From dd6b69b1da34e9b1e79044daabd78860f7270368 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 4 Dec 2025 13:21:10 -0800 Subject: [PATCH 1/4] add output files to gitignore --- .gitignore | 25 ++++++++++ ahfe_tutorial/ahfe_json/benzene.json | 1 - openmm_septop/ligand_network.graphml | 73 ---------------------------- 3 files changed, 25 insertions(+), 74 deletions(-) delete mode 100644 ahfe_tutorial/ahfe_json/benzene.json delete mode 100644 openmm_septop/ligand_network.graphml diff --git a/.gitignore b/.gitignore index a54bae6..26e5a4d 100644 --- a/.gitignore +++ b/.gitignore @@ -228,3 +228,28 @@ $RECYCLE.BIN/ *.lnk # End of https://www.toptal.com/developers/gitignore/api/osx,python,jupyternotebooks,windows,linux + +# Files generated by example notebooks +*.zip +*.tsv +*.graphml +*.tar.gz +abfe_tutorial/abfe_results/ +abfe_tutorial/abfe_json/ +ahfe_tutorial/ahfe_json/ +cookbook/assets/of3_output/ +cookbook/dg.png +cookbook/queries.json +networks/transformations/ +openmm_md/md_input/ +openmm_md/shared* +openmm_septop/septop_results/ +openmm_septop/transformations/ +plotting_rbfes_with_cinnabar/cinnabar_input.csv +plotting_rbfes_with_cinnabar/*.dat +rbfe_tutorial/transformations/ +showcase/db.json +showcase/hybrid_system.pdb +showcase/results/ +showcase/tyk2_edge.png +showcase/tyk2_json/ diff --git a/ahfe_tutorial/ahfe_json/benzene.json b/ahfe_tutorial/ahfe_json/benzene.json deleted file mode 100644 index 3d2684d..0000000 --- a/ahfe_tutorial/ahfe_json/benzene.json +++ /dev/null @@ -1 +0,0 @@ -{":version:": 1, "__module__": "gufe.transformations.transformation", "__qualname__": "Transformation", "mapping": null, "name": "benzene", "protocol": {":version:": 1, "__module__": "openfe.protocols.openmm_afe.equil_solvation_afe_method", "__qualname__": "AbsoluteSolvationProtocol", "settings": {":is_custom:": true, "__class__": "AbsoluteSolvationSettings", "__module__": "openfe.protocols.openmm_afe.equil_afe_settings", "alchemical_settings": 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22], [23, 23], [24, 24], [25, 26], [26, 25], [27, 29], [29, 27], [30, 28], [31, 31], [32, 32], [33, 33], [34, 34], [35, 35]] - {"score": 0.9048374180359595} - - - [[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5], [6, 6], [7, 7], [8, 8], [9, 9], [10, 10], [11, 11], [12, 12], [13, 13], [14, 14], [15, 15], [16, 16], [17, 17], [18, 18], [19, 19], [20, 20], [21, 21], [22, 22], [23, 23], [24, 24], [25, 26], [26, 25], [27, 29], [29, 27], [30, 28], [31, 31], [32, 32], [33, 33], [34, 34], [35, 35]] - {"score": 0.9048374180359595} - - - \ No newline at end of file From baa1747a45cef3cc0aa1042df6a83370371404cd Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 9 Dec 2025 12:15:28 -0800 Subject: [PATCH 4/4] more specific about of3 assets --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 0a693e3..7249396 100644 --- a/.gitignore +++ b/.gitignore @@ -237,7 +237,8 @@ $RECYCLE.BIN/ abfe_tutorial/abfe_results/ abfe_tutorial/abfe_json/ ahfe_tutorial/ahfe_json/ -cookbook/assets/of3_output/ +cookbook/assets/of3_output/temp_ligands/ +cookbook/assets/of3_output/p_aligned/ cookbook/dg.png cookbook/queries.json networks/transformations/