Open cyan-moma opened 1 month ago
Hi cyan-moma, I'm afraid I can't be of much help with your yaml/toml issues. But I did find your comment on the docking score being returned as 'nan' noteworthy, as I've been struggling with exactly that issue. Please see here: https://github.com/MolecularAI/maize-contrib/issues/1
Regarding the last issue, there was a fix in maize 0.5.0 about a "- Temporary fix for paths not being parsed from YAML files". Maybe it's connected?
I am finding setting up docking with maize to be quite difficult tbf, especially since the last version of REINVENT has completely different configuration syntax if comapred to the 3.2 that was used for maize examples.
@tlhr Can you please have a look into this and comment?
Hi!
Sorry for the late reply. I have updated both maize
and maize-contrib
now, this should resolve some of those issues. Can you try with the new versions for both?
Hi, I am interested in using maize for docking as a scoring function for molecular generation using REINVENT4. I got an error message when calling
maize
from CLI, even through I can run through the same workflow with success from jupyter notebook (although the docking score is found to be "nan" inout.json
).Here is the
workflow.yml
fileI got a different error when running the same workflow in toml format:
I also attached all the input and output files maize_vina_workflow.zip
I installed the conda environment of maize and maize-contrib following instructions from https://github.com/MolecularAI/maize-contrib/tree/public.
Thank you in advance for your help! Please let me know if you need additional information.