From b45d4572df17cff4cb2e01845ccaf8ab9e2ab7c5 Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Fri, 12 May 2023 13:13:34 -0400 Subject: [PATCH 1/2] correct cli tutorial name of directory --- rbfe_tutorial/cli_tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index f8c6809..a83cb25 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -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/$dirpath done @@ -121,9 +121,9 @@ and submit a job script for the simplest SLURM use case: ```bash for file in setup/transformations/*.json; do - relpath=${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 From 653d708d35a2aa2477406946004ee423813e4212 Mon Sep 17 00:00:00 2001 From: "David W.H. Swenson" Date: Sat, 13 May 2023 08:36:17 -0400 Subject: [PATCH 2/2] ligand-network-viewer => view-ligand-network --- rbfe_tutorial/cli_tutorial.md | 2 +- rbfe_tutorial/python_tutorial.ipynb | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index a83cb25..f3a96b8 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -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 diff --git a/rbfe_tutorial/python_tutorial.ipynb b/rbfe_tutorial/python_tutorial.ipynb index a36034e..ae9c74a 100644 --- a/rbfe_tutorial/python_tutorial.ipynb +++ b/rbfe_tutorial/python_tutorial.ipynb @@ -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." ] }, {