From bf5fc1503c7ebd4d0ddb9089e6e2f506ce3af718 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 17 Sep 2015 15:02:44 +0200
Subject: [PATCH] Updated documentation
---
.../_modules/promod3/rawmodel/_closegaps.html | 82 +++++++++++++++++-
doc/html/_sources/rawmodel/index.txt | 2 +
doc/html/genindex.html | 4 +
doc/html/objects.inv | Bin 2854 -> 2869 bytes
doc/html/rawmodel/index.html | 31 +++++++
doc/html/searchindex.js | 2 +-
6 files changed, 117 insertions(+), 4 deletions(-)
diff --git a/doc/html/_modules/promod3/rawmodel/_closegaps.html b/doc/html/_modules/promod3/rawmodel/_closegaps.html
index c274c0cd..57caaa23 100644
--- a/doc/html/_modules/promod3/rawmodel/_closegaps.html
+++ b/doc/html/_modules/promod3/rawmodel/_closegaps.html
@@ -52,8 +52,9 @@
<div class="body" role="main">
<h1>Source code for promod3.rawmodel._closegaps</h1><div class="highlight"><pre>
-<span class="sd">'''Single function to be 'injected' into the RawModellingResult class in the</span>
-<span class="sd">__init__.py file.</span>
+<span class="sd">'''Functions to be 'injected' into the RawModellingResult class in the</span>
+<span class="sd">__init__.py file. Do not use directly, they belong to the RawModellingResult</span>
+<span class="sd">class and are to be called as class method, for instances of this class.</span>
<span class="sd">'''</span>
<span class="kn">import</span> <span class="nn">ost</span>
@@ -207,7 +208,82 @@
<span class="k">return</span> <span class="n">scorer</span>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">'_CloseSmallDeletions'</span><span class="p">]</span>
+<span class="k">def</span> <span class="nf">_MergeGapsByDistance</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">distance</span><span class="p">):</span>
+ <span class="sd">'''Merge 2 neighbouring gaps by deleting residues in-between.</span>
+
+<span class="sd"> Check if two neighbouring gaps are at max. *distance* residues apart from</span>
+<span class="sd"> each other. Then delete the residues and store a new gap spanning the whole</span>
+<span class="sd"> stretch of original gaps and the deleted region. Original gaps will be</span>
+<span class="sd"> removed. Stem residues count to the gap, so **A-A-A** has a distance of 0.</span>
+
+<span class="sd"> .. testcode:: mergegapsbydist</span>
+<span class="sd"> :hide:</span>
+
+<span class="sd"> from promod3 import rawmodel</span>
+
+<span class="sd"> tpl = ost.io.LoadPDB('../tests/rawmodel/data/raw-modeling/1mcg.pdb')</span>
+<span class="sd"> aln = ost.seq.CreateAlignment(ost.seq.CreateSequence('trg',</span>
+<span class="sd"> 'DDFAGDTKNLGHN'),</span>
+<span class="sd"> ost.seq.CreateSequence('tpl',</span>
+<span class="sd"> 'NN----A----LF'))</span>
+<span class="sd"> aln.AttachView(1, tpl.CreateFullView())</span>
+<span class="sd"> rmodel = rawmodel.BuildRawModel(aln)</span>
+<span class="sd"> assert len(rmodel.gaps) == 2</span>
+<span class="sd"> rmodel.MergeGapsByDistance(0)</span>
+<span class="sd"> assert len(rmodel.gaps) == 1</span>
+
+<span class="sd"> .. doctest:: mergegapsbydist</span>
+
+<span class="sd"> import ost</span>
+<span class="sd"> from promod3 import rawmodel</span>
+
+<span class="sd"> tpl = ost.io.LoadPDB('1mcg.pdb')</span>
+<span class="sd"> aln = ost.io.LoadAlignment('1mcg_aln.fasta')</span>
+<span class="sd"> aln.AttachView(1, tpl.CreateFullView())</span>
+<span class="sd"> rmodel = rawmodel.BuildRawModel(aln)</span>
+<span class="sd"> rmodel.MergeGapsByDistance(0)</span>
+
+<span class="sd"> :param distance: The max. no. of residues between two gaps up to which</span>
+<span class="sd"> merge happens.</span>
+<span class="sd"> :type distance: :class:`int`</span>
+
+<span class="sd"> :return: Nothing.</span>
+<span class="sd"> '''</span>
+ <span class="c"># IMPORTANT: the assumption is that RawModelingResult stores gaps</span>
+ <span class="c"># sequentially</span>
+
+ <span class="c"># indicate if we merged gaps and should check for more</span>
+ <span class="n">try_again</span> <span class="o">=</span> <span class="bp">True</span>
+
+ <span class="c"># The number of gaps changes on merge, so we cannot just iterate them.</span>
+ <span class="c"># If we merged gaps, we do not know if this was the last one so try_again</span>
+ <span class="c"># is set to True. If no more gaps were merged, we stop by leaving try_again</span>
+ <span class="c"># as False.</span>
+ <span class="k">while</span> <span class="n">try_again</span><span class="p">:</span>
+ <span class="n">try_again</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="c"># iterate all but the last gap, since we are always looking ahead</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="n">current_gap</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="n">next_gap</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span>
+ <span class="c"># check that we are on the same chain</span>
+ <span class="k">if</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span> <span class="o">!=</span> <span class="n">next_gap</span><span class="o">.</span><span class="n">GetChain</span><span class="p">():</span>
+ <span class="k">continue</span>
+ <span class="c"># no merging of gaps at the end AND the start :)</span>
+ <span class="k">if</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">IsNTerminal</span><span class="p">()</span> <span class="ow">and</span> <span class="n">next_gap</span><span class="o">.</span><span class="n">IsCTerminal</span><span class="p">():</span>
+ <span class="k">continue</span>
+ <span class="c"># get the distance between the gaps</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">next_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span> \
+ <span class="o">-</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">dist</span> <span class="o"><=</span> <span class="n">distance</span><span class="p">:</span>
+ <span class="c"># gaps are close enough, combine! combine!</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">MergeGaps</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Merged gap </span><span class="si">%s</span><span class="s"> and </span><span class="si">%s</span><span class="s"> into </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> \
+ <span class="p">(</span><span class="n">current_gap</span><span class="p">,</span> <span class="n">next_gap</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
+ <span class="n">try_again</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="k">break</span>
+
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">'_CloseSmallDeletions'</span><span class="p">,</span> <span class="s">'_MergeGapsByDistance'</span><span class="p">]</span>
<span class="c"># LocalWords: modeling stereochemically param</span>
</pre></div>
diff --git a/doc/html/_sources/rawmodel/index.txt b/doc/html/_sources/rawmodel/index.txt
index 21267831..939917b5 100644
--- a/doc/html/_sources/rawmodel/index.txt
+++ b/doc/html/_sources/rawmodel/index.txt
@@ -95,6 +95,8 @@ Raw Coordinate Modeling API
.. automethod:: CloseSmallDeletions
+ .. automethod:: MergeGapsByDistance
+
.. LocalWords: currentmodule promod aln AttachView BuildRawModel pdb calpha
.. LocalWords: RawModelingResult StructuralGapList rawmodel Modeling os ost
.. LocalWords: testcode tempfile io LoadAlignment LoadPDB fh fn doctest API
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 240c6966..1265ed7c 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -1157,6 +1157,10 @@
</dl></dd>
+ <dt><a href="rawmodel/index.html#promod3.rawmodel.RawModelingResult.MergeGapsByDistance">MergeGapsByDistance() (promod3.rawmodel.RawModelingResult method)</a>
+ </dt>
+
+
<dt><a href="rawmodel/index.html#promod3.rawmodel.RawModelingResult.model">model (promod3.rawmodel.RawModelingResult attribute)</a>
</dt>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
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diff --git a/doc/html/rawmodel/index.html b/doc/html/rawmodel/index.html
index 7cf292f1..074ba58c 100644
--- a/doc/html/rawmodel/index.html
+++ b/doc/html/rawmodel/index.html
@@ -200,6 +200,37 @@ returned.</p>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.rawmodel.RawModelingResult.MergeGapsByDistance">
+<code class="descname">MergeGapsByDistance</code><span class="sig-paren">(</span><em>distance</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.rawmodel.RawModelingResult.MergeGapsByDistance" title="Permalink to this definition">ΒΆ</a></dt>
+<dd><p>Merge 2 neighbouring gaps by deleting residues in-between.</p>
+<p>Check if two neighbouring gaps are at max. <em>distance</em> residues apart from
+each other. Then delete the residues and store a new gap spanning the whole
+stretch of original gaps and the deleted region. Original gaps will be
+removed. Stem residues count to the gap, so <strong>A-A-A</strong> has a distance of 0.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ost</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">rawmodel</span>
+
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">ost</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'1mcg.pdb'</span><span class="p">)</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">ost</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="s">'1mcg_aln.fasta'</span><span class="p">)</span>
+<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
+<span class="n">rmodel</span> <span class="o">=</span> <span class="n">rawmodel</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
+<span class="n">rmodel</span><span class="o">.</span><span class="n">MergeGapsByDistance</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+</pre></div>
+</div>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The max. no. of residues between two gaps up to which
+merge happens.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Nothing.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
</div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index a324233e..b6eb116c 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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class=\"docutils literal\"><span class=\"pre\">test_actions.ActionTestCase</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Contributing","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","Documentation For Developes","Welcome To ProMod3’s Documentation!","Backbone","Loop Scoring","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Modelling","Load Loop Objects","Loop Candidates","Loop Closing","Monte Carlo Sampling","Structural Database","Torsion Sampler","<code class=\"docutils literal\"><span class=\"pre\">pipeline</span></code> - ProMod3 Modelling Pipeline","<code class=\"docutils literal\"><span class=\"pre\">run_engine</span></code> - Build Models From Various Starting Points","<code class=\"docutils literal\"><span class=\"pre\">rawmodel</span></code> - Coordinate Modeling","Disulfid Bond Evaluation","Frame","Coming to a solution","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Rotamers","RotamerID","Rotamer Library","Rotamer Settings","Documentation For Users"],titleterms:{"class":19,"function":[3,5,6,24,27],acid:19,action:[0,3,4],actiontestcas:0,amino:19,api:[0,22],argument:7,backbon:[11,16,29],backboneloopscor:12,base:18,basic:11,block:[11,27],bond:23,branch:4,build:[1,11,21,27],can:28,candid:15,carlo:17,catchphras:[],ccd:16,chain:18,chang:2,changelog:2,close:16,closer:17,cmake:[0,1,3,4],come:25,command:7,construct:[24,27],contribut:4,conveni:[24,27],cooler:17,coordin:22,core:6,creat:0,databas:18,defin:[18,19],depend:[1,29],develop:9,directori:4,disulfid:23,document:[3,4,9,10,31],edit:11,entri:29,evalu:23,everyth:5,execut:0,featur:18,file:5,find:18,fragment:18,frame:24,from:21,full:11,geometr:18,get:28,git:4,graph:25,group:27,have:0,helper:5,hook:4,how:[4,28],indic:10,integr:0,interact:25,introduct:[3,5,7,21],iou:[],issu:4,kic:16,librari:29,licens:4,line:7,load:14,loop:[12,13,14,15,16],mainten:3,make:[0,1],messag:5,model:[13,20,21,22,26],modul:[3,4],mont:17,must:0,object:[14,17,24],output:0,own:4,pars:7,parser:7,parti:4,particl:27,pipelin:20,pm3argpars:7,point:21,promod3:[1,3,6,10,20],raw:22,rawmodel:22,relax:16,releas:2,residu:[11,24],rotam:[27,29,30],rotamerid:28,run:[0,1],run_engin:21,sampl:17,sampler:[17,19],score:12,scorer:17,script:0,sequenc:18,set:30,setcompoundschemlib:8,share:[3,5],sidechain:26,smallest:27,solut:25,stage:4,start:[4,21],stretch:11,structur:[4,18],subclass:0,tabl:10,test:[0,3,4,5],test_act:0,third:4,torsion:19,triplet:19,type:29,unit:[0,3,4],user:31,variou:21,welcom:10,write:4,your:4}})
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