diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst index a1e8c12cb3f41381185e1d467da36f7a31a6464c..cd006fdb96d1e5f14a1bb50653a5ac8f436ac109 100644 --- a/doc/container/singularity.rst +++ b/doc/container/singularity.rst @@ -57,6 +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 --------------------