Singularity¶

Available apps¶

This container includes the following apps:

• OST - OpenStructure executable
• PM - ProMod3 executable
• IPython - OST/ProMod3-powered iPython shell
• Notebook - A Jupyter notebook playground with OST, ProMod3 and nglview
• lDDT - The Local Distance Difference Test
• Molck - Molecular checker
• ChemdictTool - Creating or update a compound library

To see the help for each individual app run:

singularity run-help --app <APP NAME> <PATH TO PROMOD IMAGE>

Eg.:

singularity run-help --app PM promod.img

To list all available ProMod3 modelling actions:

singularity run --app PM promod.img help

The Compound Library¶

You’ll have the exact same problem with outdated compound libraries as in the raw Docker image. You can find more information on that matter in the Docker section of the documentation: The Compound Library.

The same trick of mounting an up to date compound library from the local host into the container applies. The two relevant commands for Singularity are building a new library and mount it.

Build a new library:

singularity run --app ChemdictTool <IMAGE> create components.cif.gz \
compounds.chemlib

Run some script with an updated compound library from localhost:

singularity run \
-B <COMPLIB_DIR_LOCALHOST>/compounds.chemlib:<COMPLIB_DIR_CONTAINER>/compounds.chemlib \
--app PM <IMAGE> my_script.py

Same as for the Docker, if you didn’t meddle with the original Dockerfile, <COMPLIB_DIR_CONTAINER> should be /usr/local/share/openstructure. <COMPLIB_DIR_LOCALHOST> is the directory that contains the compound lib with the name compounds.chemlib that you created before. Make sure that everything works as expected by executing the exact same lines of Python code as described in the Docker documentation: The Compound Library.