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[WIP] Fixes for feedback #62

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Merged
dwhswenson merged 2 commits into from
May 13, 2023
Merged

[WIP] Fixes for feedback #62

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b45d457
correct cli tutorial name of directory
dwhswenson May 12, 2023
653d708
ligand-network-viewer => view-ligand-network
dwhswenson May 13, 2023
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10 changes: 5 additions & 5 deletions rbfe_tutorial/cli_tutorial.md
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Expand Up @@ -68,7 +68,7 @@ network_setup
```

The `ligand_network.graphml` file describes the atom mappings between the
ligands. We can visualize it with the `openfe ligand-network-viewer` command:
ligands. We can visualize it with the `openfe view-ligand-network` command:

```bash
openfe ligand-network-viewer network_setup/ligand_network.graphml
Expand Down Expand Up @@ -104,8 +104,8 @@ run each simulation on your local machine with something like:

```bash
# this will take a very long time! don't actually do it!
for file in setup/transformations/*.json; do
relpath=${file:22} # strip off "setup/transformations/"
for file in network_setup/transformations/*.json; do
relpath=${file:30} # strip off "network_setup/transformations/"
dirpath=${relpath%.*} # strip off final ".json"
openfe quickrun $file -o results/$relpath -d results/$dirpath
done
Expand All @@ -121,9 +121,9 @@ and submit a job script for the simplest SLURM use case:

```bash
for file in setup/transformations/*.json; do
relpath=${file:22} # strip off "setup/transformations/"
relpath=${file:30} # strip off "network_setup/transformations/"
dirpath=${relpath%.*} # strip off final ".json"
jobpath="setup/transformations/${dirpath}.job"
jobpath="network_setup/transformations/${dirpath}.job"
cmd="openfe quickrun $file -o results/$relpath -d results/$dirpath"
echo -e "#!/usr/bin/env bash\n${cmd}" > $jobpath
sbatch $jobpath
Expand Down
4 changes: 1 addition & 3 deletions rbfe_tutorial/python_tutorial.ipynb
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Expand Up @@ -191,9 +191,7 @@
"\n",
"That information in included in a `Transformation`. Each of these transformations corresponds to a single leg of the simulation campaign, so for each edge in the `LigandNetwork`, we will create two `Transformation`s: one for vacuum and one for solvent.\n",
"\n",
"In practice, this will be done for each edge of the `LigandNetwork` in a loop, but for illustrative purposes we'll dive into the details of creating a single transformation. In particular, we'll create the solvent leg for the pair of molecules we selecting for the mapping above.\n",
"\n",
"TODO: SWITCH TO PROTEIN COMPLEX LEG"
"In practice, this will be done for each edge of the `LigandNetwork` in a loop, but for illustrative purposes we'll dive into the details of creating a single transformation. In particular, we'll create the solvent leg for the pair of molecules we selecting for the mapping above."
]
},
{
Expand Down