You are reading the documentation for version 3.0 of ProMod3.
You may also want to read the documentation for:
1.3
2.0
2.1
3.1
3.2
Singularity¶We do not provide a “standalone” Singularity image, but rather bootstrap from a Docker image. Build the image with: sudo singularity build promod.img Singularity
Available apps¶
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The Compound Library¶You’ll have the exact same problem with outdated compound libraries as in the raw Docker image.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. |
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