Updated compiled doc.

doc/html/_sources/buildsystem.txt → doc/html/_sources/buildsystem.rst.txt

@@ -40,7 +40,7 @@ The currently preferred versions are:
 * |python|_ 3.6.0
 * |boost|_ 1.68.0
 * |eigen3|_ 3.3.1
-* |sphinx|_ 1.3.1
+* |sphinx|_ 1.4.9
 
 --------------------------------------------------------------------------------
  Using |cmake|

doc/html/_sources/changelog.txt → doc/html/_sources/changelog.rst.txt

@@ -5,6 +5,20 @@
 Changelog
 ================================================================================
 
+Release 3.1.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: reintroduces backwards compatibility in BuildRawModel.
+  See commit 0288eced23a9a541a88005a7ed30b8f019e06226 for details
+
+
+Release 3.1.0
+--------------------------------------------------------------------------------
+
+* Introduce alignment processing steps in BuildRawModel
+* Several minor bug fixes, improvements, and speed-ups.
+
+
 Release 3.0.0
 --------------------------------------------------------------------------------
 

doc/html/_sources/container/index.txt → doc/html/_sources/container/index.rst.txt

@@ -13,6 +13,7 @@
 ..  See the License for the specific language governing permissions and
 ..  limitations under the License.
 
+.. _container:
 
 |project| and Containers
 ========================

doc/html/_sources/container/singularity.txt → doc/html/_sources/container/singularity.rst.txt

@@ -20,7 +20,8 @@ Singularity
 We do not provide a "standalone" Singularity image, but rather bootstrap from a 
 Docker image.
 
-Build the image with:
+Change to the directory containing the Singularity file
+(<PROMOD3_CHECKOUT>/container) and build the image with:
 
 .. code-block:: bash
 
@@ -56,6 +57,43 @@ To list all available |project| modelling actions:
 
     singularity run --app PM promod.img help
 
+So you can either run an action with:
+
+.. code-block:: bash
+
+    singularity run --app PM promod.img build-model [options]
+
+or an arbitrary Python script using OpenStructure / |project| with:
+
+.. code-block:: bash
+
+    singularity run --app PM promod.img my_script.py [options] 
+
+The Notebook app provides a jupyter notebook playground with OST, |project|, and
+nglview available. You can fire it up with:
+
+.. code-block:: bash
+
+    singularity run --app Notebook promod.img
+
+connect to the notebook, start a new OST kernel and test it with the following 
+code snippet:
+
+.. code-block:: python
+
+    from ost import io
+    from promod3 import loop
+    import nglview
+
+    # generate backbone with dihedrals of a helix and store it
+    sequence = "HELLYEAH"
+    bb_list = loop.BackboneList(sequence)
+    io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+    # display stored file
+    view = nglview.show_file("test.pdb")
+    view
+
 The Compound Library
 --------------------
 

doc/html/_sources/gettingstarted.txt → doc/html/_sources/gettingstarted.rst.txt

@@ -19,7 +19,7 @@ Getting Started
 
 Get and Run |project|
 --------------------------------------------------------------------------------
-First steps to get |project| up and running:
+Either utilize :ref:`containers <container>` or start from source code:
 
 #. Fetch the source code from https://git.scicore.unibas.ch/schwede/ProMod3.git.
    Or directly pull it with git: