="csb.apps.AppRunner.exit
csb.apps.Application.exit
csb.build.Console.exit" class="py-name" href="#" onclick="return doclink('link-39', 'exit', 'link-39');">exit</a></tt><tt class="py-op">(</tt><tt class="py-string">'PDB file parsing failed\n'</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">e</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Variable csb.core.EnumItem.value=csb.core.EnumItem-class.html#value,Variable csb.statistics.pdf.parameterized.AbstractParameter.value=csb.statistics.pdf.parameterized.AbstractParameter-class.html#value"><a title="csb.core.EnumItem.value
csb.statistics.pdf.parameterized.AbstractParameter.value" class="py-name" href="#" onclick="return doclink('link-40', 'value', 'link-40');">value</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-41" class="py-name" targets="Class csb.apps.ExitCodes=csb.apps.ExitCodes-class.html,Class csb.apps.bfit.ExitCodes=csb.apps.bfit.ExitCodes-class.html,Class csb.apps.bfite.ExitCodes=csb.apps.bfite.ExitCodes-class.html,Class csb.apps.buildhmm.ExitCodes=csb.apps.buildhmm.ExitCodes-class.html,Class csb.apps.csfrag.ExitCodes=csb.apps.csfrag.ExitCodes-class.html,Class csb.apps.embd.ExitCodes=csb.apps.embd.ExitCodes-class.html,Class csb.apps.helloworld.ExitCodes=csb.apps.helloworld.ExitCodes-class.html,Class csb.apps.hhfrag.ExitCodes=csb.apps.hhfrag.ExitCodes-class.html,Class csb.apps.hhsearch.ExitCodes=csb.apps.hhsearch.ExitCodes-class.html,Class csb.apps.precision.ExitCodes=csb.apps.precision.ExitCodes-class.html,Class csb.apps.promix.ExitCodes=csb.apps.promix.ExitCodes-class.html"><a title="csb.apps.ExitCodes
csb.apps.bfit.ExitCodes
csb.apps.bfite.ExitCodes
csb.apps.buildhmm.ExitCodes
csb.apps.csfrag.ExitCodes
csb.apps.embd.ExitCodes
csb.apps.helloworld.ExitCodes
csb.apps.hhfrag.ExitCodes
csb.apps.hhsearch.ExitCodes
csb.apps.precision.ExitCodes
csb.apps.promix.ExitCodes" class="py-name" href="#" onclick="return doclink('link-41', 'ExitCodes', 'link-41');">ExitCodes</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="csb.apps.bfit.ExitCodes.IO_ERROR
csb.apps.bfite.ExitCodes.IO_ERROR
csb.apps.buildhmm.ExitCodes.IO_ERROR
csb.apps.csfrag.ExitCodes.IO_ERROR
csb.apps.embd.ExitCodes.IO_ERROR
csb.apps.hhfrag.ExitCodes.IO_ERROR
csb.apps.hhsearch.ExitCodes.IO_ERROR
csb.apps.precision.ExitCodes.IO_ERROR
csb.apps.promix.ExitCodes.IO_ERROR" class="py-name" href="#" onclick="return doclink('link-42', 'IO_ERROR', 'link-21');">IO_ERROR</a></tt><tt class="py-op">)</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-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="csb.bio.io.wwpdb.AbstractStructureParser.models
csb.bio.structure.Ensemble.models" class="py-name" href="#" onclick="return doclink('link-43', 'models', 'link-36');">models</a></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="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="csb.apps.AppRunner.exit
csb.apps.Application.exit
csb.build.Console.exit" class="py-name" href="#" onclick="return doclink('link-44', 'exit', 'link-39');">exit</a></tt><tt class="py-op">(</tt><tt class="py-string">'PDB file contains only one model'</tt><tt class="py-op">,</tt> <tt id="link-45" class="py-name"><a title="csb.apps.ExitCodes
csb.apps.bfit.ExitCodes
csb.apps.bfite.ExitCodes
csb.apps.buildhmm.ExitCodes
csb.apps.csfrag.ExitCodes
csb.apps.embd.ExitCodes
csb.apps.helloworld.ExitCodes
csb.apps.hhfrag.ExitCodes
csb.apps.hhsearch.ExitCodes
csb.apps.precision.ExitCodes
csb.apps.promix.ExitCodes" class="py-name" href="#" onclick="return doclink('link-45', 'ExitCodes', 'link-41');">ExitCodes</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Variable csb.apps.ExitCodes.USAGE_ERROR=csb.apps.ExitCodes-class.html#USAGE_ERROR"><a title="csb.apps.ExitCodes.USAGE_ERROR" class="py-name" href="#" onclick="return doclink('link-46', 'USAGE_ERROR', 'link-46');">USAGE_ERROR</a></tt><tt class="py-op">)</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-name">ensemble</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="csb.apps.ArgHandler.parser
csb.apps.hhsearch.HHsearch.parser" class="py-name" href="#" onclick="return doclink('link-47', 'parser', 'link-33');">parser</a></tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Method csb.bio.io.wwpdb.AbstractStructureParser.parse_models()=csb.bio.io.wwpdb.AbstractStructureParser-class.html#parse_models"><a title="csb.bio.io.wwpdb.AbstractStructureParser.parse_models" class="py-name" href="#" onclick="return doclink('link-48', 'parse_models', 'link-48');">parse_models</a></tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="csb.bio.io.wwpdb.AbstractStructureParser.models
csb.bio.structure.Ensemble.models" class="py-name" href="#" onclick="return doclink('link-49', 'models', 'link-36');">models</a></tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">X</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Static Method csb.io.tsv.Expression.array()=csb.io.tsv.Expression-class.html#array"><a title="csb.io.tsv.Expression.array" class="py-name" href="#" onclick="return doclink('link-50', 'array', 'link-50');">array</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-51" class="py-name" targets="Variable csb.statistics.maxent.MaxentPosterior.model=csb.statistics.maxent.MaxentPosterior-class.html#model"><a title="csb.statistics.maxent.MaxentPosterior.model" class="py-name" href="#" onclick="return doclink('link-51', 'model', 'link-51');">model</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="csb.apps.AppRunner.args
csb.apps.Application.args" class="py-name" href="#" onclick="return doclink('link-52', 'args', 'link-35');">args</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Variable csb.bio.fragments.rosetta.RosettaFragment.chain=csb.bio.fragments.rosetta.RosettaFragment-class.html#chain,Method csb.bio.hmm.ProfileHMM.chain()=csb.bio.hmm.ProfileHMM-class.html#chain,Variable csb.bio.io.wwpdb.EntryID.chain=csb.bio.io.wwpdb.EntryID-class.html#chain,Variable csb.bio.io.wwpdb.ResidueInfo.chain=csb.bio.io.wwpdb.ResidueInfo-class.html#chain,Variable csb.bio.nmr.ContactMap.chain=csb.bio.nmr.ContactMap-class.html#chain"><a title="csb.bio.fragments.rosetta.RosettaFragment.chain
csb.bio.hmm.ProfileHMM.chain
csb.bio.io.wwpdb.EntryID.chain
csb.bio.io.wwpdb.ResidueInfo.chain
csb.bio.nmr.ContactMap.chain" class="py-name" href="#" onclick="return doclink('link-53', 'chain', 'link-53');">chain</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method csb.bio.structure.AbstractEntity.get_coordinates()=csb.bio.structure.AbstractEntity-class.html#get_coordinates,Method csb.bio.structure.Atom.get_coordinates()=csb.bio.structure.Atom-class.html#get_coordinates,Method csb.bio.structure.Residue.get_coordinates()=csb.bio.structure.Residue-class.html#get_coordinates"><a title="csb.bio.structure.AbstractEntity.get_coordinates
csb.bio.structure.Atom.get_coordinates
csb.bio.structure.Residue.get_coordinates" class="py-name" href="#" onclick="return doclink('link-54', 'get_coordinates', 'link-54');">get_coordinates</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'CA'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">True</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-55" class="py-name"><a title="csb.statistics.maxent.MaxentPosterior.model" class="py-name" href="#" onclick="return doclink('link-55', 'model', 'link-51');">model</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">ensemble</tt><tt class="py-op">]</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">x_mu</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="csb.bio.utils.average_structure" class="py-name" href="#" onclick="return doclink('link-56', 'average_structure', 'link-13');">average_structure</a></tt><tt class="py-op">(</tt><tt class="py-name">X</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-comment">#n = X.shape[1]</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">X</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Variable csb.statistics.pdf.InverseGaussian.shape=csb.statistics.pdf.InverseGaussian-class.html#shape"><a title="csb.statistics.pdf.InverseGaussian.shape" class="py-name" href="#" onclick="return doclink('link-57', 'shape', 'link-57');">shape</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt id="link-58" class="py-name" targets="Variable csb.statistics.mixtures.AbstractStructureMixture.R=csb.statistics.mixtures.AbstractStructureMixture-class.html#R"><a title="csb.statistics.mixtures.AbstractStructureMixture.R" class="py-name" href="#" onclick="return doclink('link-58', 'R', 'link-58');">R</a></tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-number">3</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 id="link-59" class="py-name" targets="Variable csb.statistics.mixtures.AbstractStructureMixture.t=csb.statistics.mixtures.AbstractStructureMixture-class.html#t"><a title="csb.statistics.mixtures.AbstractStructureMixture.t" class="py-name" href="#" onclick="return doclink('link-59', 't', 'link-59');">t</a></tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</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>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt id="link-60" class="py-name" targets="Variable csb.statistics.scalemixture.ScaleMixture.prior=csb.statistics.scalemixture.ScaleMixture-class.html#prior"><a title="csb.statistics.scalemixture.ScaleMixture.prior" class="py-name" href="#" onclick="return doclink('link-60', 'prior', 'link-60');">prior</a></tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="csb.statistics.scalemixture.GammaPrior" class="py-name" href="#" onclick="return doclink('link-61', 'GammaPrior', 'link-20');">GammaPrior</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">mixture</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name"><a title="csb.statistics.scalemixture.ScaleMixture" class="py-name" href="#" onclick="return doclink('link-62', 'ScaleMixture', 'link-19');">ScaleMixture</a></tt><tt class="py-op">(</tt><tt id="link-63" class="py-name" targets="Variable csb.statistics.mixtures.GaussianMixture.scales=csb.statistics.mixtures.GaussianMixture-class.html#scales,Variable csb.statistics.scalemixture.ScaleMixture.scales=csb.statistics.scalemixture.ScaleMixture-class.html#scales"><a title="csb.statistics.mixtures.GaussianMixture.scales
csb.statistics.scalemixture.ScaleMixture.scales" class="py-name" href="#" onclick="return doclink('link-63', 'scales', 'link-63');">scales</a></tt><tt class="py-op">=</tt><tt class="py-name">X</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="csb.statistics.pdf.InverseGaussian.shape" class="py-name" href="#" onclick="return doclink('link-64', 'shape', 'link-57');">shape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt id="link-65" class="py-name"><a title="csb.statistics.scalemixture.ScaleMixture.prior" class="py-name" href="#" onclick="return doclink('link-65', 'prior', 'link-60');">prior</a></tt><tt class="py-op">=</tt><tt id="link-66" class="py-name"><a title="csb.statistics.scalemixture.ScaleMixture.prior" class="py-name" href="#" onclick="return doclink('link-66', 'prior', 'link-60');">prior</a></tt><tt class="py-op">,</tt> <tt class="py-name">d</tt><tt class="py-op">=</tt><tt class="py-number">3</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt id="link-67" class="py-name"><a title="csb.statistics.mixtures.AbstractStructureMixture.R" class="py-name" href="#" onclick="return doclink('link-67', 'R', 'link-58');">R</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-68" class="py-name"><a title="csb.statistics.mixtures.AbstractStructureMixture.t" class="py-name" href="#" onclick="return doclink('link-68', 't', 'link-59');">t</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name"><a title="csb.bio.utils.fit" class="py-name" href="#" onclick="return doclink('link-69', 'fit', 'link-14');">fit</a></tt><tt class="py-op">(</tt><tt class="py-name">x_mu</tt><tt class="py-op">,</tt> <tt class="py-name">X</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># gibbs sampling cycle</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="csb.apps.AppRunner.args
csb.apps.Application.args" class="py-name" href="#" onclick="return doclink('link-70', 'args', 'link-35');">args</a></tt><tt class="py-op">.</tt><tt class="py-name">niter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-comment"># apply rotation</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt id="link-71" class="py-name" targets="Variable csb.apps.embd.Deconvolution.data=csb.apps.embd.Deconvolution-class.html#data,Variable csb.io.tsv.Expression.data=csb.io.tsv.Expression-class.html#data,Variable csb.statistics.maxent.MaxentPosterior.data=csb.statistics.maxent.MaxentPosterior-class.html#data,Variable csb.test.Config.data=csb.test.Config-class.html#data"><a title="csb.apps.embd.Deconvolution.data
csb.io.tsv.Expression.data
csb.statistics.maxent.MaxentPosterior.data
csb.test.Config.data" class="py-name" href="#" onclick="return doclink('link-71', 'data', 'link-71');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="csb.io.tsv.Expression.array" class="py-name" href="#" onclick="return doclink('link-72', 'array', 'link-50');">array</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">x_mu</tt> <tt class="py-op">-</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">dot</tt><tt class="py-op">(</tt><tt class="py-name">X</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt id="link-73" class="py-name"><a title="csb.statistics.mixtures.AbstractStructureMixture.R" class="py-name" href="#" onclick="return doclink('link-73', 'R', 'link-58');">R</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt id="link-74" class="py-name"><a title="csb.statistics.mixtures.AbstractStructureMixture.t" class="py-name" href="#" onclick="return doclink('link-74', 't', 'link-59');">t</a></tt><tt class="py-op">[</tt><tt class="py-name">i</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-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">**</tt> <tt class="py-number">0.5</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">T</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-comment"># sample scales</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">mixture</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Method csb.statistics.pdf.AbstractDensity.estimate()=csb.statistics.pdf.AbstractDensity-class.html#estimate,Method csb.statistics.pdf.AbstractEstimator.estimate()=csb.statistics.pdf.AbstractEstimator-class.html#estimate,Method csb.statistics.pdf.DirichletEstimator.estimate()=csb.statistics.pdf.DirichletEstimator-class.html#estimate,Method csb.statistics.pdf.GammaMLEstimator.estimate()=csb.statistics.pdf.GammaMLEstimator-class.html#estimate,Method csb.statistics.pdf.GaussianMLEstimator.estimate()=csb.statistics.pdf.GaussianMLEstimator-class.html#estimate,Method csb.statistics.pdf.GenNormalBruteForceEstimator.estimate()=csb.statistics.pdf.GenNormalBruteForceEstimator-class.html#estimate,Method csb.statistics.pdf.GumbelMaxMomentsEstimator.estimate()=csb.statistics.pdf.GumbelMaxMomentsEstimator-class.html#estimate,Method csb.statistics.pdf.GumbelMinMomentsEstimator.estimate()=csb.statistics.pdf.GumbelMinMomentsEstimator-class.html#estimate,Method csb.statistics.pdf.InverseGaussianMLEstimator.estimate()=csb.statistics.pdf.InverseGaussianMLEstimator-class.html#estimate,Method csb.statistics.pdf.LaplaceMLEstimator.estimate()=csb.statistics.pdf.LaplaceMLEstimator-class.html#estimate,Method csb.statistics.pdf.MultivariateGaussianMLEstimator.estimate()=csb.statistics.pdf.MultivariateGaussianMLEstimator-class.html#estimate,Method csb.statistics.pdf.NullEstimator.estimate()=csb.statistics.pdf.NullEstimator-class.html#estimate,Method csb.statistics.scalemixture.GammaPosteriorMAP.estimate()=csb.statistics.scalemixture.GammaPosteriorMAP-class.html#estimate,Method csb.statistics.scalemixture.GammaPosteriorSampler.estimate()=csb.statistics.scalemixture.GammaPosteriorSampler-class.html#estimate,Method csb.statistics.scalemixture.GammaScaleMAP.estimate()=csb.statistics.scalemixture.GammaScaleMAP-class.html#estimate,Method csb.statistics.scalemixture.GammaScaleSampler.estimate()=csb.statistics.scalemixture.GammaScaleSampler-class.html#estimate,Method csb.statistics.scalemixture.InvGammaPosteriorMAP.estimate()=csb.statistics.scalemixture.InvGammaPosteriorMAP-class.html#estimate,Method csb.statistics.scalemixture.InvGammaPosteriorSampler.estimate()=csb.statistics.scalemixture.InvGammaPosteriorSampler-class.html#estimate,Method csb.statistics.scalemixture.InvGammaScaleMAP.estimate()=csb.statistics.scalemixture.InvGammaScaleMAP-class.html#estimate,Method csb.statistics.scalemixture.InvGammaScaleSampler.estimate()=csb.statistics.scalemixture.InvGammaScaleSampler-class.html#estimate,Method csb.statmech.wham.AbstractWHAM.estimate()=csb.statmech.wham.AbstractWHAM-class.html#estimate,Method csb.statmech.wham.NonparametricWHAM.estimate()=csb.statmech.wham.NonparametricWHAM-class.html#estimate,Method csb.statmech.wham.WHAM.estimate()=csb.statmech.wham.WHAM-class.html#estimate"><a title="csb.statistics.pdf.AbstractDensity.estimate
csb.statistics.pdf.AbstractEstimator.estimate
csb.statistics.pdf.DirichletEstimator.estimate
csb.statistics.pdf.GammaMLEstimator.estimate
csb.statistics.pdf.GaussianMLEstimator.estimate
csb.statistics.pdf.GenNormalBruteForceEstimator.estimate
csb.statistics.pdf.GumbelMaxMomentsEstimator.estimate
csb.statistics.pdf.GumbelMinMomentsEstimator.estimate
csb.statistics.pdf.InverseGaussianMLEstimator.estimate
csb.statistics.pdf.LaplaceMLEstimator.estimate
csb.statistics.pdf.MultivariateGaussianMLEstimator.estimate
csb.statistics.pdf.NullEstimator.estimate
csb.statistics.scalemixture.GammaPosteriorMAP.estimate
csb.statistics.scalemixture.GammaPosteriorSampler.estimate
csb.statistics.scalemixture.GammaScaleMAP.estimate
csb.statistics.scalemixture.GammaScaleSampler.estimate
csb.statistics.scalemixture.InvGammaPosteriorMAP.estimate
csb.statistics.scalemixture.InvGammaPosteriorSampler.estimate
csb.statistics.scalemixture.InvGammaScaleMAP.estimate
csb.statistics.scalemixture.InvGammaScaleSampler.estimate
csb.statmech.wham.AbstractWHAM.estimate
csb.statmech.wham.NonparametricWHAM.estimate
csb.statmech.wham.WHAM.estimate" class="py-name" href="#" onclick="return doclink('link-75', 'estimate', 'link-75');">estimate</a></tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="csb.apps.embd.Deconvolution.data
csb.io.tsv.Expression.data
csb.statistics.maxent.MaxentPosterior.data
csb.test.Config.data" class="py-name" href="#" onclick="return doclink('link-76', 'data', 'link-71');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-comment"># sample rotations</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-77" class="py-name"><a title="csb.statistics.mixtures.AbstractStructureMixture.R" class="py-name" href="#" onclick="return doclink('link-77', 'R', 'link-58');">R</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-78" class="py-name"><a title="csb.statistics.mixtures.AbstractStructureMixture.t" class="py-name" href="#" onclick="return doclink('link-78', 't', 'link-59');">t</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-79" class="py-name"><a title="csb.bio.utils.wfit" class="py-name" href="#" onclick="return doclink('link-79', 'wfit', 'link-15');">wfit</a></tt><tt class="py-op">(</tt><tt class="py-name">x_mu</tt><tt class="py-op">,</tt> <tt class="py-name">X</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">mixture</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="csb.statistics.mixtures.GaussianMixture.scales
csb.statistics.scalemixture.ScaleMixture.scales" class="py-name" href="#" onclick="return doclink('link-80', 'scales', 'link-63');">scales</a></tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">out_ensemble</tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name"><a title="csb" class="py-name" href="#" onclick="return doclink('link-81', 'csb', 'link-0');">csb</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="csb.bio" class="py-name" href="#" onclick="return doclink('link-82', 'bio', 'link-3');">bio</a></tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="csb.bio.fragments.BenchmarkAdapter.structure
csb.bio.hmm.ProfileHMM.structure
csb.bio.structure" class="py-name" href="#" onclick="return doclink('link-83', 'structure', 'link-4');">structure</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Class csb.bio.structure.Ensemble=csb.bio.structure.Ensemble-class.html"><a title="csb.bio.structure.Ensemble" class="py-name" href="#" onclick="return doclink('link-84', 'Ensemble', 'link-84');">Ensemble</a></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>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt id="link-85" class="py-name"><a title="csb.statistics.maxent.MaxentPosterior.model" class="py-name" href="#" onclick="return doclink('link-85', 'model', 'link-51');">model</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">ensemble</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt id="link-86" class="py-name"><a title="csb.statistics.maxent.MaxentPosterior.model" class="py-name" href="#" onclick="return doclink('link-86', 'model', 'link-51');">model</a></tt><tt class="py-op">.</tt><tt id="link-87" class="py-name" targets="Method csb.bio.fragments.Assignment.transform()=csb.bio.fragments.Assignment-class.html#transform,Method csb.bio.structure.AbstractEntity.transform()=csb.bio.structure.AbstractEntity-class.html#transform,Method csb.bio.structure.Atom.transform()=csb.bio.structure.Atom-class.html#transform,Method csb.bio.structure.DisorderedAtom.transform()=csb.bio.structure.DisorderedAtom-class.html#transform,Function csb.bio.utils.transform()=csb.bio.utils-module.html#transform"><a title="csb.bio.fragments.Assignment.transform
csb.bio.structure.AbstractEntity.transform
csb.bio.structure.Atom.transform
csb.bio.structure.DisorderedAtom.transform
csb.bio.utils.transform" class="py-name" href="#" onclick="return doclink('link-87', 'transform', 'link-87');">transform</a></tt><tt class="py-op">(</tt><tt id="link-88" class="py-name"><a title="csb.statistics.mixtures.AbstractStructureMixture.R" class="py-name" href="#" onclick="return doclink('link-88', 'R', 'link-58');">R</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-89" class="py-name"><a title="csb.statistics.mixtures.AbstractStructureMixture.t" class="py-name" href="#" onclick="return doclink('link-89', 't', 'link-59');">t</a></tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">out_ensemble</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="csb.bio.io.wwpdb.AbstractStructureParser.models
csb.bio.structure.Ensemble.models" class="py-name" href="#" onclick="return doclink('link-90', 'models', 'link-36');">models</a></tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Method csb.bio.fragments.rosetta.RosettaFragmentMap.append()=csb.bio.fragments.rosetta.RosettaFragmentMap-class.html#append,Method csb.bio.hmm.EmissionTable.append()=csb.bio.hmm.EmissionTable-class.html#append,Method csb.bio.hmm.HMMLayer.append()=csb.bio.hmm.HMMLayer-class.html#append,Method csb.bio.hmm.TransitionTable.append()=csb.bio.hmm.TransitionTable-class.html#append,Method csb.bio.structure.ChainResiduesCollection.append()=csb.bio.structure.ChainResiduesCollection-class.html#append,Method csb.bio.structure.DisorderedAtom.append()=csb.bio.structure.DisorderedAtom-class.html#append,Method csb.bio.structure.EnsembleModelsCollection.append()=csb.bio.structure.EnsembleModelsCollection-class.html#append,Method csb.bio.structure.ResidueAtomsTable.append()=csb.bio.structure.ResidueAtomsTable-class.html#append,Method csb.bio.structure.SecondaryStructure.append()=csb.bio.structure.SecondaryStructure-class.html#append,Method csb.bio.structure.StructureChainsTable.append()=csb.bio.structure.StructureChainsTable-class.html#append,Method csb.core.CollectionContainer.append()=csb.core.CollectionContainer-class.html#append,Method csb.core.DictionaryContainer.append()=csb.core.DictionaryContainer-class.html#append"><a title="csb.bio.fragments.rosetta.RosettaFragmentMap.append
csb.bio.hmm.EmissionTable.append
csb.bio.hmm.HMMLayer.append
csb.bio.hmm.TransitionTable.append
csb.bio.structure.ChainResiduesCollection.append
csb.bio.structure.DisorderedAtom.append
csb.bio.structure.EnsembleModelsCollection.append
csb.bio.structure.ResidueAtomsTable.append
csb.bio.structure.SecondaryStructure.append
csb.bio.structure.StructureChainsTable.append
csb.core.CollectionContainer.append
csb.core.DictionaryContainer.append" class="py-name" href="#" onclick="return doclink('link-91', 'append', 'link-91');">append</a></tt><tt class="py-op">(</tt><tt id="link-92" class="py-name"><a title="csb.statistics.maxent.MaxentPosterior.model" class="py-name" href="#" onclick="return doclink('link-92', 'model', 'link-51');">model</a></tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">out_ensemble</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name" targets="Method csb.bio.structure.Ensemble.to_pdb()=csb.bio.structure.Ensemble-class.html#to_pdb,Method csb.bio.structure.Structure.to_pdb()=csb.bio.structure.Structure-class.html#to_pdb"><a title="csb.bio.structure.Ensemble.to_pdb
csb.bio.structure.Structure.to_pdb" class="py-name" href="#" onclick="return doclink('link-93', 'to_pdb', 'link-93');">to_pdb</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="csb.apps.AppRunner.args
csb.apps.Application.args" class="py-name" href="#" onclick="return doclink('link-94', 'args', 'link-35');">args</a></tt><tt class="py-op">.</tt><tt class="py-name">outfile</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="csb.apps.bfite-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main-expanded"><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt id="link-95" class="py-name" targets="Class csb.apps.AppRunner=csb.apps.AppRunner-class.html,Class csb.apps.bfit.AppRunner=csb.apps.bfit.AppRunner-class.html,Class csb.apps.bfite.AppRunner=csb.apps.bfite.AppRunner-class.html,Class csb.apps.buildhmm.AppRunner=csb.apps.buildhmm.AppRunner-class.html,Class csb.apps.csfrag.AppRunner=csb.apps.csfrag.AppRunner-class.html,Class csb.apps.embd.AppRunner=csb.apps.embd.AppRunner-class.html,Class csb.apps.helloworld.AppRunner=csb.apps.helloworld.AppRunner-class.html,Class csb.apps.hhfrag.AppRunner=csb.apps.hhfrag.AppRunner-class.html,Class csb.apps.hhsearch.AppRunner=csb.apps.hhsearch.AppRunner-class.html,Class csb.apps.precision.AppRunner=csb.apps.precision.AppRunner-class.html,Class csb.apps.promix.AppRunner=csb.apps.promix.AppRunner-class.html"><a title="csb.apps.AppRunner
csb.apps.bfit.AppRunner
csb.apps.bfite.AppRunner
csb.apps.buildhmm.AppRunner
csb.apps.csfrag.AppRunner
csb.apps.embd.AppRunner
csb.apps.helloworld.AppRunner
csb.apps.hhfrag.AppRunner
csb.apps.hhsearch.AppRunner
csb.apps.precision.AppRunner
csb.apps.promix.AppRunner" class="py-name" href="#" onclick="return doclink('link-95', 'AppRunner', 'link-95');">AppRunner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Method csb.apps.AppRunner.run()=csb.apps.AppRunner-class.html#run,Method csb.apps.buildhmm.ProfileBuilder.run()=csb.apps.buildhmm.ProfileBuilder-class.html#run,Method csb.apps.embd.Deconvolution.run()=csb.apps.embd.Deconvolution-class.html#run,Method csb.apps.embd.DeconvolutionApp.run()=csb.apps.embd.DeconvolutionApp-class.html#run,Method csb.apps.hhsearch.HHsearch.run()=csb.apps.hhsearch.HHsearch-class.html#run,Method csb.apps.precision.LibrarySuperimposer.run()=csb.apps.precision.LibrarySuperimposer-class.html#run,Method csb.bio.io.procheck.ProcheckParser.run()=csb.bio.io.procheck.ProcheckParser-class.html#run,Method csb.bio.io.whatif.WhatCheckParser.run()=csb.bio.io.whatif.WhatCheckParser-class.html#run,Static Method csb.build.Console.run()=csb.build.Console-class.html#run,Method csb.core.InterruptibleThread.run()=csb.core.InterruptibleThread-class.html#run,Static Method csb.io.Shell.run()=csb.io.Shell-class.html#run,Method csb.io.plots.Backend.run()=csb.io.plots.Backend-class.html#run,Method csb.test.Console.run()=csb.test.Console-class.html#run"><a title="csb.apps.AppRunner.run
csb.apps.buildhmm.ProfileBuilder.run
csb.apps.embd.Deconvolution.run
csb.apps.embd.DeconvolutionApp.run
csb.apps.hhsearch.HHsearch.run
csb.apps.precision.LibrarySuperimposer.run
csb.bio.io.procheck.ProcheckParser.run
csb.bio.io.whatif.WhatCheckParser.run
csb.build.Console.run
csb.core.InterruptibleThread.run
csb.io.Shell.run
csb.io.plots.Backend.run
csb.test.Console.run" class="py-name" href="#" onclick="return doclink('link-96', 'run', 'link-96');">run</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</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="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt id="link-97" class="py-name" targets="Method csb.apps.Application.main()=csb.apps.Application-class.html#main,Method csb.apps.bfit.BFitApp.main()=csb.apps.bfit.BFitApp-class.html#main,Function csb.apps.bfit.main()=csb.apps.bfit-module.html#main,Method csb.apps.bfite.BFitApp.main()=csb.apps.bfite.BFitApp-class.html#main,Function csb.apps.bfite.main()=csb.apps.bfite-module.html#main,Method csb.apps.buildhmm.BuildProfileApp.main()=csb.apps.buildhmm.BuildProfileApp-class.html#main,Function csb.apps.buildhmm.main()=csb.apps.buildhmm-module.html#main,Method csb.apps.csfrag.CSfragApp.main()=csb.apps.csfrag.CSfragApp-class.html#main,Function csb.apps.csfrag.main()=csb.apps.csfrag-module.html#main,Method csb.apps.embd.DeconvolutionApp.main()=csb.apps.embd.DeconvolutionApp-class.html#main,Function csb.apps.embd.main()=csb.apps.embd-module.html#main,Method csb.apps.helloworld.HelloWorldApp.main()=csb.apps.helloworld.HelloWorldApp-class.html#main,Function csb.apps.helloworld.main()=csb.apps.helloworld-module.html#main,Method csb.apps.hhfrag.HHfragApp.main()=csb.apps.hhfrag.HHfragApp-class.html#main,Function csb.apps.hhfrag.main()=csb.apps.hhfrag-module.html#main,Method csb.apps.hhsearch.HHsearchApp.main()=csb.apps.hhsearch.HHsearchApp-class.html#main,Function csb.apps.hhsearch.main()=csb.apps.hhsearch-module.html#main,Method csb.apps.precision.PrecisionApp.main()=csb.apps.precision.PrecisionApp-class.html#main,Function csb.apps.precision.main()=csb.apps.precision-module.html#main,Method csb.apps.promix.ProMixApp.main()=csb.apps.promix.ProMixApp-class.html#main,Function csb.apps.promix.main()=csb.apps.promix-module.html#main,Function csb.build.main()=csb.build-module.html#main,Function csb.test.app.main()=csb.test.app-module.html#main"><a title="csb.apps.Application.main
csb.apps.bfit.BFitApp.main
csb.apps.bfit.main
csb.apps.bfite.BFitApp.main
csb.apps.bfite.main
csb.apps.buildhmm.BuildProfileApp.main
csb.apps.buildhmm.main
csb.apps.csfrag.CSfragApp.main
csb.apps.csfrag.main
csb.apps.embd.DeconvolutionApp.main
csb.apps.embd.main
csb.apps.helloworld.HelloWorldApp.main
csb.apps.helloworld.main
csb.apps.hhfrag.HHfragApp.main
csb.apps.hhfrag.main
csb.apps.hhsearch.HHsearchApp.main
csb.apps.hhsearch.main
csb.apps.precision.PrecisionApp.main
csb.apps.precision.main
csb.apps.promix.ProMixApp.main
csb.apps.promix.main
csb.build.main
csb.test.app.main" class="py-name" href="#" onclick="return doclink('link-97', 'main', 'link-97');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt><script type="text/javascript">
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