Commit de4ceb7a authored by Studer Gabriel's avatar Studer Gabriel
Browse files

Updated compiled doc.

parent 386ae091
......@@ -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|
......
......@@ -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
--------------------------------------------------------------------------------
......
......@@ -13,6 +13,7 @@
.. See the License for the specific language governing permissions and
.. limitations under the License.
.. _container:
|project| and Containers
========================
......
......@@ -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
--------------------
......
......@@ -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:
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment