update cli docs for clarity and accuracy #283
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IAlibay
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IAlibay
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Couple of things, otherwise it looks good to me.
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| This opens an interactive viewer. You can move the ligand names around to get a | ||
| better view of the structure, and if you click on the edge, you will see the | ||
| to open an interactive viewer. |
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move this to the sentence on line 93? It feels a bit jarring to just have the end of a sentence after the method is being shown.
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| Let's assume you want to exchange the kartograf atom mapper with the LOMAP atom mapper, the Minimal Spanning Tree | ||
| Network Planner with the Maximal Network Planner and the am1bcc charge method with [OpenFF NAGL](https://docs.openforcefield.org/projects/nagl/): |
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Jumping into 1/2/3 seems to be missing something here. Maybe in this sentence you should something like "to achieve this, you would do the following N steps:"
| want to create a new job script for each simulation JSON file, and the core of | ||
| that job script will be to run the `openfe quickrun` command above. | ||
| When running a complete network of simulations, it is important to ensure that the file name for the result JSON and name of the working directory are different for each leg and each repeat, otherwise you'll overwrite results. | ||
| We recommend doing this programmatically, such as the example below, which uses the fact that the JSON files in `network_setup/transformations/` have unique names, and creates directories |
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I don't think it's a good idea to just have the slurm example be the one that shows this off. Partly this is because a lot of folks just don't have any clue about slurm. I would re-add the bash example that demonstrates how to do this and loop over all the files.
this is likely where users will start, so we should make sure it's up to date and clear!