From 386ae0915df7c546c5d9e1a5b72d43019d929ed5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 27 Jul 2020 12:39:35 +0200
Subject: [PATCH] add examples in the Singularity documentation
---
doc/container/singularity.rst | 37 +++++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst
index a1e8c12c..cd006fdb 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
--------------------
--
GitLab