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Verified Commit 67fb44bd authored by Xavier Robin's avatar Xavier Robin
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doc: reorganize and add links to main sections

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......@@ -16,10 +16,12 @@ a link to OpenStructure's own `GitLab Docker registry <https://git.scicore.uniba
If you wish to compile OpenStructure outside of a container, you need to follow
the steps which we describe in detail below. In essence, these steps are:
* Installing the Dependencies
* Checking out the source code from GIT
* Configuring the build with cmake
* Compiling an Linking
* `Installing the Dependencies`_
* `Getting the Source Code`_
* `Configuring the build`_
* `Building the Project`_
* `Building the Compound Library`_
* `Running the tests`_
Installing the Dependencies
......@@ -109,7 +111,7 @@ specific features. To change to a specific branch, use
git checkout <branch-name>
Configuring
Configuring the build
--------------------------------------------------------------------------------
OpenStructure uses `CMake <http://cmake.org>`_ for compiling and building the
......@@ -339,8 +341,11 @@ Building the Project
Type ``make``. If you are using a multi-core machine, you can use the `-j` flag
to run multiple jobs at once.
.. code-block:: bash
What's next?
make
Building the Compound Library
--------------------------------------------------------------------------------
One thing is missing for a fully functional OpenStructure installation.
......@@ -353,16 +358,29 @@ into our internal format:
.. code-block:: bash
wget https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
stage/bin/chemdict_tool create components.cif.gz <compounds.chemlib>
stage/bin/chemdict_tool create components.cif.gz compounds.chemlib
We can rerun cmake and make. All cmake parameters from the original
configuration remain in the cache.
.. code-block:: bash
cmake .. -DCOMPOUND_LIB=<compounds.chemlib>
cmake .. -DCOMPOUND_LIB=compounds.chemlib
make
Running the tests
--------------------------------------------------------------------------------
Many parts of OpenStructure are covered by unit tests. You can run them with:
.. code-block:: bash
make check
What's next?
--------------------------------------------------------------------------------
On Linux and macOS, you can start dng from the command-line. The binaries are
all located in stage/bin:
......@@ -375,13 +393,7 @@ or, to start the command-line interpreter:
.. code-block:: bash
stage/bin/ost
But hey, good citizen run the unit tests first:
.. code-block:: bash
make check
If you repeatedly use OpenStructure, it is recommended to add
/path/to/ost/stage/bin to your path.
......@@ -401,6 +413,7 @@ And then you can simply import ost as a module:
import ost
Getting the newest changes
--------------------------------------------------------------------------------
......
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