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diff --git a/doc/html/.doctrees/meld/loop.doctree b/doc/html/.doctrees/meld/loop.doctree
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diff --git a/doc/html/.doctrees/meld/rawmodel.doctree b/doc/html/.doctrees/meld/rawmodel.doctree
index 4e8f300f4bc8581cb59b45ed848ee7bef730b0dd..78503f04f2aba7fcffafc912c4227cd0be08e307 100644
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diff --git a/doc/html/.doctrees/users.doctree b/doc/html/.doctrees/users.doctree
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diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index e70c128d53fe4064b75459b77bfba3938432881a..30923bd52cb8a7c485414dfc7c06005493f56d59 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 May 09 14:45, 2014.
+ Last updated on May 26 14:31, 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 7983666a30c0a07057b7c24326d486c489bbe924..c91c0ab7ccc167f704ea65318ffba146d8339b70 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -173,7 +173,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 09 14:45, 2014.
+ Last updated on May 26 14:31, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index 8d59f3b901d2b65d796687817a2791c872afd9b6..c4124270a1741bec5e4448b7ca28d39b0f812fe3 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -5,7 +5,7 @@ Dependencies
--------------------------------------------------------------------------------
|project| is build on top of |ost_l|_ (|ost_s|) and needs at least version
1.4. To create the build system, |cmake|_ is required in version 2.8.7 or
-higher. |python|_ works well from version 2.7. For |ost_s| and the C++ bit of
+higher. |python|_ works well from version 2.7. For |ost_s| and the |C++| bit of
|project|, |boost|_ is required in version 1.47.0. To build documentation,
|sphinx|_ 1.2b1 is used.
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt
index abea2cec422d0ec556ffc5817888ee2e624e499a..7891e86c9f6605b36114b1a4d6d2a14eec0a52aa 100644
--- a/doc/html/_sources/changelog.txt
+++ b/doc/html/_sources/changelog.txt
@@ -11,4 +11,8 @@ Changes in Release 0.1
* first idea of the documentation system
* meld included from SMNG as first module (to be modified/ renamed)
+Changes in Release 0.2
+--------------------------------------------------------------------------------
+ * added html documentation to repository
+
.. LocalWords: Changelog reStructuredText changelog txt
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index c4ba7c73478aee3dbd85fa8a2bb3dec1036b1a79..869300d8702b2334086fa46095eebe7cfa8eac00 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -11,6 +11,9 @@ documented inline. One exception exists on the example-driven approach:
following the :mod:`~promod3.core` module for your setup is not advisable. This
one is a bit special and provides core functionality to everybody else.
+In the end of this chapter you will find a little walk-through on how to get
+started.
+
--------------------------------------------------------------------------------
|git| Branches
--------------------------------------------------------------------------------
@@ -201,16 +204,17 @@ will provide you with a target ``test_awesome_feature.py_run``.
--------------------------------------------------------------------------------
Writing Documentation
--------------------------------------------------------------------------------
-To create documentation, we use |sphinx|_ to go from |restructuredtext|_ files
-and API documentation in source files to HTML or man pages.
-
-For each module, at least one |restructuredtext| document exists, that gives an
-idea of concepts and pulls in interfaces from source. Copying files to the
-build directory, issuing the |sphinx| call and everything else that is needed
-to create the actual documentation is done by |cmake| and its makefiles. Hence,
-the :file:`CMakeLists.txt` of the :file:`doc` directory of a module is crucial.
-For documentation which does not relate to a particular module, the repository
-comes with a top-level :file:`doc` directory.
+To create documentation, we use |sphinx|_ to go from |restructuredtext|_
+(|restructuredtext_abrv|) files and API documentation in source files to HTML
+or man pages.
+
+For each module, at least one |restructuredtext_abrv| document exists, that
+gives an idea of concepts and pulls in interfaces from source. Copying files to
+the build directory, issuing the |sphinx| call and everything else that is
+needed to create the actual documentation is done by |cmake| and its makefiles.
+Hence, the :file:`CMakeLists.txt` of the :file:`doc` directory of a module is
+crucial. For documentation which does not relate to a particular module, the
+repository comes with a top-level :file:`doc` directory.
While you should not spend to much time thinking about how to format
documentation, here is a helpful list of standard formatters:
@@ -219,8 +223,272 @@ http://sphinx-doc.org/markup/inline.html
If you write new functionality for |project|, or fix bugs, feel free to extend
the Changelog. It will be automatically pulled into the documentation.
+--------------------------------------------------------------------------------
+How To Start Your Own Module
+--------------------------------------------------------------------------------
+This is just a walk-through how the topics from above work together when you
+start your own module. For the entry point, lets assume that you already cloned
+the repository into a directory and just changed into it.
+
+All new features should take off from the ``develop`` branch. That way, they
+work fine with all the other new fellows waiting for release right from the
+beginning. Therefore you need to switch branches as a first step. |git| will
+tell you for which branch you went, a story of failure otherwise.
+
+.. code-block:: console
+
+ $ git checkout develop
+ Switched to branch 'develop'
+ $
+
+Sitting on top of the right code basis, you should just spawn your own branch
+from it. As an example, your feature will go by the name of 'sidechains'.
+
+.. code-block:: console
+
+ $ git checkout -b sidechains
+ Switched to a new branch 'sidechains'
+ $
+
+This time, |git| should tell you about going for **a new** branch.
+
+Now create the directory structure where your project will live. Here is the
+list of directories which are likely to be used in every project.
+
+.. code-block:: console
+
+ $ mkdir -p sidechains/doc
+ $ mkdir -p sidechains/pymod
+ $ mkdir -p sidechains/tests
+ $
+
+If you run ``git status`` at this point, you will see basically nothing. That
+is, |git| does not admire empty directories. Before you bring your module under
+version control, create a couple of files which are always needed.
+
+.. code-block:: console
+
+ $ touch sidechains/pymod/__init__.py
+ $ echo "FOO" >> sidechains/doc/index.rst
+ $ echo ":mod:\`~promod3.sidechains\` - ProMod3 side chain optimiser" >> sidechains/doc/index.rst
+ $ echo "================================================================================" >> sidechains/doc/index.rst
+ $
+
+Having an empty :file:`__init__.py` is perfectly fine for |python|, it just
+announces a directory as a module. But a blank :file:`index.rst` has the chance
+to give |sphinx| quite a headache so you already fill it with a headline for
+your documentation.
+
+For integration with :command:`make`, the build system needs to now about the
+new module and its members. This goes for setting up new |cmake| files and
+extending some around the directory root.
+
+.. code-block:: console
+
+ $ touch sidechains/CMakeLists.txt
+ $ touch sidechains/pymod/CMakeLists.txt
+ $ touch sidechains/doc/CMakeLists.txt
+ $
+
+Each of those files still needs a bit of content. The simplest one comes from
+the module's root, :file:`sidechains/CMakeLists.txt`:
+
+.. code-block:: cmake
+ :linenos:
+
+ add_subdirectory(pymod)
+ add_subdirectory(doc)
+
+Those two directives just tell |cmake| to go and look in directories
+:file:`pymod` and :file:`doc` below the current path for more |cmake|
+configurations. The next level in :file:`CMakeLists.txt` magic comes for the
+:file:`doc` directory:
+
+.. code-block:: cmake
+ :linenos:
+
+ set(SIDECHAINS_RST
+ index.rst
+ )
+
+ add_doc_source(NAME sidechains RST ${SIDECHAINS_RST})
+
+``add_doc_source`` is our custom |cmake| macro to register
+|restructuredtext_abrv| files for the documentation. On running
+:command:`make`, those files are placed in a :file:`doc/source` directory tree
+within the build directory. Each new submodule in your project should be
+covered by its own documentation entity, extending the list in ``RST``.
+Maintaining readability, its good practice to store this list in a separate
+variable, called ``SIDECHAINS_RST`` here.
+
+For the actual code, you should keep in mind that a |python| module may be
+rather complex. There is for sure |python| code, there could be a bit of |C++|
+and conditional compilation. In rare cases you also want to modify the
+directory structure of the package. All this has to be declared in the
+:file:`pymod` subtree. We cannot enumerate all specialities but there should be
+a couple of examples around in this repository. Here is the most basic
+:file:`CMakeLists.txt`:
+
+.. code-block:: cmake
+ :linenos:
+
+ set(SIDECHAINS_PYMOD
+ __init__.py
+ )
+
+ pymod(NAME sidechains PY ${SIDECHAINS_PYMOD})
+
+Source files should be again listed in a dedicated variable. Later, you
+probably add some |C++| code and settings diverging from the defaults via the
+``pymod`` macro. This is where things clutter up quite quickly. As set up here,
+your project would be added as a module ``sidechains`` in the |project|
+|python| package tree.
+
+The final step towards |cmake| is to register your module's directory in the
+top level :file:`CMakeLists.txt`:
+
+.. code-block:: cmake
+ :linenos:
+ :emphasize-lines: 80
+
+ #-------------------------------------------------------------------------------
+ # Author: Bienchen
+ #-------------------------------------------------------------------------------
+ # Options to CMake:
+ # DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx
+ # DISABLE_DOCTEST: Don't run example code from documentation on 'make check'
+ # DISABLE_LINKCHECK: Don't test links from documentation on 'make check'
+ # (if documentation is disabled, there is no doctest, linkcheck at all)
+ cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
+ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
+
+ project(PROMOD3 CXX C)
+
+ include(PROMOD3)
+
+ set(PROMOD3_VERSION_MAJOR 0)
+ set(PROMOD3_VERSION_MINOR 1)
+ set(PROMOD3_VERSION_PATCH 0)
+ set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}.${PROMOD3_VERSION_PATCH})
+
+ if (CMAKE_COMPILER_IS_GNUCXX)
+ exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
+ if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
+ set(PROMOD_GCC_45 true)
+ else()
+ set(PROMOD_GCC_45 false)
+ endif()
+ endif()
+
+ if (OPTIMIZE)
+ set(CMAKE_BUILD_TYPE Release)
+ set(_OPT ON)
+ else()
+ set(CMAKE_BUILD_TYPE Debug)
+ set(_OPT OFF)
+ endif()
+
+ setup_stage()
+ file(MAKE_DIRECTORY ${STAGE_DIR}
+ ${EXECUTABLE_OUTPUT_PATH}
+ ${HEADER_STAGE_PATH}
+ ${LIB_STAGE_PATH}
+ ${LIBEXEC_STAGE_PATH})
+
+ setup_compiler_flags()
+ setup_boost()
+
+ find_package(Python 2.7 REQUIRED)
+ if(NOT DISABLE_DOCUMENTATION)
+ find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
+ set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
+ # set this to the URL corresponding to the version of OST you are using
+ set(OST_DOC_URL "http://www.openstructure.org/docs/1.3")
+ endif()
+ find_package(OPENSTRUCTURE 1.4 REQUIRED
+ COMPONENTS io mol seq seq_alg mol_alg conop)
+
+ if (CMAKE_COMPILER_IS_GNUCXX)
+ # do not write back into cache, otherwise the compile command line gets
+ # expanded with multiple -fno-strict-aliasing flags, triggering a complete
+ # rebuild whenever cmake is run
+ set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing")
+ if("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-attributes")
+ endif("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
+ endif()
+
+ # basic environment
+ include_directories(${Boost_INCLUDE_DIRS}
+ ${OST_INCLUDE_DIR})
+
+ set(FILES_TO_BE_REMOVED ${PROJECT_BINARY_DIR}/stage)
+ set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
+ "${FILES_TO_BE_REMOVED}")
+
+ ## sub dirs to be recognised by CMake
+ ## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
+ add_subdirectory(config)
+ add_subdirectory(core)
+ add_subdirectory(sidechains)
+ add_subdirectory(scripts)
+ add_subdirectory(actions)
+ if(NOT DISABLE_DOCUMENTATION)
+ add_changelog_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG")
+ add_subdirectory(doc)
+ endif()
+
+ ## report setup
+ message(STATUS "PROMOD3 will be built with the following options:\n"
+ " OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
+ " Optimized (-DOPTIMIZE) : ${_OPT}\n"
+ " Python : ${PYTHON_BINARY}\n")
+
+All that needs to be done for |cmake| to recognise your module is adding its
+directory as shown in line 80.
+
+This was the final step to set up the build system. Running |cmake| at this
+point would create the build environment in place. But building software in
+your code repository has several drawbacks. First of all, it puts all kind of
+new files in the directory tree and ``git status`` would show them all. Then
+its very likely, that manual intervention is needed after ``make clean``. Plus,
+this would be very static. Imagine at one point you want to switch on all
+debugging flags for your |C++| code. So you either clean the whole repository
+and rebuild or you go by two separated repositories copying code changes from A
+to B. The solution to this is instead of 'in place' you go 'out of source'. You
+still can stay in your repository while being out of the source tree by using
+sub-directories. |project| comes with a dedicated prefix 'build*' in
+:file:`.gitignore`. Have a directory :file:`build` and :file:`build-dbg` and it
+will not show up in ``git status``.
+
+.. code-block:: console
+
+ $ mkdir build
+ $ cd build
+ $
+
+To actually create all the makefiles and generated files, you may use one of
+the configuration scripts from the :file:`conf-scripts` directory. Usually
+those scripts only need to be pointed to an |ost_s| staging tree. Even if you
+are on a system not covered by available scripts, their code may help you at
+the |cmake| command. Once you managed to conquer a new system, feel free to add
+a new configuration script. The following example assumes |fedora| 19.
+
+.. code-block:: console
+
+ $ ../conf-scripts/fedora-19-conf ../../ost.git/stage
+
+From this point, :command:`make` should work and you could start adding your
+files to the repository using ``git add``.
+
+
.. _restructuredtext: http://docutils.sourceforge.net/rst.html
+.. |fedora| replace:: Fedora
+
.. LocalWords: cmake hotfix doctest linkcheck rebase BRANCHNAME rebasing py
.. LocalWords: CMakeLists txt rst pymod init submodule src restructuredtext
-.. LocalWords: makefiles formatters Changelog codetest promod
+.. LocalWords: makefiles formatters Changelog codetest promod sidechains io
+.. LocalWords: mkdir linenos subdirectory abrv emphasize CXX GNUCXX gcc fno
+.. LocalWords: ARGS endif OPTIMIZE LIBEXEC Wno DIRS dirs subdirs config dbg
+.. LocalWords: changelog Optimized DOPTIMIZE gitignore cd conf
diff --git a/doc/html/_sources/meld/index.txt b/doc/html/_sources/meld/index.txt
index fec388e6369affe35445eb20f171bdac43ad71a4..148e9702d21b56fadee106c99930b2053775bb89 100644
--- a/doc/html/_sources/meld/index.txt
+++ b/doc/html/_sources/meld/index.txt
@@ -1,7 +1,7 @@
-:mod:`~sm.meld` - Coordinate modeling
+:mod:`~promod3.meld` - Coordinate modeling
================================================================================
-.. module:: sm.meld
+.. module:: promod3.meld
:synopsis: Coordinate modeling and sampling
This module contains functions and classes to model protein structures from sequence.
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 9d3a59c3c7f615273ee80e1aa1a62670f94433dc..e38c28162d03ba1653564dd8d407b4ebcd14f3b6 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -186,7 +186,7 @@ configuration also Sphinx with the <tt class="docutils literal"><span class="pre
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 08 10:47, 2014.
+ Last updated on May 26 14:31, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index ba32c057a85f890973aa2415896cd2e47d73cdf7..abd8194403d23abe1f5fdfdcda2bbb58d6f34ed4 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -60,6 +60,14 @@
</ul>
</div></blockquote>
</div>
+<div class="section" id="changes-in-release-0-2">
+<h2>Changes in Release 0.2<a class="headerlink" href="#changes-in-release-0-2" title="Permalink to this headline">¶</a></h2>
+<blockquote>
+<div><ul class="simple">
+<li>added html documentation to repository</li>
+</ul>
+</div></blockquote>
+</div>
</div>
@@ -72,6 +80,7 @@
<ul>
<li><a class="reference internal" href="#">Changelog</a><ul>
<li><a class="reference internal" href="#changes-in-release-0-1">Changes in Release 0.1</a></li>
+<li><a class="reference internal" href="#changes-in-release-0-2">Changes in Release 0.2</a></li>
</ul>
</li>
</ul>
@@ -118,7 +127,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 08 10:47, 2014.
+ Last updated on May 26 13:39, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 14622752d530083782888067fb2d7f69c9886152..559d94b89daddd9ff7b6392e561dcbe06615621f 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -66,6 +66,8 @@ explaining what a whole module is supposed to do usually goes into a
documented inline. One exception exists on the example-driven approach:
following the <a class="reference internal" href="core/index.html#module-promod3.core" title="promod3.core: Basic functionality, supporting standard tasks in your code."><tt class="xref py py-mod docutils literal"><span class="pre">core</span></tt></a> module for your setup is not advisable. This
one is a bit special and provides core functionality to everybody else.</p>
+<p>In the end of this chapter you will find a little walk-through on how to get
+started.</p>
<div class="section" id="git-branches">
<h2>Git Branches<a class="headerlink" href="#git-branches" title="Permalink to this headline">¶</a></h2>
<p>Basically we have two, sometimes three major branches. <tt class="docutils literal"><span class="pre">master</span></tt>, <tt class="docutils literal"><span class="pre">develop</span></tt>
@@ -230,21 +232,346 @@ will provide you with a target <tt class="docutils literal"><span class="pre">te
</div>
<div class="section" id="writing-documentation">
<h2>Writing Documentation<a class="headerlink" href="#writing-documentation" title="Permalink to this headline">¶</a></h2>
-<p>To create documentation, we use <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> to go from <a class="reference external" href="http://docutils.sourceforge.net/rst.html">reStructuredText</a> files
-and API documentation in source files to HTML or man pages.</p>
-<p>For each module, at least one reStructuredText document exists, that gives an
-idea of concepts and pulls in interfaces from source. Copying files to the
-build directory, issuing the Sphinx call and everything else that is needed
-to create the actual documentation is done by CMake and its makefiles. Hence,
-the <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt> of the <tt class="file docutils literal"><span class="pre">doc</span></tt> directory of a module is crucial.
-For documentation which does not relate to a particular module, the repository
-comes with a top-level <tt class="file docutils literal"><span class="pre">doc</span></tt> directory.</p>
+<p>To create documentation, we use <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> to go from <a class="reference external" href="http://docutils.sourceforge.net/rst.html">reStructuredText</a>
+(reST) files and API documentation in source files to HTML
+or man pages.</p>
+<p>For each module, at least one reST document exists, that
+gives an idea of concepts and pulls in interfaces from source. Copying files to
+the build directory, issuing the Sphinx call and everything else that is
+needed to create the actual documentation is done by CMake and its makefiles.
+Hence, the <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt> of the <tt class="file docutils literal"><span class="pre">doc</span></tt> directory of a module is
+crucial. For documentation which does not relate to a particular module, the
+repository comes with a top-level <tt class="file docutils literal"><span class="pre">doc</span></tt> directory.</p>
<p>While you should not spend to much time thinking about how to format
documentation, here is a helpful list of standard formatters:
<a class="reference external" href="http://sphinx-doc.org/markup/inline.html">http://sphinx-doc.org/markup/inline.html</a></p>
<p>If you write new functionality for ProMod3, or fix bugs, feel free to extend
the Changelog. It will be automatically pulled into the documentation.</p>
</div>
+<div class="section" id="how-to-start-your-own-module">
+<h2>How To Start Your Own Module<a class="headerlink" href="#how-to-start-your-own-module" title="Permalink to this headline">¶</a></h2>
+<p>This is just a walk-through how the topics from above work together when you
+start your own module. For the entry point, lets assume that you already cloned
+the repository into a directory and just changed into it.</p>
+<p>All new features should take off from the <tt class="docutils literal"><span class="pre">develop</span></tt> branch. That way, they
+work fine with all the other new fellows waiting for release right from the
+beginning. Therefore you need to switch branches as a first step. Git will
+tell you for which branch you went, a story of failure otherwise.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout develop
+<span class="go">Switched to branch 'develop'</span>
+<span class="gp">$</span>
+</pre></div>
+</div>
+<p>Sitting on top of the right code basis, you should just spawn your own branch
+from it. As an example, your feature will go by the name of ‘sidechains’.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout -b sidechains
+<span class="go">Switched to a new branch 'sidechains'</span>
+<span class="gp">$</span>
+</pre></div>
+</div>
+<p>This time, Git should tell you about going for <strong>a new</strong> branch.</p>
+<p>Now create the directory structure where your project will live. Here is the
+list of directories which are likely to be used in every project.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> mkdir -p sidechains/doc
+<span class="gp">$</span> mkdir -p sidechains/pymod
+<span class="gp">$</span> mkdir -p sidechains/tests
+<span class="gp">$</span>
+</pre></div>
+</div>
+<p>If you run <tt class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></tt> at this point, you will see basically nothing. That
+is, Git does not admire empty directories. Before you bring your module under
+version control, create a couple of files which are always needed.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch sidechains/pymod/__init__.py
+<span class="gp">$</span> <span class="nb">echo</span> <span class="s2">"FOO"</span> >> sidechains/doc/index.rst
+<span class="gp">$</span> <span class="nb">echo</span> <span class="s2">":mod:\`~promod3.sidechains\` - ProMod3 side chain optimiser"</span> >> sidechains/doc/index.rst
+<span class="gp">$</span> <span class="nb">echo</span> <span class="s2">"================================================================================"</span> >> sidechains/doc/index.rst
+<span class="gp">$</span>
+</pre></div>
+</div>
+<p>Having an empty <tt class="file docutils literal"><span class="pre">__init__.py</span></tt> is perfectly fine for Python, it just
+announces a directory as a module. But a blank <tt class="file docutils literal"><span class="pre">index.rst</span></tt> has the chance
+to give Sphinx quite a headache so you already fill it with a headline for
+your documentation.</p>
+<p>For integration with <strong class="command">make</strong>, the build system needs to now about the
+new module and its members. This goes for setting up new CMake files and
+extending some around the directory root.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch sidechains/CMakeLists.txt
+<span class="gp">$</span> touch sidechains/pymod/CMakeLists.txt
+<span class="gp">$</span> touch sidechains/doc/CMakeLists.txt
+<span class="gp">$</span>
+</pre></div>
+</div>
+<p>Each of those files still needs a bit of content. The simplest one comes from
+the module’s root, <tt class="file docutils literal"><span class="pre">sidechains/CMakeLists.txt</span></tt>:</p>
+<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+2</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
+</pre></div>
+</td></tr></table></div>
+<p>Those two directives just tell CMake to go and look in directories
+<tt class="file docutils literal"><span class="pre">pymod</span></tt> and <tt class="file docutils literal"><span class="pre">doc</span></tt> below the current path for more CMake
+configurations. The next level in <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt> magic comes for the
+<tt class="file docutils literal"><span class="pre">doc</span></tt> directory:</p>
+<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+2
+3
+4
+5</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAINS_RST</span>
+<span class="s">index.rst</span>
+<span class="p">)</span>
+
+<span class="nb">add_doc_source</span><span class="p">(</span><span class="s">NAME</span> <span class="s">sidechains</span> <span class="s">RST</span> <span class="o">${</span><span class="nv">SIDECHAINS_RST</span><span class="o">}</span><span class="p">)</span>
+</pre></div>
+</td></tr></table></div>
+<p><tt class="docutils literal"><span class="pre">add_doc_source</span></tt> is our custom CMake macro to register
+reST files for the documentation. On running
+<strong class="command">make</strong>, those files are placed in a <tt class="file docutils literal"><span class="pre">doc/source</span></tt> directory tree
+within the build directory. Each new submodule in your project should be
+covered by its own documentation entity, extending the list in <tt class="docutils literal"><span class="pre">RST</span></tt>.
+Maintaining readability, its good practice to store this list in a separate
+variable, called <tt class="docutils literal"><span class="pre">SIDECHAINS_RST</span></tt> here.</p>
+<p>For the actual code, you should keep in mind that a Python module may be
+rather complex. There is for sure Python code, there could be a bit of C++
+and conditional compilation. In rare cases you also want to modify the
+directory structure of the package. All this has to be declared in the
+<tt class="file docutils literal"><span class="pre">pymod</span></tt> subtree. We cannot enumerate all specialities but there should be
+a couple of examples around in this repository. Here is the most basic
+<tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt>:</p>
+<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+2
+3
+4
+5</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAINS_PYMOD</span>
+<span class="s">__init__.py</span>
+<span class="p">)</span>
+
+<span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">sidechains</span> <span class="s">PY</span> <span class="o">${</span><span class="nv">SIDECHAINS_PYMOD</span><span class="o">}</span><span class="p">)</span>
+</pre></div>
+</td></tr></table></div>
+<p>Source files should be again listed in a dedicated variable. Later, you
+probably add some C++ code and settings diverging from the defaults via the
+<tt class="docutils literal"><span class="pre">pymod</span></tt> macro. This is where things clutter up quite quickly. As set up here,
+your project would be added as a module <tt class="docutils literal"><span class="pre">sidechains</span></tt> in the ProMod3
+Python package tree.</p>
+<p>The final step towards CMake is to register your module’s directory in the
+top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt>:</p>
+<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+ 2
+ 3
+ 4
+ 5
+ 6
+ 7
+ 8
+ 9
+10
+11
+12
+13
+14
+15
+16
+17
+18
+19
+20
+21
+22
+23
+24
+25
+26
+27
+28
+29
+30
+31
+32
+33
+34
+35
+36
+37
+38
+39
+40
+41
+42
+43
+44
+45
+46
+47
+48
+49
+50
+51
+52
+53
+54
+55
+56
+57
+58
+59
+60
+61
+62
+63
+64
+65
+66
+67
+68
+69
+70
+71
+72
+73
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+76
+77
+78
+79
+80
+81
+82
+83
+84
+85
+86
+87
+88
+89
+90
+91
+92</pre></div></td><td class="code"><div class="highlight"><pre><span class="c">#-------------------------------------------------------------------------------</span>
+<span class="c"># Author: Bienchen</span>
+<span class="c">#-------------------------------------------------------------------------------</span>
+<span class="c"># Options to CMake:</span>
+<span class="c"># DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx</span>
+<span class="c"># DISABLE_DOCTEST: Don't run example code from documentation on 'make check'</span>
+<span class="c"># DISABLE_LINKCHECK: Don't test links from documentation on 'make check'</span>
+<span class="c"># (if documentation is disabled, there is no doctest, linkcheck at all)</span>
+<span class="nb">cmake_minimum_required</span><span class="p">(</span><span class="s">VERSION</span> <span class="s">2.6.4</span> <span class="s">FATAL_ERROR</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_MODULE_PATH</span> <span class="o">${</span><span class="nv">CMAKE_MODULE_PATH</span><span class="o">}</span> <span class="o">${</span><span class="nv">CMAKE_SOURCE_DIR</span><span class="o">}</span><span class="s">/cmake_support</span><span class="p">)</span>
+
+<span class="nb">project</span><span class="p">(</span><span class="s">PROMOD3</span> <span class="s">CXX</span> <span class="s">C</span><span class="p">)</span>
+
+<span class="nb">include</span><span class="p">(</span><span class="s">PROMOD3</span><span class="p">)</span>
+
+<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MAJOR</span> <span class="s">0</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MINOR</span> <span class="s">1</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_PATCH</span> <span class="s">0</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_STRING</span> <span class="o">${</span><span class="nv">PROMOD3_VERSION_MAJOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_MINOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_PATCH</span><span class="o">}</span><span class="p">)</span>
+
+<span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
+ <span class="nb">exec_program</span><span class="p">(</span><span class="s">gcc</span> <span class="s">ARGS</span> <span class="s">--version</span> <span class="s">OUTPUT_VARIABLE</span> <span class="s">CMAKE_C_COMPILER_VERSION</span><span class="p">)</span>
+ <span class="nb">if</span><span class="p">(</span><span class="s">CMAKE_C_COMPILER_VERSION</span> <span class="s">MATCHES</span> <span class="s2">".*4\\.[5-9].*"</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">true</span><span class="p">)</span>
+ <span class="nb">else</span><span class="p">()</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">false</span><span class="p">)</span>
+ <span class="nb">endif</span><span class="p">()</span>
+<span class="nb">endif</span><span class="p">()</span>
+
+<span class="nb">if</span> <span class="p">(</span><span class="s">OPTIMIZE</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Release</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">ON</span><span class="p">)</span>
+<span class="nb">else</span><span class="p">()</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Debug</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">OFF</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
+
+<span class="nb">setup_stage</span><span class="p">()</span>
+<span class="nb">file</span><span class="p">(</span><span class="s">MAKE_DIRECTORY</span> <span class="o">${</span><span class="nv">STAGE_DIR</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">EXECUTABLE_OUTPUT_PATH</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">HEADER_STAGE_PATH</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">LIB_STAGE_PATH</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">LIBEXEC_STAGE_PATH</span><span class="o">}</span><span class="p">)</span>
+
+<span class="nb">setup_compiler_flags</span><span class="p">()</span>
+<span class="nb">setup_boost</span><span class="p">()</span>
+
+<span class="nb">find_package</span><span class="p">(</span><span class="s">Python</span> <span class="s">2.7</span> <span class="s">REQUIRED</span><span class="p">)</span>
+<span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
+ <span class="nb">find_package</span><span class="p">(</span><span class="s">Sphinx</span> <span class="o">${</span><span class="nv">PYTHON_VERSION</span><span class="o">}</span> <span class="s">REQUIRED</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PYTHON_DOC_URL</span> <span class="s2">"https://docs.python.org/${PYTHON_VERSION}"</span><span class="p">)</span>
+ <span class="c"># set this to the URL corresponding to the version of OST you are using</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">OST_DOC_URL</span> <span class="s2">"http://www.openstructure.org/docs/1.3"</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
+<span class="nb">find_package</span><span class="p">(</span><span class="s">OPENSTRUCTURE</span> <span class="s">1.4</span> <span class="s">REQUIRED</span>
+ <span class="s">COMPONENTS</span> <span class="s">io</span> <span class="s">mol</span> <span class="s">seq</span> <span class="s">seq_alg</span> <span class="s">mol_alg</span> <span class="s">conop</span><span class="p">)</span>
+
+<span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
+ <span class="c"># do not write back into cache, otherwise the compile command line gets</span>
+ <span class="c"># expanded with multiple -fno-strict-aliasing flags, triggering a complete</span>
+ <span class="c"># rebuild whenever cmake is run</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS_RELEASE</span> <span class="s2">"${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing"</span><span class="p">)</span>
+ <span class="nb">if</span><span class="p">(</span><span class="s2">"${CMAKE_CXX_COMPILER_VERSION}"</span> <span class="s">VERSION_GREATER</span> <span class="s2">"4.6"</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS</span> <span class="s2">"${CMAKE_CXX_FLAGS} -Wno-attributes"</span><span class="p">)</span>
+ <span class="nb">endif</span><span class="p">(</span><span class="s2">"${CMAKE_CXX_COMPILER_VERSION}"</span> <span class="s">VERSION_GREATER</span> <span class="s2">"4.6"</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
+
+<span class="c"># basic environment</span>
+<span class="nb">include_directories</span><span class="p">(</span><span class="o">${</span><span class="nv">Boost_INCLUDE_DIRS</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">OST_INCLUDE_DIR</span><span class="o">}</span><span class="p">)</span>
+
+<span class="nb">set</span><span class="p">(</span><span class="s">FILES_TO_BE_REMOVED</span> <span class="o">${</span><span class="nv">PROJECT_BINARY_DIR</span><span class="o">}</span><span class="s">/stage</span><span class="p">)</span>
+<span class="nb">set_directory_properties</span><span class="p">(</span><span class="s">PROPERTIES</span> <span class="s">ADDITIONAL_MAKE_CLEAN_FILES</span>
+ <span class="s2">"${FILES_TO_BE_REMOVED}"</span><span class="p">)</span>
+
+<span class="c">## sub dirs to be recognised by CMake</span>
+<span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">config</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">core</span><span class="p">)</span>
+<span class="hll"><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
+</span><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">scripts</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">actions</span><span class="p">)</span>
+<span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
+ <span class="nb">add_changelog_to_doc</span><span class="p">(</span><span class="s">FILE</span> <span class="s2">"${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG"</span><span class="p">)</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
+
+<span class="c">## report setup</span>
+<span class="nb">message</span><span class="p">(</span><span class="s">STATUS</span> <span class="s2">"PROMOD3 will be built with the following options:\n"</span>
+ <span class="s2">" OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"</span>
+ <span class="s2">" Optimized (-DOPTIMIZE) : ${_OPT}\n"</span>
+ <span class="s2">" Python : ${PYTHON_BINARY}\n"</span><span class="p">)</span>
+</pre></div>
+</td></tr></table></div>
+<p>All that needs to be done for CMake to recognise your module is adding its
+directory as shown in line 80.</p>
+<p>This was the final step to set up the build system. Running CMake at this
+point would create the build environment in place. But building software in
+your code repository has several drawbacks. First of all, it puts all kind of
+new files in the directory tree and <tt class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></tt> would show them all. Then
+its very likely, that manual intervention is needed after <tt class="docutils literal"><span class="pre">make</span> <span class="pre">clean</span></tt>. Plus,
+this would be very static. Imagine at one point you want to switch on all
+debugging flags for your C++ code. So you either clean the whole repository
+and rebuild or you go by two separated repositories copying code changes from A
+to B. The solution to this is instead of ‘in place’ you go ‘out of source’. You
+still can stay in your repository while being out of the source tree by using
+sub-directories. ProMod3 comes with a dedicated prefix ‘build*’ in
+<tt class="file docutils literal"><span class="pre">.gitignore</span></tt>. Have a directory <tt class="file docutils literal"><span class="pre">build</span></tt> and <tt class="file docutils literal"><span class="pre">build-dbg</span></tt> and it
+will not show up in <tt class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></tt>.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> mkdir build
+<span class="gp">$</span> <span class="nb">cd </span>build
+<span class="gp">$</span>
+</pre></div>
+</div>
+<p>To actually create all the makefiles and generated files, you may use one of
+the configuration scripts from the <tt class="file docutils literal"><span class="pre">conf-scripts</span></tt> directory. Usually
+those scripts only need to be pointed to an OST staging tree. Even if you
+are on a system not covered by available scripts, their code may help you at
+the CMake command. Once you managed to conquer a new system, feel free to add
+a new configuration script. The following example assumes Fedora 19.</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> ../conf-scripts/fedora-19-conf ../../ost.git/stage
+</pre></div>
+</div>
+<p>From this point, <strong class="command">make</strong> should work and you could start adding your
+files to the repository using <tt class="docutils literal"><span class="pre">git</span> <span class="pre">add</span></tt>.</p>
+</div>
</div>
@@ -262,6 +589,7 @@ the Changelog. It will be automatically pulled into the documentation.</p>
<li><a class="reference internal" href="#the-stage-directory">The <tt class="file docutils literal"><span class="pre">stage</span></tt> Directory</a></li>
<li><a class="reference internal" href="#unit-tests">Unit Tests</a></li>
<li><a class="reference internal" href="#writing-documentation">Writing Documentation</a></li>
+<li><a class="reference internal" href="#how-to-start-your-own-module">How To Start Your Own Module</a></li>
</ul>
</li>
</ul>
@@ -315,7 +643,7 @@ the Changelog. It will be automatically pulled into the documentation.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 09 14:45, 2014.
+ Last updated on May 26 14:31, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index 5335428067aca8869aa8a841341175ad61117fbd..1b5d174d8f2ddffebb4204680e5e81b8957a0521 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 May 08 15:38, 2014.
+ Last updated on May 26 13:39, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index f29228abce94c08a0f7cfc16bb7c64272852af8c..14636e68b6d3287570b9f6896a115ee65475c9bb 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -123,7 +123,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 08 15:38, 2014.
+ Last updated on May 26 13:39, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 3d5b6e38e663c832d1f91b102dcc0c82b785d35a..58fcbad03d41bb38b379c61bee613e1199869c6f 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -78,6 +78,7 @@
<li class="toctree-l2"><a class="reference internal" href="contributing.html#the-stage-directory">The <tt class="file docutils literal"><span class="pre">stage</span></tt> Directory</a></li>
<li class="toctree-l2"><a class="reference internal" href="contributing.html#unit-tests">Unit Tests</a></li>
<li class="toctree-l2"><a class="reference internal" href="contributing.html#writing-documentation">Writing Documentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="contributing.html#how-to-start-your-own-module">How To Start Your Own Module</a></li>
</ul>
</li>
</ul>
@@ -138,7 +139,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 09 14:45, 2014.
+ Last updated on May 26 14:31, 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 0b29f2bdbeee864ebe13e337c276f1484b96f95d..ec5e6d559ac9eda6398e3ba29df95f5e9de619d3 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -198,10 +198,14 @@
<dt><a href="meld/loop.html#sm.meld.LoopCandidate.packing_score">packing_score (sm.meld.LoopCandidate attribute)</a>
</dt>
+
+ <dt><a href="core/index.html#module-promod3.core">promod3.core (module)</a>
+ </dt>
+
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="core/index.html#module-promod3.core">promod3.core (module)</a>
+ <dt><a href="meld/index.html#module-promod3.meld">promod3.meld (module)</a>
</dt>
</dl></td>
@@ -235,16 +239,12 @@
</dt>
- <dt><a href="meld/index.html#module-sm.meld">sm.meld (module)</a>
+ <dt><a href="meld/loop.html#sm.meld.LoopCandidates.SortByCorrel">SortByCorrel() (sm.meld.LoopCandidates method)</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="meld/loop.html#sm.meld.LoopCandidates.SortByCorrel">SortByCorrel() (sm.meld.LoopCandidates method)</a>
- </dt>
-
-
<dt><a href="meld/loop.html#sm.meld.LoopCandidates.SortByScore">SortByScore() (sm.meld.LoopCandidates method)</a>
</dt>
@@ -308,7 +308,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 09 14:45, 2014.
+ Last updated on May 26 14:31, 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 29ff149490c5b27c7fb9eb77c55fc1b8ce53e074..9ff48fa481b166eebb839b9572531746d5476eca 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -63,6 +63,7 @@
</li>
<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#changes-in-release-0-1">Changes in Release 0.1</a></li>
+<li class="toctree-l2"><a class="reference internal" href="changelog.html#changes-in-release-0-2">Changes in Release 0.2</a></li>
</ul>
</li>
</ul>
@@ -133,7 +134,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 09 14:45, 2014.
+ Last updated on May 26 14:31, 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 c51bc70c22a95c4d55faa8fa27cf9c2d13e7e422..99d458aac43c2b1120f9a4316f0f11ef9a4f3f09 100644
--- a/doc/html/meld/index.html
+++ b/doc/html/meld/index.html
@@ -54,8 +54,8 @@
<div class="bodywrapper">
<div class="body">
- <div class="section" id="module-sm.meld">
-<span id="meld-coordinate-modeling"></span><h1><a class="reference internal" href="#module-sm.meld" title="sm.meld: Coordinate modeling and sampling"><tt class="xref py py-mod docutils literal"><span class="pre">meld</span></tt></a> - Coordinate modeling<a class="headerlink" href="#module-sm.meld" title="Permalink to this headline">¶</a></h1>
+ <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: Coordinate modeling and sampling"><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>
<p>This module contains functions and classes to model protein structures from sequence.</p>
<div class="toctree-wrapper compound">
<ul>
@@ -127,7 +127,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 08 10:47, 2014.
+ Last updated on May 26 13:39, 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 542b8e3032dc46e909987180c7539e7e5b901fea..0c2db6ed37b75b55029348284503ded02a730ff9 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 May 08 10:47, 2014.
+ Last updated on May 26 13:39, 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 a923efc24c5d62560d2badb890281c69ebf64a18..1838d45abb78a9fad790227c95272082e928e7c3 100644
--- a/doc/html/meld/rawmodel.html
+++ b/doc/html/meld/rawmodel.html
@@ -221,7 +221,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 08 10:47, 2014.
+ Last updated on May 26 13:39, 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 9edb0b756a685738eb8d0edad56c9be36e9bc55c..12044229f7d8f4641a521777fef1c1f27935d098 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 823015676683c75ecfcb1177a3e74896ac362cc9..c4ea1c8467e4804ea9ba47182cb319fa090ef1b1 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -51,8 +51,7 @@
<h1>Python Module Index</h1>
<div class="modindex-jumpbox">
- <a href="#cap-p"><strong>p</strong></a> |
- <a href="#cap-s"><strong>s</strong></a>
+ <a href="#cap-p"><strong>p</strong></a>
</div>
<table class="indextable modindextable" cellspacing="0" cellpadding="2">
@@ -70,19 +69,10 @@
<td>
<a href="core/index.html#module-promod3.core"><tt class="xref">promod3.core</tt></a></td><td>
<em>Basic functionality, supporting standard tasks in your code.</em></td></tr>
- <tr class="pcap"><td></td><td> </td><td></td></tr>
- <tr class="cap" id="cap-s"><td></td><td>
- <strong>s</strong></td><td></td></tr>
- <tr>
- <td><img src="_static/minus.png" class="toggler"
- id="toggle-2" style="display: none" alt="-" /></td>
- <td>
- <tt class="xref">sm</tt></td><td>
- <em></em></td></tr>
- <tr class="cg-2">
+ <tr class="cg-1">
<td></td>
<td>
- <a href="meld/index.html#module-sm.meld"><tt class="xref">sm.meld</tt></a></td><td>
+ <a href="meld/index.html#module-promod3.meld"><tt class="xref">promod3.meld</tt></a></td><td>
<em>Coordinate modeling and sampling</em></td></tr>
</table>
@@ -123,7 +113,7 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on May 09 14:45, 2014.
+ Last updated on May 26 14:31, 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 3f771e55c1d5aa742c01fe5a24609b46112609a3..88fa4ab3f67685c4a2cd853f97ff8a546ef341f5 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 May 09 14:45, 2014.
+ Last updated on May 26 14:31, 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 d1a7a707fd99e812b8eba088f7aedada584b2775..30fd4ffdeac1b7bf9050732d2f18a16b22b291b7 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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diff --git a/doc/html/users.html b/doc/html/users.html
index d68bc59d27636a9674a905631202526225852700..4de84604288434d99ec0071cccb779830e684a63 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 May 08 10:47, 2014.
+ Last updated on May 26 13:39, 2014.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
</div>
</body>