diff --git a/CHANGELOG b/CHANGELOG
index 7891e86c9f6605b36114b1a4d6d2a14eec0a52aa..d0336bb6c605f6eef99d72f5a79aa195e1731ba1 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -14,5 +14,6 @@ Changes in Release 0.1
Changes in Release 0.2
--------------------------------------------------------------------------------
* added html documentation to repository
+ * meld renamed to rawmodel
.. LocalWords: Changelog reStructuredText changelog txt
diff --git a/actions/pm-build-rawmodel b/actions/pm-build-rawmodel
index 29486cf6478dca87982adf01363813d5a8e48dd8..282de6573db79600a6a1fb70e312cb0829555fae 100755
--- a/actions/pm-build-rawmodel
+++ b/actions/pm-build-rawmodel
@@ -1,7 +1,7 @@
#!/usr/bin/env ost
import os, argparse
-from promod3 import meld
+from promod3 import rawmodel
from promod3.core import argcheck, helper
### CHANGELOG - START
@@ -68,7 +68,7 @@ aln = io.LoadAlignment(opts.alignment_file)
# how can we do multi-whatever things?
aln.AttachView(1, tpl.CreateFullView())
-result = meld.BuildRawModel(aln)
+result = rawmodel.BuildRawModel(aln)
io.SavePDB(result.model, opts.model_file)
if not os.path.isfile(opts.model_file):
helper.MsgErrorAndExit("Failed to write model file '%s'." % opts.model_file, 5)
diff --git a/doc/contributing.rst b/doc/contributing.rst
index d536b3ff6619c56d093554eac5454f97916a33b9..42a8b8e81a32261643026b016f87f2709c7b1aa7 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -44,7 +44,14 @@ what goes into this branch:
* Your project needs documentation
* It must not break the ability of out-of-source builds
-The reason to be a bit restrictive on branches which end up in actual releases, should be mostly obvious: |project| is used by productive services as a third party toolbox. There it is not an item of active development and people probably have no insight in its internals. So messing up a new release creates a lot of extra work for a lot of people. First for the developer of a service to find out that |project| has turned malicious, then for the maintainer of this package to figure out that its your contribution messing things up and in the end for you, fixing the problems.
+The reason to be a bit restrictive on branches which end up in actual releases,
+should be mostly obvious: |project| is used by productive services as a third
+party toolbox. There it is not an item of active development and people
+probably have no insight in its internals. So messing up a new release creates
+a lot of extra work for a lot of people. First for the developer of a service
+to find out that |project| has turned malicious, then for the maintainer of
+this package to figure out that its your contribution messing things up and in
+the end for you, fixing the problems.
The place where you may get messy is your own |git| branch within the |project|
repository. This is basically where you should develop your project. Once you
@@ -463,7 +470,7 @@ top level :file:`CMakeLists.txt`:
## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
add_subdirectory(config)
add_subdirectory(core)
- add_subdirectory(meld)
+ add_subdirectory(rawmodel)
add_subdirectory(sidechains)
add_subdirectory(loop)
add_subdirectory(scripts)
diff --git a/doc/developers.rst b/doc/developers.rst
index 71d0344731b59d15b1f80d99f37d97bf27245f74..850cac5a81f2f205d1464e9ffeafe006ca76714b 100644
--- a/doc/developers.rst
+++ b/doc/developers.rst
@@ -10,7 +10,7 @@ Contents:
:maxdepth: 2
core/index
- meld/index
+ rawmodel/index
buildsystem
contributing
diff --git a/doc/html/.doctrees/buildsystem.doctree b/doc/html/.doctrees/buildsystem.doctree
deleted file mode 100644
index f1321adc41fa0acb10d413ccb1f2a44da6533ff4..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/buildsystem.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/changelog.doctree b/doc/html/.doctrees/changelog.doctree
deleted file mode 100644
index 772282020fa6c54823f32bbe75fcde5fa4af1dd2..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/changelog.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/contributing.doctree b/doc/html/.doctrees/contributing.doctree
deleted file mode 100644
index f366d50d132d1436a2df8c5f88c0dcf4e2976e41..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/contributing.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/core/argcheck.doctree b/doc/html/.doctrees/core/argcheck.doctree
deleted file mode 100644
index cc6ee6ecf1f02017213224ff911405d18f5f7b71..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/core/argcheck.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/core/index.doctree b/doc/html/.doctrees/core/index.doctree
deleted file mode 100644
index 6bd9c5aa11f20af5893d6a6ceadb6b3f81af93ad..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/core/index.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/developers.doctree b/doc/html/.doctrees/developers.doctree
deleted file mode 100644
index fbc187423a62425ad358535e126934a861f89510..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/developers.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/environment.pickle b/doc/html/.doctrees/environment.pickle
deleted file mode 100644
index 44a4e0a1fb1596c3d4b5513a43b67b41b75be1f1..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/environment.pickle and /dev/null differ
diff --git a/doc/html/.doctrees/index.doctree b/doc/html/.doctrees/index.doctree
deleted file mode 100644
index 8158249bd3a69b4b315366e3298db906fac8928a..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/index.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/meld/index.doctree b/doc/html/.doctrees/meld/index.doctree
deleted file mode 100644
index 88082b335d2070c895461f6aa03c5cd2c4ab4260..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/meld/index.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/meld/loop.doctree b/doc/html/.doctrees/meld/loop.doctree
deleted file mode 100644
index 4cc8bfc83abfa4be99db345c22061f220c25097a..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/meld/loop.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/meld/rawmodel.doctree b/doc/html/.doctrees/meld/rawmodel.doctree
deleted file mode 100644
index 479f721d34ccdeda4a35f29a559025761c87fa63..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/meld/rawmodel.doctree and /dev/null differ
diff --git a/doc/html/.doctrees/users.doctree b/doc/html/.doctrees/users.doctree
deleted file mode 100644
index f7ce8119c9596087cf9d1a9246dd1d3353cde392..0000000000000000000000000000000000000000
Binary files a/doc/html/.doctrees/users.doctree and /dev/null differ
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 25f32be06c34e046e6b30ed687d71e6321ad772f..d8763d02825cad686def1ec06e52aa645a93da2c 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -47,7 +47,7 @@
<h1>All modules for which code is available</h1>
<ul><li><a href="promod3/core/argcheck.html">promod3.core.argcheck</a></li>
<li><a href="promod3/core/helper.html">promod3.core.helper</a></li>
-<li><a href="promod3/meld.html">promod3.meld</a></li>
+<li><a href="promod3/rawmodel.html">promod3.rawmodel</a></li>
</ul>
</div>
@@ -86,7 +86,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index 592540390350fb1055b9c63ab0434c83a9e1221d..52e2bef873e7be5609774caf928c69baa7e7f9be 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 Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index 847a3a085dcbf916abfb88b9e0fdcd688da9a898..3cb6679ebd4560682de10f1c1fae033cc638965b 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -113,7 +113,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt
index 7891e86c9f6605b36114b1a4d6d2a14eec0a52aa..d0336bb6c605f6eef99d72f5a79aa195e1731ba1 100644
--- a/doc/html/_sources/changelog.txt
+++ b/doc/html/_sources/changelog.txt
@@ -14,5 +14,6 @@ Changes in Release 0.1
Changes in Release 0.2
--------------------------------------------------------------------------------
* added html documentation to repository
+ * meld renamed to rawmodel
.. LocalWords: Changelog reStructuredText changelog txt
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index d536b3ff6619c56d093554eac5454f97916a33b9..ba4eef099de448c977745221edbcebd67eddd174 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -463,7 +463,7 @@ top level :file:`CMakeLists.txt`:
## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
add_subdirectory(config)
add_subdirectory(core)
- add_subdirectory(meld)
+ add_subdirectory(rawmodel)
add_subdirectory(sidechains)
add_subdirectory(loop)
add_subdirectory(scripts)
diff --git a/doc/html/_sources/core/helper.txt b/doc/html/_sources/core/helper.txt
index c790f0ab5a8f3c4465f858bcbbd89c5264035444..3108fb5c90323978cba701325291b749931906f5 100644
--- a/doc/html/_sources/core/helper.txt
+++ b/doc/html/_sources/core/helper.txt
@@ -26,6 +26,11 @@ Messages
else:
raise
+.. testoutput:: helper
+ :hide:
+
+ Something failed!
+
.. doctest:: helper
from promod3.core import helper
diff --git a/doc/html/_sources/developers.txt b/doc/html/_sources/developers.txt
index 71d0344731b59d15b1f80d99f37d97bf27245f74..850cac5a81f2f205d1464e9ffeafe006ca76714b 100644
--- a/doc/html/_sources/developers.txt
+++ b/doc/html/_sources/developers.txt
@@ -10,7 +10,7 @@ Contents:
:maxdepth: 2
core/index
- meld/index
+ rawmodel/index
buildsystem
contributing
diff --git a/doc/html/_sources/meld/index.txt b/doc/html/_sources/rawmodel/index.txt
similarity index 87%
rename from doc/html/_sources/meld/index.txt
rename to doc/html/_sources/rawmodel/index.txt
index b90b30a29ef5d31edfaae116dae846ae4ebe5400..6ac1a6d1e7f1556439d1fea676bb3349071c1725 100644
--- a/doc/html/_sources/meld/index.txt
+++ b/doc/html/_sources/rawmodel/index.txt
@@ -1,40 +1,40 @@
-:mod:`~promod3.meld` - Coordinate modeling
+:mod:`~promod3.rawmodel` - Coordinate modeling
================================================================================
-.. module:: promod3.meld
+.. module:: promod3.rawmodel
:synopsis: Raw Coordinate Model
-.. currentmodule:: promod3.meld
+.. currentmodule:: promod3.rawmodel
Functionality 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.
-.. testcode:: meld
+.. testcode:: rawmodel
:hide:
import os
import tempfile
from ost import io
- from promod3 import meld
+ from promod3 import rawmodel
- aln = io.LoadAlignment('../tests/meld/data/raw-modeling/seq.fasta')
- template_structure = io.LoadPDB('../tests/meld/data/raw-modeling/gly.pdb',
+ aln = io.LoadAlignment('../tests/rawmodel/data/raw-modeling/seq.fasta')
+ template_structure = io.LoadPDB('../tests/rawmodel/data/raw-modeling/gly.pdb',
restrict_chains='A')
aln.AttachView(1, template_structure.Select('peptide=true'))
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
(fh, fn) = tempfile.mkstemp(suffix='.pdb')
io.SavePDB(result.model, fn)
os.remove(fn)
-.. doctest:: meld
+.. doctest:: rawmodel
from ost import io
- from promod3 import meld
+ from promod3 import rawmodel
aln = io.LoadAlignment('seq.fasta')
template_structure = io.LoadPDB('gly.pdb', restrict_chains='A')
aln.AttachView(1, template_structure.Select('peptide=true'))
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
io.SavePDB(result.model, 'model.pdb')
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index d29ed22750b76d52d47d637f7c61008ee7494ca8..f37c2969255884b5691a1774fa249ffdd425c2dd 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -26,7 +26,7 @@
<link rel="top" title="ProMod3 0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developes" href="developers.html" />
<link rel="next" title="Contributing" href="contributing.html" />
- <link rel="prev" title="meld - Coordinate modeling" href="meld/index.html" />
+ <link rel="prev" title="rawmodel - Coordinate modeling" href="rawmodel/index.html" />
</head>
<body>
<div class="related">
@@ -42,7 +42,7 @@
<a href="contributing.html" title="Contributing"
accesskey="N">next</a> |</li>
<li class="right" >
- <a href="meld/index.html" title="meld - Coordinate modeling"
+ <a href="rawmodel/index.html" title="rawmodel - Coordinate modeling"
accesskey="P">previous</a> |</li>
<li><a href="index.html">ProMod3 0 documentation</a> »</li>
<li><a href="developers.html" accesskey="U">Documentation For Developes</a> »</li>
@@ -164,8 +164,8 @@ builder</li>
</ul>
<h4>Previous topic</h4>
- <p class="topless"><a href="meld/index.html"
- title="previous chapter"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a></p>
+ <p class="topless"><a href="rawmodel/index.html"
+ title="previous chapter"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="contributing.html"
title="next chapter">Contributing</a></p>
@@ -204,7 +204,7 @@ builder</li>
<a href="contributing.html" title="Contributing"
>next</a> |</li>
<li class="right" >
- <a href="meld/index.html" title="meld - Coordinate modeling"
+ <a href="rawmodel/index.html" title="rawmodel - Coordinate modeling"
>previous</a> |</li>
<li><a href="index.html">ProMod3 0 documentation</a> »</li>
<li><a href="developers.html" >Documentation For Developes</a> »</li>
@@ -212,7 +212,7 @@ builder</li>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index fb2834449dfa3b851ec0159a0be9bd5767e01755..5a038a74750a7d78e57cf9a59bc15eb4e6c75b38 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -65,6 +65,7 @@
<blockquote>
<div><ul class="simple">
<li>added html documentation to repository</li>
+<li>meld renamed to rawmodel</li>
</ul>
</div></blockquote>
</div>
@@ -127,7 +128,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index c07a094c1f0f6375d4483dc7e303224abc9d405a..9738ae3e51f9adb3c9bc89f8c04d2563352caf2a 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -582,7 +582,7 @@ top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</sp
<span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">config</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">core</span><span class="p">)</span>
-<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">meld</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">rawmodel</span><span class="p">)</span>
<span class="hll"><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
</span><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">loop</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">scripts</span><span class="p">)</span>
@@ -795,7 +795,7 @@ contributions to web pages using ProMod3.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index 1a628fdbbbc2c1c1c41d848a128b8f5d34dcfd21..5e31b3c93f1b37e71eecf568f97c336b35d81908 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -217,7 +217,7 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 7af2deb5b156b43f5797d725b631c493be3c54ac..9bec665fc2eb6310a06291ef648b1ec2048dfc6a 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -25,7 +25,7 @@
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 core functionality" href="index.html" />
- <link rel="next" title="meld - Coordinate modeling" href="../meld/index.html" />
+ <link rel="next" title="rawmodel - Coordinate modeling" href="../rawmodel/index.html" />
<link rel="prev" title="argcheck - Standard tests for command line arguments" href="argcheck.html" />
</head>
<body>
@@ -39,7 +39,7 @@
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="../meld/index.html" title="meld - Coordinate modeling"
+ <a href="../rawmodel/index.html" title="rawmodel - Coordinate modeling"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="argcheck.html" title="argcheck - Standard tests for command line arguments"
@@ -114,8 +114,8 @@ traditionally reserved to successful commands.</li>
<p class="topless"><a href="argcheck.html"
title="previous chapter"><tt class="docutils literal"><span class="pre">argcheck</span></tt> - Standard tests for command line arguments</a></p>
<h4>Next topic</h4>
- <p class="topless"><a href="../meld/index.html"
- title="next chapter"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a></p>
+ <p class="topless"><a href="../rawmodel/index.html"
+ title="next chapter"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="../_sources/core/helper.txt"
@@ -148,7 +148,7 @@ traditionally reserved to successful commands.</li>
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="../meld/index.html" title="meld - Coordinate modeling"
+ <a href="../rawmodel/index.html" title="rawmodel - Coordinate modeling"
>next</a> |</li>
<li class="right" >
<a href="argcheck.html" title="argcheck - Standard tests for command line arguments"
@@ -160,7 +160,7 @@ traditionally reserved to successful commands.</li>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 0f1d5a6abf8889372a81ecad14605c453217a411..a0238bad9fea4dd03e724ea509a192a97212f450 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -129,7 +129,7 @@ modeling per se but cover standard programming issues.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index f999557c69bb510223f004b05548e27be2a74d75..f54f20e8adce6a64e2d4aa902abd628e27651213 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -62,8 +62,8 @@
<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><tt class="docutils literal"><span class="pre">helper</span></tt> - Shared functionality for the everything</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="meld/index.html"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="meld/index.html#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="rawmodel/index.html"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="buildsystem.html">Building ProMod3</a><ul>
@@ -140,7 +140,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 00249f62eaf8438f2d207f09fc0cfcb5ddac3de9..310c27eb27bc3de0fcfa5b09084bd2360bc9ed4a 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -61,7 +61,7 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="meld/index.html#promod3.meld.BuildRawModel">BuildRawModel() (in module promod3.meld)</a>
+ <dt><a href="rawmodel/index.html#promod3.rawmodel.BuildRawModel">BuildRawModel() (in module promod3.rawmodel)</a>
</dt>
</dl></td>
@@ -87,7 +87,7 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="meld/index.html#promod3.meld.RawModelingResult.gaps">gaps (promod3.meld.RawModelingResult attribute)</a>
+ <dt><a href="rawmodel/index.html#promod3.rawmodel.RawModelingResult.gaps">gaps (promod3.rawmodel.RawModelingResult attribute)</a>
</dt>
</dl></td>
@@ -123,7 +123,7 @@
</dt>
- <dt><a href="meld/index.html#promod3.meld.RawModelingResult.model">model (promod3.meld.RawModelingResult attribute)</a>
+ <dt><a href="rawmodel/index.html#promod3.rawmodel.RawModelingResult.model">model (promod3.rawmodel.RawModelingResult attribute)</a>
</dt>
@@ -143,7 +143,7 @@
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="meld/index.html#module-promod3.meld">promod3.meld (module)</a>
+ <dt><a href="rawmodel/index.html#module-promod3.rawmodel">promod3.rawmodel (module)</a>
</dt>
</dl></td>
@@ -153,7 +153,7 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="meld/index.html#promod3.meld.RawModelingResult">RawModelingResult (class in promod3.meld)</a>
+ <dt><a href="rawmodel/index.html#promod3.rawmodel.RawModelingResult">RawModelingResult (class in promod3.rawmodel)</a>
</dt>
</dl></td>
@@ -200,7 +200,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/index.html b/doc/html/index.html
index 728d4c3131da60adb60b6894859717ea708927eb..e34abe0418a8882fb270684df43b4d451fb5ec1d 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -56,7 +56,7 @@
<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a><ul>
<li class="toctree-l2"><a class="reference internal" href="core/index.html"><tt class="docutils literal"><span class="pre">core</span></tt> - ProMod3 core functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="meld/index.html"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="contributing.html">Contributing</a></li>
</ul>
@@ -132,7 +132,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 74174deab424a13c6f3e3035ccaeffedc1a058f7..afa275d05d2acaac2ddc795850a6c91f6ce02318 100644
--- a/doc/html/objects.inv
+++ b/doc/html/objects.inv
@@ -2,4 +2,5 @@
# Project: ProMod3
# Version: 0.1
# The remainder of this file is compressed using zlib.
-xڭP�N�0��+,�5��[o �C%T����bmGO\'
큛5���� 6T{@ѬE����Cv��Fl���@+ �hF'E����Sb�&�[%�* �>�1�A�`��5�^��y�hnEs�x@s�)�M��*Y݁���� ���{��{] ��e�ܩ�q%@�(#��h4X���~��l�H�K|���!�-�6�� �i��n��W^ ���(�����6�E 1�ǜ���\j�
�0��
\ No newline at end of file
+xڝ��N�0��}
+Kp����HA� �O�ڋc��Ѯ��oO��(����l���~��+� ���Yq˪-��U7
x:{�������W���V���j��d;dëа�яk ��#î�K�Y�V�yPݲjɠ8��`��� ��� Բ�Ο��z��x��ޢ�!��dq~�� �S4V�ũ��V %� �l��5��G��������e�0N
|9��1�֕>-z�k]�����P�GZAt�����
\ No newline at end of file
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 2fbe71259e595d59d1f39f1349f136e232eb4b37..f1d5cd039e01423bb0b396bb8b1d01c4347e8688 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -72,7 +72,7 @@
<tr class="cg-1">
<td></td>
<td>
- <a href="meld/index.html#module-promod3.meld"><tt class="xref">promod3.meld</tt></a></td><td>
+ <a href="rawmodel/index.html#module-promod3.rawmodel"><tt class="xref">promod3.rawmodel</tt></a></td><td>
<em>Raw Coordinate Model</em></td></tr>
</table>
@@ -113,7 +113,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/meld/index.html b/doc/html/rawmodel/index.html
similarity index 82%
rename from doc/html/meld/index.html
rename to doc/html/rawmodel/index.html
index 0f71bc8f67df5016a6aecc0450597170a46c5178..f90af7dcb22bc41b869810d8bb047468a3e0b3c1 100644
--- a/doc/html/meld/index.html
+++ b/doc/html/rawmodel/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>meld - Coordinate modeling — ProMod3 0 documentation</title>
+ <title>rawmodel - Coordinate modeling — ProMod3 0 documentation</title>
<link rel="stylesheet" href="../_static/default.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -54,27 +54,27 @@
<div class="bodywrapper">
<div class="body">
- <div class="section" id="module-promod3.meld">
-<span id="meld-coordinate-modeling"></span><h1><a class="reference internal" href="#module-promod3.meld" title="promod3.meld: Raw Coordinate Model"><tt class="xref py py-mod docutils literal"><span class="pre">meld</span></tt></a> - Coordinate modeling<a class="headerlink" href="#module-promod3.meld" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="module-promod3.rawmodel">
+<span id="rawmodel-coordinate-modeling"></span><h1><a class="reference internal" href="#module-promod3.rawmodel" title="promod3.rawmodel: Raw Coordinate Model"><tt class="xref py py-mod docutils literal"><span class="pre">rawmodel</span></tt></a> - Coordinate modeling<a class="headerlink" href="#module-promod3.rawmodel" title="Permalink to this headline">¶</a></h1>
<p>Functionality 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">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">meld</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">rawmodel</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">'seq.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">'gly.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">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">result</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">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>
</pre></div>
</div>
<div class="section" id="raw-coordinate-modeling-api">
<h2>Raw Coordinate Modeling API<a class="headerlink" href="#raw-coordinate-modeling-api" title="Permalink to this headline">¶</a></h2>
<dl class="function">
-<dt id="promod3.meld.BuildRawModel">
-<tt class="descclassname">promod3.meld.</tt><tt class="descname">BuildRawModel</tt><big>(</big><em>alignment</em>, <em>calpha_only=False</em><big>)</big><a class="headerlink" href="#promod3.meld.BuildRawModel" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.rawmodel.BuildRawModel">
+<tt class="descclassname">promod3.rawmodel.</tt><tt class="descname">BuildRawModel</tt><big>(</big><em>alignment</em>, <em>calpha_only=False</em><big>)</big><a class="headerlink" href="#promod3.rawmodel.BuildRawModel" title="Permalink to this definition">¶</a></dt>
<dt>
-<tt class="descclassname">promod3.meld.</tt><tt class="descname">BuildRawModel</tt><big>(</big><em>alignments</em>, <em>calpha_only=False</em><big>)</big></dt>
+<tt class="descclassname">promod3.rawmodel.</tt><tt class="descname">BuildRawModel</tt><big>(</big><em>alignments</em>, <em>calpha_only=False</em><big>)</big></dt>
<dd><p>Builds a raw (pseudo) model from the alignment. Can either take a single
alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.</p>
@@ -94,7 +94,7 @@ phosphoserine are copied as a whole with the modifications stripped off.</li>
<p>Residue numbers are set such that missing residue in gaps are honoured and
subsequent loop modeling can insert new residues without having to
renumber.</p>
-<p>The returned <a class="reference internal" href="#promod3.meld.RawModelingResult" title="promod3.meld.RawModelingResult"><tt class="xref py py-class docutils literal"><span class="pre">RawModelingResult</span></tt></a> stores the obtained raw model as well
+<p>The returned <a class="reference internal" href="#promod3.rawmodel.RawModelingResult" title="promod3.rawmodel.RawModelingResult"><tt class="xref py py-class docutils literal"><span class="pre">RawModelingResult</span></tt></a> stores the obtained raw model as well
as information about insertions and deletions in the gaps list.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -111,14 +111,14 @@ attached structure</td>
</dd></dl>
<dl class="class">
-<dt id="promod3.meld.RawModelingResult">
-<em class="property">class </em><tt class="descclassname">promod3.meld.</tt><tt class="descname">RawModelingResult</tt><a class="headerlink" href="#promod3.meld.RawModelingResult" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.rawmodel.RawModelingResult">
+<em class="property">class </em><tt class="descclassname">promod3.rawmodel.</tt><tt class="descname">RawModelingResult</tt><a class="headerlink" href="#promod3.rawmodel.RawModelingResult" title="Permalink to this definition">¶</a></dt>
<dd><p>Holds the result of raw model building. Incredibly minimalistic for now. Will
most likely grow a few more members over time to, e.g. to store a detailed
report.</p>
<dl class="attribute">
-<dt id="promod3.meld.RawModelingResult.model">
-<tt class="descname">model</tt><a class="headerlink" href="#promod3.meld.RawModelingResult.model" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.rawmodel.RawModelingResult.model">
+<tt class="descname">model</tt><a class="headerlink" href="#promod3.rawmodel.RawModelingResult.model" title="Permalink to this definition">¶</a></dt>
<dd><p>The resulting model.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -131,8 +131,8 @@ report.</p>
</dd></dl>
<dl class="attribute">
-<dt id="promod3.meld.RawModelingResult.gaps">
-<tt class="descname">gaps</tt><a class="headerlink" href="#promod3.meld.RawModelingResult.gaps" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.rawmodel.RawModelingResult.gaps">
+<tt class="descname">gaps</tt><a class="headerlink" href="#promod3.rawmodel.RawModelingResult.gaps" title="Permalink to this definition">¶</a></dt>
<dd><p>List of gaps in the model that could not be copied from the template. These
gaps may be the result of insertions/deletions in the alignment or due to
missing or incomplete backbone coordinates in the template structure.</p>
@@ -159,7 +159,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">meld</span></tt> - Coordinate modeling</a><ul>
+<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">rawmodel</span></tt> - Coordinate modeling</a><ul>
<li><a class="reference internal" href="#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
</ul>
</li>
@@ -173,7 +173,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
title="next chapter">Building ProMod3</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
- <li><a href="../_sources/meld/index.txt"
+ <li><a href="../_sources/rawmodel/index.txt"
rel="nofollow">Show Source</a></li>
</ul>
<div id="searchbox" style="display: none">
@@ -214,7 +214,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/search.html b/doc/html/search.html
index 7f012f8889852082fea816a4d9f89a1d04168153..22dc512c584eda6a35cebb06b93796cd761340e3 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 Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 4fe49b1d6804d89cb18e206ca7e671794e3140a8..eb581bef306b7215be2d1f3d2cd697ebd7f18b26 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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+Search.setIndex({envversion:42,terms:{aln:8,all:[7,1,4,8],code:[7,1,4,5],forget:[7,4],chain:[7,8],messi:7,skip:7,forbidden:7,sidechains_unit_test:7,ost:[0,1,2,3,4,5,6,7,8,9],disable_document:[7,4],prefix:[7,1],concept:7,legal:7,abil:7,follow:[7,8],middl:7,readabl:7,send:5,init:7,program:6,under:7,introduc:7,sourc:[7,1,4,5],everi:[7,8],string:1,fals:[7,1,8],internet:7,worst:7,failur:[7,1],veri:[7,1],affect:7,solver:7,runnabl:7,tri:8,magic:7,level:[7,4],did:7,list:[7,1,4,8],assertequ:7,item:[7,8],fileextens:1,align:8,dir:7,malici:7,promod_gcc_45:7,your_modul:7,direct:7,past:7,second:8,design:1,pass:7,download:4,acid:8,even:[7,4],index:[7,3],what:[7,1,4],hide:7,sub:7,resembl:7,exot:7,"while":[7,1],find:7,current:7,delet:8,version:[7,4],"new":[7,8],boost:[0,1,2,3,4,5,6,7,8,9],meld:0,subtre:7,submodule1:7,honour:8,gener:7,never:7,here:[7,1,4,5,8],sphinx:[0,1,2,3,4,5,6,7,8,9],save:7,lib_stage_path:7,let:7,set_directory_properti:7,path:[7,1,4],along:7,modifi:[7,8,0],implicit:4,valu:[4,1,5],wait:7,headlin:7,search:[7,3,4],produc:4,executable_output_path:7,setup_boost:7,promod3_version_minor:7,gly:8,doctest:[7,4],action:7,implement:7,chanc:7,spawn:7,via:7,extra:7,activ:7,modul:0,submodul:7,put:[7,1,4],unix:7,api:[7,9],instal:[7,4],smallish:[7,4],unit:4,highli:4,yourself:[7,4],fed:7,from:[1,0,4,5,8,7],describ:1,would:[7,4,5],regist:7,two:7,next:7,everybodi:7,few:[7,4,8],live:7,call:[7,4],recommend:4,msg:5,loadalign:8,checkout:7,tell:[7,1],tightli:7,more:[7,4,8],chapter:7,peopl:7,relat:7,notic:7,warn:7,flag:[7,1],include_directori:7,particular:7,known:1,actual:7,hold:8,cach:[7,4],must:7,ost_double_precis:4,py_run:7,hous:7,setup:[7,0],work:[7,4],histori:7,paragraph:7,can:[7,1,4,8],purpos:7,root:7,fetch:[7,1],def:7,control:7,give:7,process:7,add_argu:1,indic:1,topic:7,abort:7,want:[7,4],phrase:7,unfortun:7,hydrogen:8,alwai:7,gcc:7,cours:7,end:[7,1,4,5],sit:7,rather:[7,5],comfort:1,sever:[7,4],verifi:1,config:7,updat:7,python_vers:7,product:7,entityhandl:8,rebas:7,mess:7,clone:7,after:[7,4],usabl:7,befor:7,wrong:4,attent:7,mai:[7,4,8],multipl:7,data:7,grow:8,man:[7,4],"short":7,essenti:7,practic:7,ost_doc_url:7,python_binari:7,correspond:7,stash:7,exclud:7,alias:7,"switch":7,maintain:7,environ:7,allow:7,exclus:7,origin:7,promod3_version_major:7,eigen:[7,4],over:[7,4,8],insight:7,becaus:[7,4],through:7,same:[7,4],rawmodel:[7,3,9,0],gitignor:7,still:7,pointer:4,disable_disable_doctest:7,entiti:7,perfect:7,output_vari:7,funni:4,fix:[7,1],selenium:8,structuralgaplist:8,relev:4,carri:[7,1],drawback:7,onc:7,bin:7,python_doc_url:7,therefor:7,linkcheck:[7,4],them:7,good:7,"return":[1,5,8],thei:[7,4],python:[0,1,2,3,4,5,6,7,8,9],dai:1,initi:0,"break":7,framework:7,conquer:7,instead:[7,1,4],front:[7,1,4],now:[7,8],minimalist:8,cmake_cxx_flags_releas:7,libexec_stage_path:7,name:[7,1],anyth:[7,4],drop:7,separ:7,easili:7,achiev:7,each:7,debug:7,found:7,went:7,complet:[7,8],side:[7,8],mean:[7,1,4],compil:7,everyth:7,monolith:7,cmake_module_path:7,test_sidechain:7,idea:[7,0],realli:[7,1,4],runtest:7,member:[7,8],"static":7,our:7,extract:7,special:[7,4],out:[7,4],variabl:[7,4],shown:7,goe:[7,4],promod3_unittest:7,crucial:7,content:[7,3,9],reader:7,print:4,got:4,exec_program:7,merg:7,dive:7,integr:7,runtimeerror:8,differ:[7,4],free:7,standard:[7,4],test_someth:7,reason:7,base:[1,8],latest:4,ask:7,org:7,basi:7,could:[7,8],insert:8,keep:7,thing:[7,4],place:[7,5],think:7,first:[7,0],oper:7,softwar:7,major:7,suffix:1,obviou:7,prevent:7,feel:7,sidechains_pymod:7,number:8,sometim:7,restrict:7,date:7,alreadi:7,done:7,least:[7,4],blank:7,stabl:7,miss:[1,8],straight:7,exit_statu:[1,5],given:1,script:[7,1,4,5],top:[7,4],perfectli:7,mkdir:7,system:[7,4,0],messag:[7,1],stack:7,attach:8,stori:7,master:7,too:7,which:[7,4,5,8,6],termin:1,scheme:7,"final":[7,8],store:[7,8],shell:[4,1,5],option:[7,1,4],tool:1,copi:[7,8],restrict_chain:8,openstructur:[0,1,2,3,4,5,6,7,8,9],part:7,pars:1,boost_include_dir:7,mostli:7,rst:7,off:[7,8],exactli:4,than:7,kind:7,grep:4,target:[7,4],whenev:7,provid:[7,4],seamlessli:7,tree:7,unrecognis:1,project:7,nevertheless:7,reus:8,str:[1,5],were:7,posit:1,toward:7,builder:4,pre:7,respons:7,mind:7,argument:4,packag:7,manner:7,have:[7,4,8],"__main__":7,need:[7,1,4],dedic:[7,4],turn:[7,1],tidi:7,cmake_current_source_dir:7,optimis:7,imagin:7,probabl:[7,4],built:7,advic:7,inform:8,diverg:7,self:7,also:[7,1,4,8],exampl:[7,4,8],take:[7,8],advis:7,thoroughli:7,noth:7,singl:[7,8],"_opt":7,sure:7,distribut:7,track:1,forg:7,compress:1,strict:7,wno:7,most:[7,1,8],eigen3_found:7,hotfix:7,"class":[7,8,6],charg:7,renam:0,bug:7,url:7,doc:[7,4],later:7,cover:[7,1,6],doe:[7,1,8],ext:1,declar:7,clean:[7,4],usual:[7,4],review:7,came:7,cmakelist:[7,4],show:7,test_suite_your_module_run:7,dbg:7,attachview:8,bring:7,permiss:7,cmake_support:7,fine:7,anywai:7,help:[7,4],involv:7,onli:[7,1,8],locat:4,explain:7,configur:[7,4],solut:7,figur:7,should:[7,1,5],suppos:7,templat:8,folder:7,move:7,hit:7,unus:7,variou:4,get:[7,4],watch:7,soon:7,cannot:7,loadpdb:8,report:[7,8],toolbox:7,requir:[7,4],setup_compiler_flag:7,add_changelog_to_doc:7,enabl:1,"2b1":4,"default":[7,4],common:[7,1],contain:[7,1,4,8],python_root:4,where:7,remov:4,view:7,set:[7,1,4,8],project_nam:7,seq:[7,8],frame:7,ost_include_dir:7,see:7,temporarili:7,mandatori:7,result:[7,4,8],smng:0,arg:7,testcas:7,close:7,sport:7,subject:7,awar:7,statu:7,detect:1,msgerrorandexit:5,someth:[7,5],version_great:7,enumer:7,label:7,state:[7,4],header_stage_path:7,subdir:7,simplest:7,"import":[7,1,4,5,8],awai:7,paramet:[1,5,8],approach:7,attribut:7,accord:7,extend:7,sole:7,cmake_cxx_compiler_vers:7,test_your_modul:7,recent:7,solv:7,come:[7,1],addit:[7,1],fail:[7,5],extens:1,alon:5,disable_doctest:[7,4],promod3_version_patch:7,tutori:7,grain:7,fno:7,mani:5,whole:[7,8],pdb:[1,8],comment:7,sidechains_rst:7,author:7,point:[7,4],cxx:7,overview:7,unittest:7,argumentpars:1,pop:7,walk:7,residu:8,header:[7,4],featur:7,littl:7,test_submodule1:7,assum:7,amino:8,quit:7,template_structur:8,creat:[7,4],coupl:7,rebuild:[7,4],three:7,been:7,sinc:[7,1,4],compon:7,trigger:7,besid:4,treat:[7,8],basic:[7,4,8],ost_root:[7,4],popul:[7,4],seq_alg:7,tini:7,quickli:7,life:7,fasta:8,convert:8,ani:7,coordin:[3,9],togeth:7,els:7,fileexist:1,educ:7,those:[7,4],"case":7,cmake_c_compiler_vers:7,uncertain:7,look:[7,1],raw:9,testfileexistsfals:7,disable_disable_linkcheck:7,servic:7,properti:7,commerci:7,formatt:7,invok:[7,4],boost_root:4,abov:7,error:[1,5],dost_root:[7,4],loop:[7,8],stage_dir:7,methionin:8,real:7,argpars:1,readi:4,sidechain:7,henc:7,non:7,itself:7,clutter:7,conf:[7,4],protein:8,vanish:7,calpha_onli:8,"__init__":7,reviv:7,parent:8,develop:7,fedora:7,etc:7,suggest:7,belong:7,savepdb:8,files_to_be_remov:7,promod3_version_str:7,binari:7,complex:7,admir:7,document:[4,0],start:4,conflict:7,higher:4,http:7,cmakecach:4,optim:[7,4],bienchen:7,make_directori:7,hand:4,driven:7,moment:7,rais:8,disable_linkcheck:[7,4],user:3,kic:7,tradition:[1,5],expand:7,codetest:7,task:7,conop:7,pymod:7,find_packag:7,macro:7,markup:7,well:[7,4,8],without:[7,1,8],command:7,branchnam:7,thi:[7,1,4,8,6],endif:7,gzip:1,model:[3,9,6],academ:7,spend:7,piec:7,left:5,interpret:5,add_doc_sourc:7,entri:7,just:[7,4],elabor:7,obtain:8,rest:[0,1,2,3,4,5,6,7,8,9],touch:7,web:[7,4],lapack:[7,4],restructuredtext:[0,1,2,3,4,5,6,7,8,9],makefil:[7,4],except:7,seem:7,add:7,eigen3:7,input:1,subsequ:8,match:[7,8],opt:1,around:7,format:7,handl:8,specimen:1,term:7,source2:7,source1:7,know:4,background:4,mol:7,bit:[7,4],you:[7,1,4],mod:7,eigen3_include_dir:[7,4],loss:7,like:[7,4,8],success:[1,5],incred:8,manual:[7,4],html:[7,4,0],test_:7,test_awesome_featur:7,collect:5,"boolean":1,either:[7,8],output:[7,1],hook:7,page:[7,3,4],www:7,right:[7,4],often:[7,1],acknowledg:7,some:[7,1,4],begin:7,resolv:7,intern:7,proper:7,librari:7,qmean:[7,4],thu:1,txt:[7,4],lead:1,avoid:7,definit:7,subclass:7,exit:[1,5],select:8,recognis:7,devot:6,condit:7,core:[7,1,5],plu:7,cmake_source_dir:7,backbon:8,step:7,promot:7,repositori:[7,0],"__name__":7,add_subdirectori:7,intervent:7,mmcif:1,stage:4,trustworthi:7,src:7,about:[7,8],rare:7,materi:7,manag:7,coars:7,commit:7,mol_alg:7,disabl:7,qmean_root:[7,4],within:[7,4],automat:[7,1],due:8,empti:[7,5],cmake_cxx_flag:7,strip:8,announc:7,your:4,per:[7,6],git:[4,0],log:[7,5],wai:[7,4],pictur:7,qmean_include_dir:7,support:[7,1],renumb:8,custom:7,avail:[7,4],lost:7,much:[7,8],interfac:7,includ:[7,1,0],lot:[7,1],suit:7,forward:7,parse_arg:1,"function":[7,1],headach:7,unexpect:4,enough:7,tupl:1,buildrawmodel:8,somethingtest:7,back:7,link:[7,4],atom:8,don:[7,4],line:7,inlin:7,"true":[7,1,8],setup_stag:7,pull:[7,4],tripl:1,immedi:7,consist:7,possibl:[7,8],whether:1,type:[1,8],displai:1,below:7,otherwis:7,problem:7,similar:4,eigenvector:7,testutil:7,reserv:[1,5],gather:[7,6],evalu:7,"int":[1,5],certain:4,utilis:[7,1],fellow:7,incomplet:8,exist:[7,1],file:[7,4],dqmean_root:[7,4],deuterium:8,check:[7,1,4],fill:7,echo:7,again:[7,4],calpha:8,modif:8,when:[7,8],detail:[7,8],other:[7,4,8],bool:1,test:4,cmake_compiler_is_gnucxx:7,phosphoserin:8,nice:7,additional_make_clean_fil:7,extern:7,determin:1,rawmodelingresult:8,sequenc:8,cmake_build_typ:7,cmake_minimum_requir:7,briefli:7,eigenvalu:7,consid:7,gap:8,homolog:6,doptim:7,fatal_error:7,stai:7,peptid:8,algorithm:[7,8],project_binary_dir:7,directori:4,descript:7,pseudo:8,rule:7,ignor:8,time:[7,8],push:7},objtypes:{"0":"py:module","1":"py:function","2":"py:attribute","3":"py:class"},objnames:{"0":["py","module","Python 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\ No newline at end of file
diff --git a/doc/html/users.html b/doc/html/users.html
index 23f886887981e1ffe430b323ccc69d2418fbb49d..34a274494c009364a0ef35e235fdf326598b8993 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -110,7 +110,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Oct 16 09:31, 2014.
+ Last updated on Nov 04 11:22, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
diff --git a/extras/pre-commit b/extras/pre-commit
index 9ede84071e6b7fd70b78fc69ea1b9ce3f8c3cdf1..6ad191d06fccde451bd265fbb6531d7fdd9c81f1 100755
--- a/extras/pre-commit
+++ b/extras/pre-commit
@@ -137,6 +137,8 @@ def GetFileType(filepath):
return "C"
elif fo == "%s: SQLite 3.x database" % filepath:
return "ukn"
+ elif fo == "%s: ASCII English text" % filepath:
+ return "text"
else:
FailMsg("Could not determine file type of '%s'. " % filepath
+"Please go to 'extras/pre-commit' and extend 'GetFileType'. "
@@ -149,6 +151,7 @@ def GetModFiles():
shell_scripts = list()
c_files = list()
ukn_files = list()
+ text_files = list()
re_excludes = list()
# get path to repo root
try:
@@ -195,10 +198,12 @@ def GetModFiles():
c_files.append(f)
elif ft == 'ukn':
ukn_files.append(f)
+ elif ft == 'text':
+ text_files.append(f)
else:
FailMsg("Not supposed to be ever seen. There must be a file type "
+"recognised by the pre-commit hook which is not handled.", 13)
- return py_files, rst_files, cmake_files, shell_scripts, c_files, ukn_files
+ return py_files, rst_files, cmake_files, shell_scripts, c_files, text_files, ukn_files
def TestLineWidthExit(line, line_no, filename):
"""
@@ -254,6 +259,14 @@ def CheckShellScript(filepath):
TestLineWidthExit(line, lno, filepath)
lno += 1
+def CheckTextFile(filepath):
+ fh = open(filepath, "U")
+ lno = 1
+ for line in fh:
+ line = line.rstrip(os.linesep)
+ TestLineWidthExit(line, lno, filepath)
+ lno += 1
+
def CheckCCode(filepath):
fh = open(filepath, "U")
lno = 1
@@ -277,6 +290,7 @@ rst_files, \
cmake_files, \
shell_scripts, \
c_files, \
+text_files, \
ukn_files = GetModFiles()
# checks on commit
print "[ Checking for trailing whitespace(s) ]"
@@ -314,6 +328,11 @@ if not len(shell_scripts):
print " Nothing to be done."
for f in shell_scripts:
CheckShellScript(f)
+print "[ Checking text files ]"
+if not len(text_files):
+ print " Nothing to be done."
+for f in text_files:
+ CheckTextFile(f)
print "[ Files modified but not checked ]"
if not len(ukn_files):
print " None."
diff --git a/loop/pymod/export_monte_carlo.cc b/loop/pymod/export_monte_carlo.cc
index 797c88c7ff37bb7b9666a5e816ac7bd2543853eb..9c7d56ed0f84b6d6f5f789863358cdad981e3a4e 100644
--- a/loop/pymod/export_monte_carlo.cc
+++ b/loop/pymod/export_monte_carlo.cc
@@ -5,7 +5,7 @@
#include <promod3/loop/monte_carlo_cooling_schedule.hh>
#include <promod3/loop/monte_carlo_scorer.hh>
#include <promod3/loop/monte_carlo_sampler.hh>
-#include <promod3/meld/gap.hh>
+#include <promod3/rawmodel/gap.hh>
using namespace promod3;
using namespace promod3::loop;
diff --git a/loop/src/CMakeLists.txt b/loop/src/CMakeLists.txt
index 2325dd9b810c316564a61963116441db2008a7e9..5de1110c418ea5bb37016dd09dc40c20fcccf5a2 100644
--- a/loop/src/CMakeLists.txt
+++ b/loop/src/CMakeLists.txt
@@ -38,7 +38,7 @@ loop_object_loader.cc
)
module(NAME loop HEADERS ${LOOP_HEADERS} SOURCES ${LOOP_SOURCES} DEPENDS_ON
- promod3_core promod3_meld LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES} ${LAPACK_LIBRARIES})
+ promod3_core promod3_rawmodel LINK ${OST_LIBRARIES} ${BOOST_LIBRARIES} ${LAPACK_LIBRARIES})
if (QMEAN_ROOT)
target_link_libraries(promod3_loop ${QMEAN_LIBRARIES})
endif()
diff --git a/loop/src/loop_candidate.hh b/loop/src/loop_candidate.hh
index ba86db9eeb129eace7e42c72982c42ce1e63372a..db666470a40af01f54abf12e3e0c53ff6eb227dd 100644
--- a/loop/src/loop_candidate.hh
+++ b/loop/src/loop_candidate.hh
@@ -11,7 +11,7 @@
#include "promod3/loop/backbone.hh"
#include "promod3/loop/frag_db.hh"
-#include "promod3/meld/gap.hh"
+#include "promod3/rawmodel/gap.hh"
#include "promod3/loop/monte_carlo.hh"
#include "promod3/loop/flame.hh"
#include "promod3/loop/loop_score.hh"
@@ -22,7 +22,7 @@ namespace promod3 { namespace loop {
using namespace promod3;
-using namespace promod3::meld;
+using namespace promod3::rawmodel;
struct LoopCandidate {
diff --git a/loop/src/loop_score.hh b/loop/src/loop_score.hh
index a983274e9b5f2634a5ca52b0dbf5426e0d6cd5f5..f1481d5cad0dc7b7ee57aca86a19895019682f9d 100644
--- a/loop/src/loop_score.hh
+++ b/loop/src/loop_score.hh
@@ -7,7 +7,7 @@
#include <ost/geom/vecmat3_op.hh>
#include <ost/mol/view_op.hh>
#include <promod3/loop/backbone.hh>
-#include <promod3/meld/gap.hh>
+#include <promod3/rawmodel/gap.hh>
#include <qmean/cbeta_potential.hh>
#include <qmean/torsion_potential.hh>
diff --git a/loop/src/monte_carlo_sampler.hh b/loop/src/monte_carlo_sampler.hh
index 18f39ce9c30390538ae96e06c9a64b97df9d46bf..7ed42f862ec4c1d7daff512644327ac3004cafbc 100644
--- a/loop/src/monte_carlo_sampler.hh
+++ b/loop/src/monte_carlo_sampler.hh
@@ -12,7 +12,7 @@
#include <ost/mol/atom_handle.hh>
#include <ost/mol/alg/construct_cbeta.hh>
-#include <promod3/meld/gap.hh>
+#include <promod3/rawmodel/gap.hh>
#include <promod3/loop/backbone.hh>
#include <promod3/loop/torsion_sampler.hh>
#include <promod3/core/message.hh>
diff --git a/loop/src/monte_carlo_scorer.hh b/loop/src/monte_carlo_scorer.hh
index a86881b218cf85be6b597704db8be0ff5ca562f1..cbd1f1cd9f99342b530722ae7838c523295a57a5 100644
--- a/loop/src/monte_carlo_scorer.hh
+++ b/loop/src/monte_carlo_scorer.hh
@@ -8,7 +8,7 @@
#include <qmean/cb_packing_potential.hh>
#include <qmean/torsion_potential.hh>
-#include <promod3/meld/gap.hh>
+#include <promod3/rawmodel/gap.hh>
#include <promod3/loop/loop_score.hh>
diff --git a/rawmodel/doc/CMakeLists.txt b/rawmodel/doc/CMakeLists.txt
index 67ee54a52efc1df30484cc2725dee66fc50b58b6..2f43617494857e74012508cf15feea63e28e6abb 100644
--- a/rawmodel/doc/CMakeLists.txt
+++ b/rawmodel/doc/CMakeLists.txt
@@ -1,5 +1,5 @@
-set(MELD_RST
+set(RAWMODEL_RST
index.rst
)
-add_doc_source(NAME meld RST ${MELD_RST})
+add_doc_source(NAME rawmodel RST ${RAWMODEL_RST})
diff --git a/rawmodel/doc/index.rst b/rawmodel/doc/index.rst
index b90b30a29ef5d31edfaae116dae846ae4ebe5400..6ac1a6d1e7f1556439d1fea676bb3349071c1725 100644
--- a/rawmodel/doc/index.rst
+++ b/rawmodel/doc/index.rst
@@ -1,40 +1,40 @@
-:mod:`~promod3.meld` - Coordinate modeling
+:mod:`~promod3.rawmodel` - Coordinate modeling
================================================================================
-.. module:: promod3.meld
+.. module:: promod3.rawmodel
:synopsis: Raw Coordinate Model
-.. currentmodule:: promod3.meld
+.. currentmodule:: promod3.rawmodel
Functionality 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.
-.. testcode:: meld
+.. testcode:: rawmodel
:hide:
import os
import tempfile
from ost import io
- from promod3 import meld
+ from promod3 import rawmodel
- aln = io.LoadAlignment('../tests/meld/data/raw-modeling/seq.fasta')
- template_structure = io.LoadPDB('../tests/meld/data/raw-modeling/gly.pdb',
+ aln = io.LoadAlignment('../tests/rawmodel/data/raw-modeling/seq.fasta')
+ template_structure = io.LoadPDB('../tests/rawmodel/data/raw-modeling/gly.pdb',
restrict_chains='A')
aln.AttachView(1, template_structure.Select('peptide=true'))
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
(fh, fn) = tempfile.mkstemp(suffix='.pdb')
io.SavePDB(result.model, fn)
os.remove(fn)
-.. doctest:: meld
+.. doctest:: rawmodel
from ost import io
- from promod3 import meld
+ from promod3 import rawmodel
aln = io.LoadAlignment('seq.fasta')
template_structure = io.LoadPDB('gly.pdb', restrict_chains='A')
aln.AttachView(1, template_structure.Select('peptide=true'))
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
io.SavePDB(result.model, 'model.pdb')
diff --git a/rawmodel/pymod/CMakeLists.txt b/rawmodel/pymod/CMakeLists.txt
index 6ab10b51b57ed8f3ede4957df891c1e86cb268c0..14a282c60232c553809d42b9772ddd1a21b18288 100644
--- a/rawmodel/pymod/CMakeLists.txt
+++ b/rawmodel/pymod/CMakeLists.txt
@@ -1,11 +1,14 @@
-set(MELD_CPP
-wrap_meld.cc
+set(RAWMODEL_CPP
+wrap_rawmodel.cc
export_model.cc
export_gap.cc
)
-set(MELD_PYMOD
+set(RAWMODEL_PYMOD
__init__.py
)
-pymod(NAME meld CPP ${MELD_CPP} PY ${MELD_PYMOD} DEPENDS_ON core_pymod)
+pymod(NAME rawmodel
+ CPP ${RAWMODEL_CPP}
+ PY ${RAWMODEL_PYMOD}
+ DEPENDS_ON core_pymod)
diff --git a/rawmodel/pymod/__init__.py b/rawmodel/pymod/__init__.py
index 78638a80b8ece882268f1ef1846c62f54b5d3424..1651376225107dea990bb0ea7eea8e66a59d5cf8 100644
--- a/rawmodel/pymod/__init__.py
+++ b/rawmodel/pymod/__init__.py
@@ -1,4 +1,4 @@
"""
-Initialise the meld module.
+Initialise the rawmodel module.
"""
-from _meld import BuildRawModel, StructuralGap, GapExtender
+from _rawmodel import BuildRawModel, StructuralGap, GapExtender
diff --git a/rawmodel/pymod/export_gap.cc b/rawmodel/pymod/export_gap.cc
index b71def8f086b0fce2163addb2bc360fa5d6b87ec..9982f1deef523a32049f22a823fd758274922e47 100644
--- a/rawmodel/pymod/export_gap.cc
+++ b/rawmodel/pymod/export_gap.cc
@@ -1,10 +1,10 @@
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-#include <promod3/meld/gap.hh>
+#include <promod3/rawmodel/gap.hh>
using namespace ost;
using namespace boost::python;
-using namespace promod3::meld;
+using namespace promod3::rawmodel;
void export_gap()
diff --git a/rawmodel/pymod/export_model.cc b/rawmodel/pymod/export_model.cc
index cc856f1674a2aeb29603f6bf08c2bf320e6781e9..c5b1eda51a578e5a2dafdd3bf64a65a1871109bd 100644
--- a/rawmodel/pymod/export_model.cc
+++ b/rawmodel/pymod/export_model.cc
@@ -1,9 +1,9 @@
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-#include <promod3/meld/model.hh>
+#include <promod3/rawmodel/model.hh>
using namespace boost::python;
-using namespace promod3::meld;
+using namespace promod3::rawmodel;
RawModelingResult (*BuildRawModelHandle)(const ost::seq::AlignmentHandle&,
bool,
diff --git a/rawmodel/pymod/wrap_meld.cc b/rawmodel/pymod/wrap_rawmodel.cc
similarity index 77%
rename from rawmodel/pymod/wrap_meld.cc
rename to rawmodel/pymod/wrap_rawmodel.cc
index 0961bcb0202a8a8beeb4b875bbd3830fa3f7c7d2..2babdad0ea3435ce1accc4d9c2928ec14710c075 100644
--- a/rawmodel/pymod/wrap_meld.cc
+++ b/rawmodel/pymod/wrap_rawmodel.cc
@@ -3,7 +3,7 @@
void export_gap();
void export_model();
-BOOST_PYTHON_MODULE(_meld)
+BOOST_PYTHON_MODULE(_rawmodel)
{
export_gap();
export_model();
diff --git a/rawmodel/src/CMakeLists.txt b/rawmodel/src/CMakeLists.txt
index f4cf454415656ea44ff019eb7499f395f1acadea..5c8b58a47399e292efbc653eb5f98b38744ecb36 100644
--- a/rawmodel/src/CMakeLists.txt
+++ b/rawmodel/src/CMakeLists.txt
@@ -1,15 +1,15 @@
-set(MELD_SOURCES
+set(RAWMODEL_SOURCES
gap.cc
model.cc
)
-set(MELD_HEADERS
+set(RAWMODEL_HEADERS
gap.hh
model.hh
)
-module(NAME meld
- HEADERS ${MELD_HEADERS}
- SOURCES ${MELD_SOURCES}
+module(NAME rawmodel
+ HEADERS ${RAWMODEL_HEADERS}
+ SOURCES ${RAWMODEL_SOURCES}
DEPENDS_ON promod3_core
LINK ${OPENGL_LIBRARIES} ${OST_LIBRARIES} ${BOOST_LIBRARIES})
diff --git a/rawmodel/src/gap.cc b/rawmodel/src/gap.cc
index 18df76c2663986a26630c9bf815d7fe06cb2c394..cd9bf861cef908d1395df091f322401b1afe3204 100644
--- a/rawmodel/src/gap.cc
+++ b/rawmodel/src/gap.cc
@@ -5,7 +5,7 @@
using namespace ost::mol;
using namespace ost;
-namespace promod3 { namespace meld {
+namespace promod3 { namespace rawmodel {
String StructuralGap::GetChain() const
{
diff --git a/rawmodel/src/gap.hh b/rawmodel/src/gap.hh
index 6bbef0fe321d14c45c4058c5a74d7736805ff532..90b6ce4669bf5454b73546148d26505579f82114 100644
--- a/rawmodel/src/gap.hh
+++ b/rawmodel/src/gap.hh
@@ -1,9 +1,9 @@
-#ifndef PM3_MELD_GAP_HH
-#define PM3_MELD_GAP_HH
+#ifndef PM3_RAWMODEL_GAP_HH
+#define PM3_RAWMODEL_GAP_HH
#include <ost/mol/mol.hh>
-namespace promod3 { namespace meld {
+namespace promod3 { namespace rawmodel {
/// Describes a structural gap, i.e. a loop to be modeled. The gap may either be
/// terminal or between two defined regions. The gap stores information of the
diff --git a/rawmodel/src/model.cc b/rawmodel/src/model.cc
index b6fdbcc30d6a331a2daacb144810a38d7f69078a..688c69ce39de52e8959bceaee254fd3cd98125d3 100644
--- a/rawmodel/src/model.cc
+++ b/rawmodel/src/model.cc
@@ -17,7 +17,7 @@ using namespace ost;
using namespace ost::seq;
using namespace ost::conop;
-namespace promod3 { namespace meld {
+namespace promod3 { namespace rawmodel {
namespace {
diff --git a/rawmodel/src/model.hh b/rawmodel/src/model.hh
index 53f456051e718f6f3126d83454524ca1634621c5..3ebfdd845446404919569e137673894fa6f38dad 100644
--- a/rawmodel/src/model.hh
+++ b/rawmodel/src/model.hh
@@ -7,7 +7,7 @@
#include "gap.hh"
-namespace promod3 { namespace meld {
+namespace promod3 { namespace rawmodel {
struct RawModelingResult {
diff --git a/rawmodel/tests/CMakeLists.txt b/rawmodel/tests/CMakeLists.txt
index bf83b9dbdaf8e85db7324d966b455916dc38bd44..66f8d50226c762dbd6dd383c9e7fb651f62381a2 100644
--- a/rawmodel/tests/CMakeLists.txt
+++ b/rawmodel/tests/CMakeLists.txt
@@ -1,9 +1,9 @@
-set(MELD_UNIT_TESTS
+set(RAWMODEL_UNIT_TESTS
test_raw_modeling.py
test_gap_extension.py
)
-set(MELD_TEST_DATA
+set(RAWMODEL_TEST_DATA
data/loop/ext.pdb
data/raw-modeling/compounds.chemlib
data/raw-modeling/gly.pdb
@@ -17,6 +17,6 @@ set(MELD_TEST_DATA
data/raw-modeling/cbeta.fasta
)
-promod3_unittest(MODULE meld
- SOURCES "${MELD_UNIT_TESTS}"
- DATA "${MELD_TEST_DATA}")
+promod3_unittest(MODULE rawmodel
+ SOURCES "${RAWMODEL_UNIT_TESTS}"
+ DATA "${RAWMODEL_TEST_DATA}")
diff --git a/rawmodel/tests/test_gap_extension.py b/rawmodel/tests/test_gap_extension.py
index cfeb92b0ff01fc07c3e3063b1a95028bbe9ca700..fecd7c3f02924f0269d6bda9cb4fc39aafca1ccc 100644
--- a/rawmodel/tests/test_gap_extension.py
+++ b/rawmodel/tests/test_gap_extension.py
@@ -1,15 +1,15 @@
import unittest
-from promod3 import meld
+from promod3 import rawmodel
from ost import io
class GapExtension(unittest.TestCase):
def testGapExtender(self):
ent = io.LoadPDB('data/loop/ext.pdb')
chain = ent.chains[0]
- gap = meld.StructuralGap(chain.FindResidue(9),
+ gap = rawmodel.StructuralGap(chain.FindResidue(9),
chain.FindResidue(11),
'X')
- ext = meld.GapExtender(gap)
+ ext = rawmodel.GapExtender(gap)
self.assertEqual(str(gap), 'A.PRO9-(X)-A.TRP11')
self.assertTrue(ext.Extend())
self.assertEqual(str(gap), 'A.THR8-(PX)-A.TRP11')
diff --git a/rawmodel/tests/test_raw_modeling.py b/rawmodel/tests/test_raw_modeling.py
index b18cc0e4c415d25309338e35ebeec799591bb576..07f900522c9e46f0742873bdbf5b42b358b9524f 100644
--- a/rawmodel/tests/test_raw_modeling.py
+++ b/rawmodel/tests/test_raw_modeling.py
@@ -1,8 +1,8 @@
"""
-Unit tests for meld.
+Unit tests for rawmodel.
"""
import unittest
-from promod3 import meld
+from promod3 import rawmodel
from ost import conop, seq, io, mol
class RawModelingTests(unittest.TestCase):
@@ -17,14 +17,14 @@ class RawModelingTests(unittest.TestCase):
# test that BuildRawModel throws exception when no view is attached
aln = seq.CreateAlignment(seq.CreateSequence('A', 'acdef'),
seq.CreateSequence('B', 'ac-ef'))
- self.assertRaises(RuntimeError, meld.BuildRawModel, aln)
+ self.assertRaises(RuntimeError, rawmodel.BuildRawModel, aln)
def testModeledSequence(self):
# test if the model has the sequence we want.
tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
aln = io.LoadAlignment('data/raw-modeling/seq.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
seq1 = seq.SequenceFromChain('MODEL', result.model.chains[0])
self.assertEqual(seq1.string, aln.sequences[0].string)
@@ -33,7 +33,7 @@ class RawModelingTests(unittest.TestCase):
tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
aln = io.LoadAlignment('data/raw-modeling/del.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before, residues[2])
@@ -45,7 +45,7 @@ class RawModelingTests(unittest.TestCase):
tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
aln = io.LoadAlignment('data/raw-modeling/ins.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before, residues[1])
@@ -58,7 +58,7 @@ class RawModelingTests(unittest.TestCase):
tpl = io.LoadPDB('data/raw-modeling/gly.pdb')
aln = io.LoadAlignment('data/raw-modeling/ter.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(result.gaps), 2)
self.assertEqual(result.gaps[0].before, mol.ResidueHandle())
@@ -73,7 +73,7 @@ class RawModelingTests(unittest.TestCase):
tpl = io.LoadPDB('data/raw-modeling/sep.pdb')
aln = io.LoadAlignment('data/raw-modeling/sep.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
residues = result.model.residues
self.assertEqual(len(residues), 1)
self.assertEqual(len(residues[0].atoms), 6)
@@ -89,7 +89,7 @@ class RawModelingTests(unittest.TestCase):
tpl = io.LoadPDB('data/raw-modeling/cbeta.pdb')
aln = io.LoadAlignment('data/raw-modeling/cbeta.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = meld.BuildRawModel(aln)
+ result = rawmodel.BuildRawModel(aln)
residues = result.model.residues
self.assertFalse(residues[0].FindAtom("CB").IsValid())
self.assertFalse(residues[1].FindAtom("CB").IsValid())