From 96405a4e545b54a57a0f2b0b8abb523e8abdbad8 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 14 Aug 2014 13:40:54 +0200
Subject: [PATCH] Updated documentation
---
doc/html/_modules/index.html | 2 +-
doc/html/_modules/promod3/core/argcheck.html | 2 +-
doc/html/_sources/meld/rawmodel.txt | 4 ++--
doc/html/developers.html | 2 +-
doc/html/genindex.html | 2 +-
doc/html/index.html | 2 +-
doc/html/meld/index.html | 2 +-
doc/html/meld/loop.html | 2 +-
doc/html/meld/rawmodel.html | 6 +++---
doc/html/objects.inv | Bin 520 -> 521 bytes
doc/html/py-modindex.html | 2 +-
doc/html/search.html | 2 +-
doc/html/searchindex.js | 2 +-
meld/doc/rawmodel.rst | 4 ++--
14 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 49c9c6c3..786dbfa9 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -85,7 +85,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 11:59, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index 4fb0e22d..e301ec0b 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -193,7 +193,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 11:59, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/_sources/meld/rawmodel.txt b/doc/html/_sources/meld/rawmodel.txt
index ebaa1420..312c6856 100644
--- a/doc/html/_sources/meld/rawmodel.txt
+++ b/doc/html/_sources/meld/rawmodel.txt
@@ -10,12 +10,12 @@ Contains function to build raw (pseudo) models based on a sequence alignment. He
.. code-block:: python
- from sm.meld import *
+ from promod3 import meld
aln=io.LoadAlignment('parwise.fasta')
template_structure=io.LoadPDB('1ake.pdb', restrict_chains='A')
aln.AttachView(1, template_structure.Select('peptide=true'))
- result=BuildRawModel(aln)
+ result=meld.BuildRawModel(aln)
io.SavePDB(result.model, 'model.pdb')
print 'remaining gaps:'
for gap in result.gaps:
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 0b6aa23b..49595aa9 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -140,7 +140,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 11:59, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index a70a13b2..47425e61 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -334,7 +334,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 11:59, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/index.html b/doc/html/index.html
index e22fde9c..ba8d5b87 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -134,7 +134,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 11:59, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/meld/index.html b/doc/html/meld/index.html
index a10156c1..a322cb8e 100644
--- a/doc/html/meld/index.html
+++ b/doc/html/meld/index.html
@@ -127,7 +127,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 08:42, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/meld/loop.html b/doc/html/meld/loop.html
index 51e549ed..2cfc4fdc 100644
--- a/doc/html/meld/loop.html
+++ b/doc/html/meld/loop.html
@@ -338,7 +338,7 @@ extension of the gap.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 08:42, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/meld/rawmodel.html b/doc/html/meld/rawmodel.html
index 0b2978a8..b28a127b 100644
--- a/doc/html/meld/rawmodel.html
+++ b/doc/html/meld/rawmodel.html
@@ -60,12 +60,12 @@
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">ΒΆ</a></h2>
<p>Contains function to build raw (pseudo) models based on a sequence alignment. Here is an example of how to build a model from an alignment and a structure.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">sm.meld</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">promod3</span> <span class="kn">import</span> <span class="n">meld</span>
<span class="n">aln</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">'parwise.fasta'</span><span class="p">)</span>
<span class="n">template_structure</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">'1ake.pdb'</span><span class="p">,</span> <span class="n">restrict_chains</span><span class="o">=</span><span class="s">'A'</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">template_structure</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">'peptide=true'</span><span class="p">))</span>
-<span class="n">result</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">result</span><span class="o">=</span><span class="n">meld</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">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="s">'model.pdb'</span><span class="p">)</span>
<span class="k">print</span> <span class="s">'remaining gaps:'</span>
<span class="k">for</span> <span class="n">gap</span> <span class="ow">in</span> <span class="n">result</span><span class="o">.</span><span class="n">gaps</span><span class="p">:</span>
@@ -221,7 +221,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 08:42, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 12044229f7d8f4641a521777fef1c1f27935d098..fa69201d044980768da879cf410081d7f709e4d1 100644
GIT binary patch
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diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 98081f3e..f3ff581b 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,7 +113,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 11:59, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/search.html b/doc/html/search.html
index 2662ebc5..58fbeca2 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,7 +99,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 11:59, 2014.
+ Last updated on Aug 14 13:38, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 9d5e7657..47c98e6e 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/meld/doc/rawmodel.rst b/meld/doc/rawmodel.rst
index ebaa1420..312c6856 100644
--- a/meld/doc/rawmodel.rst
+++ b/meld/doc/rawmodel.rst
@@ -10,12 +10,12 @@ Contains function to build raw (pseudo) models based on a sequence alignment. He
.. code-block:: python
- from sm.meld import *
+ from promod3 import meld
aln=io.LoadAlignment('parwise.fasta')
template_structure=io.LoadPDB('1ake.pdb', restrict_chains='A')
aln.AttachView(1, template_structure.Select('peptide=true'))
- result=BuildRawModel(aln)
+ result=meld.BuildRawModel(aln)
io.SavePDB(result.model, 'model.pdb')
print 'remaining gaps:'
for gap in result.gaps:
--
GitLab