Skip to content

Commit

Permalink
update documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
@gqdong
gqdong committed Jun 17, 2014
1 parent 7c26cc4 commit b45aa2b
Show file tree
Hide file tree
Showing 15 changed files with 13 additions and 360 deletions.
Binary file modified doc/_build/doctrees/environment.pickle
View file
Binary file not shown.
Binary file modified doc/_build/doctrees/loop.doctree
View file
Binary file not shown.
Binary file modified doc/_build/doctrees/mhc2.doctree
View file
Binary file not shown.
Binary file modified doc/_build/doctrees/sampling.doctree
View file
Binary file not shown.
Binary file modified doc/_build/doctrees/statsTable.doctree
View file
Binary file not shown.
Binary file modified doc/_build/doctrees/utility.doctree
View file
Binary file not shown.
144 changes: 5 additions & 139 deletions doc/_build/html/genindex.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -65,12 +65,10 @@ <h1 id="index">Index</h1>
| <a href="#K"><strong>K</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#O"><strong>O</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>

</div>
<h2 id="A">A</h2>
Expand Down Expand Up @@ -130,18 +128,10 @@ <h2 id="C">C</h2>
<dt><a href="rankScore.html#rankScores.spdsscore.calc_score">calc_score() (rankScores.spdsscore method)</a>
</dt>


<dt><a href="rankScore.html#rankScores.spdsscore.calc_score_fromlist">calc_score_fromlist() (rankScores.spdsscore method)</a>
</dt>

</dl></td>
<td style="width: 33%" valign="top"><dl>

<dt><a href="statsTable.html#statsTable.rawsp.calc_sp_all">calc_sp_all() (statsTable.rawsp method)</a>
</dt>


<dt><a href="loop.html#loop.checkRMSD">checkRMSD (class in loop)</a>
<dt><a href="rankScore.html#rankScores.spdsscore.calc_score_fromlist">calc_score_fromlist() (rankScores.spdsscore method)</a>
</dt>


Expand All @@ -155,23 +145,19 @@ <h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>

<dt><a href="utility.html#utility.decode_genmethod">decode_genmethod() (in module utility)</a>
</dt>


<dt><a href="decoys.html#module-decoys">decoys (module)</a>
</dt>


<dt><a href="decoys.html#decoys.decoys4single">decoys4single (class in decoys)</a>
</dt>

</dl></td>
<td style="width: 33%" valign="top"><dl>

<dt><a href="decoys.html#decoys.decoyset">decoyset (class in decoys)</a>
</dt>

</dl></td>
<td style="width: 33%" valign="top"><dl>

<dt><a href="rankScore.html#rankScores.dsscore">dsscore (class in rankScores)</a>
</dt>
Expand Down Expand Up @@ -216,16 +202,6 @@ <h2 id="G">G</h2>
<dt><a href="jobSchedule.html#jobSchedule.generate_job_submit_script">generate_job_submit_script() (in module jobSchedule)</a>
</dt>


<dt><a href="loop.html#loop.MyLoop.get_loop_actions">get_loop_actions() (loop.MyLoop method)</a>
</dt>

<dd><dl>

<dt><a href="loop.html#loop.ORLoop.get_loop_actions">(loop.ORLoop method)</a>
</dt>

</dl></dd>
</dl></td>
<td style="width: 33%" valign="top"><dl>

Expand Down Expand Up @@ -279,87 +255,27 @@ <h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>

<dt><a href="utility.html#utility.load_scorer">load_scorer() (in module utility)</a>
</dt>


<dt><a href="jobSchedule.html#jobSchedule.localtask">localtask (class in jobSchedule)</a>
</dt>

</dl></td>
<td style="width: 33%" valign="top"><dl>

<dt><a href="loop.html#module-loop">loop (module)</a>
</dt>


<dt><a href="loop.html#loop.MyLoop.loop_model_analysis">loop_model_analysis() (loop.MyLoop method)</a>
</dt>

<dd><dl>

<dt><a href="loop.html#loop.ORLoop.loop_model_analysis">(loop.ORLoop method)</a>
</dt>

</dl></dd>
</dl></td>
</tr></table>

<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>

<dt><a href="utility.html#utility.MemoryMonitor">MemoryMonitor (class in utility)</a>
</dt>


<dt><a href="modelSelection.html#module-modelSelection">modelSelection (module)</a>
</dt>


<dt><a href="jobSchedule.html#jobSchedule.task.monitor">monitor() (jobSchedule.task method)</a>
</dt>


<dt><a href="jobSchedule.html#jobSchedule.tasklist.monitor2end">monitor2end() (jobSchedule.tasklist method)</a>
</dt>

</dl></td>
<td style="width: 33%" valign="top"><dl>

<dt><a href="loop.html#loop.MyLoop.multiple_loop_models">multiple_loop_models() (loop.MyLoop method)</a>
</dt>


<dt><a href="loop.html#loop.MyLoop">MyLoop (class in loop)</a>
</dt>


<dt><a href="utility.html#utility.Mymodel">Mymodel (class in utility)</a>
</dt>


<dt><a href="utility.html#utility.mypickle">mypickle (class in utility)</a>
</dt>

</dl></td>
</tr></table>

<h2 id="O">O</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>

<dt><a href="sampling.html#sampling.optimizer.optimize">optimize() (sampling.optimizer method)</a>
</dt>


<dt><a href="sampling.html#sampling.optimizer">optimizer (class in sampling)</a>
</dt>

</dl></td>
<td style="width: 33%" valign="top"><dl>

<dt><a href="loop.html#loop.ORLoop">ORLoop (class in loop)</a>
<dt><a href="jobSchedule.html#jobSchedule.tasklist.monitor2end">monitor2end() (jobSchedule.tasklist method)</a>
</dt>

</dl></td>
Expand All @@ -383,10 +299,6 @@ <h2 id="R">R</h2>
</dt>


<dt><a href="statsTable.html#statsTable.rawsp">rawsp (class in statsTable)</a>
</dt>


<dt><a href="recoveryFucntion.html#module-recoveryFunction">recoveryFunction (module)</a>
</dt>

Expand All @@ -407,14 +319,6 @@ <h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>

<dt><a href="sampling.html#module-sampling">sampling (module)</a>
</dt>


<dt><a href="statsTable.html#statsTable.scaledsp">scaledsp (class in statsTable)</a>
</dt>


<dt><a href="scorer.html#scorer.scorer">scorer (class in scorer)</a>
</dt>

Expand All @@ -437,34 +341,16 @@ <h2 id="S">S</h2>
</dt>


<dt><a href="loop.html#loop.sgmd">sgmd() (in module loop)</a>
</dt>


<dt><a href="loop.html#loop.MyLoop.single_loop_model">single_loop_model() (loop.MyLoop method)</a>
</dt>

<dd><dl>

<dt><a href="loop.html#loop.ORLoop.single_loop_model">(loop.ORLoop method)</a>
<dt><a href="env.html#envConfig.SOAPenv">SOAPenv (class in envConfig)</a>
</dt>

</dl></dd>
</dl></td>
<td style="width: 33%" valign="top"><dl>

<dt><a href="env.html#envConfig.SOAPenv">SOAPenv (class in envConfig)</a>
</dt>


<dt><a href="rankScore.html#rankScores.spdsscore">spdsscore (class in rankScores)</a>
</dt>


<dt><a href="loop.html#loop.sprefine">sprefine (class in loop)</a>
</dt>


<dt><a href="refineScore.html#refineScores.sprefinescore">sprefinescore (class in refineScores)</a>
</dt>

Expand All @@ -476,10 +362,6 @@ <h2 id="S">S</h2>
<dt><a href="modelSelection.html#modelSelection.spss">spss (class in modelSelection)</a>
</dt>


<dt><a href="statsTable.html#module-statsTable">statsTable (module)</a>
</dt>

</dl></td>
</tr></table>

Expand All @@ -500,22 +382,6 @@ <h2 id="T">T</h2>
<dt><a href="jobSchedule.html#jobSchedule.tasklist">tasklist (class in jobSchedule)</a>
</dt>

</dl></td>
</tr></table>

<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>

<dt><a href="utility.html#utility.MemoryMonitor.usage">usage() (utility.MemoryMonitor method)</a>
</dt>

</dl></td>
<td style="width: 33%" valign="top"><dl>

<dt><a href="utility.html#module-utility">utility (module)</a>
</dt>

</dl></td>
</tr></table>

Expand Down
77 changes: 2 additions & 75 deletions doc/_build/html/loop.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,81 +55,8 @@ <h3>Navigation</h3>
<div class="bodywrapper">
<div class="body">

<div class="section" id="module-loop">
<span id="loop-modeling"></span><h1>Loop modeling<a class="headerlink" href="#module-loop" title="Permalink to this headline"></a></h1>
<p>SOAP loop model.</p>
<dl class="class">
<dt id="loop.MyLoop">
<em class="property">class </em><tt class="descclassname">loop.</tt><tt class="descname">MyLoop</tt><big>(</big><em>env, sequence, alnfile=None, knowns=[], inimodel=None, deviation=None, library_schedule=None, csrfile=None, inifile=None, assess_methods=None, loop_assess_methods=None, refinepot=['$(LIB)/atmcls-mf.lib', '$(LIB)/dist-mf.lib'], loops=[], calcrmsds='111', nonbond_spine=0.1, contact_shell=12.0, deviations=50, energytrace=False, assess_trace=True</em><big>)</big><a class="reference internal" href="_modules/loop.html#MyLoop"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loop.MyLoop" title="Permalink to this definition"></a></dt>
<dd><p>SOAP loop modeling class</p>
<dl class="method">
<dt id="loop.MyLoop.get_loop_actions">
<tt class="descname">get_loop_actions</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/loop.html#MyLoop.get_loop_actions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loop.MyLoop.get_loop_actions" title="Permalink to this definition"></a></dt>
<dd><p>Get actions to carry out during loop optimization</p>
</dd></dl>

<dl class="method">
<dt id="loop.MyLoop.loop_model_analysis">
<tt class="descname">loop_model_analysis</tt><big>(</big><em>atmsel</em>, <em>ini_model</em>, <em>filename</em>, <em>out</em>, <em>id1</em>, <em>num</em><big>)</big><a class="reference internal" href="_modules/loop.html#MyLoop.loop_model_analysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loop.MyLoop.loop_model_analysis" title="Permalink to this definition"></a></dt>
<dd><p>Energy evaluation and assessment, and write out the loop model</p>
</dd></dl>

<dl class="method">
<dt id="loop.MyLoop.multiple_loop_models">
<tt class="descname">multiple_loop_models</tt><big>(</big><em>atmsel</em>, <em>ini_model</em>, <em>num</em>, <em>sched</em><big>)</big><a class="reference internal" href="_modules/loop.html#MyLoop.multiple_loop_models"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loop.MyLoop.multiple_loop_models" title="Permalink to this definition"></a></dt>
<dd><p>Build all loop models for a given initial model</p>
</dd></dl>

<dl class="method">
<dt id="loop.MyLoop.single_loop_model">
<tt class="descname">single_loop_model</tt><big>(</big><em>atmsel</em>, <em>ini_model</em>, <em>num</em>, <em>id1</em>, <em>sched</em>, <em>parallel=False</em><big>)</big><a class="reference internal" href="_modules/loop.html#MyLoop.single_loop_model"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loop.MyLoop.single_loop_model" title="Permalink to this definition"></a></dt>
<dd><p>Build a single loop model</p>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="loop.ORLoop">
<em class="property">class </em><tt class="descclassname">loop.</tt><tt class="descname">ORLoop</tt><big>(</big><em>env, sequence, alnfile=None, knowns=[], inimodel=None, deviation=None, library_schedule=None, csrfile=None, inifile=None, assess_methods=None, loop_assess_methods=None, refinepot=['$(LIB)/atmcls-mf.lib', '$(LIB)/dist-mf.lib'], assess_trace=False, loops=[], calcrmsds='111', nonbond_spine=0.1, contact_shell=12.0, deviations=50, energytrace=False</em><big>)</big><a class="headerlink" href="#loop.ORLoop" title="Permalink to this definition"></a></dt>
<dd><p>Original loop modeling class</p>
<dl class="method">
<dt id="loop.ORLoop.get_loop_actions">
<tt class="descname">get_loop_actions</tt><big>(</big><big>)</big><a class="headerlink" href="#loop.ORLoop.get_loop_actions" title="Permalink to this definition"></a></dt>
<dd><p>Get actions to carry out during loop optimization</p>
</dd></dl>

<dl class="method">
<dt id="loop.ORLoop.loop_model_analysis">
<tt class="descname">loop_model_analysis</tt><big>(</big><em>atmsel</em>, <em>ini_model</em>, <em>filename</em>, <em>out</em>, <em>id1</em>, <em>num</em><big>)</big><a class="headerlink" href="#loop.ORLoop.loop_model_analysis" title="Permalink to this definition"></a></dt>
<dd><p>Energy evaluation and assessment, and write out the loop model</p>
</dd></dl>

<dl class="method">
<dt id="loop.ORLoop.single_loop_model">
<tt class="descname">single_loop_model</tt><big>(</big><em>atmsel</em>, <em>ini_model</em>, <em>num</em>, <em>id1</em>, <em>sched</em>, <em>parallel=False</em><big>)</big><a class="headerlink" href="#loop.ORLoop.single_loop_model" title="Permalink to this definition"></a></dt>
<dd><p>Build a single loop model</p>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="loop.checkRMSD">
<em class="property">class </em><tt class="descclassname">loop.</tt><tt class="descname">checkRMSD</tt><big>(</big><em>skip</em>, <em>loopObj</em>, <em>first=False</em>, <em>last=False</em>, <em>start=0</em><big>)</big><a class="reference internal" href="_modules/loop.html#checkRMSD"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loop.checkRMSD" title="Permalink to this definition"></a></dt>
<dd><p>calcualte the RMSDs of intermediate loops</p>
</dd></dl>

<dl class="function">
<dt id="loop.sgmd">
<tt class="descclassname">loop.</tt><tt class="descname">sgmd</tt><big>(</big><em>atmsel</em>, <em>actions</em><big>)</big><a class="reference internal" href="_modules/loop.html#sgmd"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loop.sgmd" title="Permalink to this definition"></a></dt>
<dd><p>Very slow MD annealing</p>
</dd></dl>

<dl class="class">
<dt id="loop.sprefine">
<em class="property">class </em><tt class="descclassname">loop.</tt><tt class="descname">sprefine</tt><big>(</big><em>dslist='101'</em>, <em>bm='loop.100.8'</em>, <em>criteria='bestrmsd'</em>, <em>nonbond_spline=0.1</em>, <em>contact_shell=12.0</em>, <em>deviations=50</em>, <em>assess=''</em>, <em>mcrmsdonly=False</em>, <em>spmodel=None</em>, <em>refineProtocal=None</em>, <em>trace=True</em>, <em>saveStructure=False</em><big>)</big><a class="reference internal" href="_modules/loop.html#sprefine"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#loop.sprefine" title="Permalink to this definition"></a></dt>
<dd><p>SOAP loop refinement benchmark class</p>
</dd></dl>

<div class="section" id="loop-modeling">
<h1>Loop modeling<a class="headerlink" href="#loop-modeling" title="Permalink to this headline"></a></h1>
</div>


Expand Down
4 changes: 2 additions & 2 deletions doc/_build/html/mhc2.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -250,7 +250,7 @@ <h1>Calcualte SOAP poential for ranking MHC2 peptides.<a class="headerlink" href
<ul class="simple">
<li>Select the best models with distance and accessbility feature, multiple recovery functions, only considering interface atom pairs.</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">sps</span> <span class="kn">import</span> <span class="o">*</span>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">SOAP</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">profile</span>
<span class="kn">import</span> <span class="nn">sys</span>
Expand Down Expand Up @@ -710,7 +710,7 @@ <h1>Calcualte SOAP poential for ranking MHC2 peptides.<a class="headerlink" href
<ol class="arabic simple" start="4">
<li>Run SOAP script to calculate the optimal statistical potential using the best model found in the last step.</li>
</ol>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">sps</span> <span class="kn">import</span> <span class="o">*</span>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">SOAP</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">profile</span>
<span class="kn">import</span> <span class="nn">sys</span>
Expand Down
Binary file modified doc/_build/html/objects.inv
View file
Binary file not shown.
Loading

0 comments on commit b45aa2b

Please sign in to comment.