From 6b36bd47d9cb9cf716d5e62fbc8482b8b5165d24 Mon Sep 17 00:00:00 2001 From: Alex Morehead Date: Fri, 21 Feb 2025 15:03:50 -0600 Subject: [PATCH] Clarify CASP15 environment install, and update docs after changing README --- README.md | 3 ++- docs/source/acknowledgements.rst | 4 ++-- docs/source/available_methods.rst | 4 ++-- docs/source/bonus.rst | 4 ++-- docs/source/citing_this_work.rst | 4 ++-- docs/source/comparative_plots.rst | 4 ++-- docs/source/data_preparation.rst | 4 ++-- docs/source/ensemble_inference.rst | 4 ++-- docs/source/for_developers.rst | 4 ++-- docs/source/installation.rst | 2 +- docs/source/method_inference.rst | 4 ++-- docs/source/sweep_inference.rst | 4 ++-- docs/source/tutorials.rst | 4 ++-- 13 files changed, 25 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 4712333..3d6f70e 100644 --- a/README.md +++ b/README.md @@ -84,7 +84,8 @@ pip install -e . --no-deps # - casp15_ligand_scoring environment (~3 GB) mamba env create -f environments/casp15_ligand_scoring_environment.yaml conda activate casp15_ligand_scoring # NOTE: one still needs to use `conda` to (de)activate environments -pip3 install -e . # NOTE: must comment out `posecheck` requirement in `pyproject.toml` beforehand and restore it thereafter +# NOTE: must comment out the `posecheck` requirement in `pyproject.toml` beforehand and restore it thereafter +pip3 install -e . # - DiffDock environment (~13 GB) mamba env create -f environments/diffdock_environment.yaml --prefix forks/DiffDock/DiffDock/ conda activate forks/DiffDock/DiffDock/ # NOTE: one still needs to use `conda` to (de)activate environments diff --git a/docs/source/acknowledgements.rst b/docs/source/acknowledgements.rst index 31f8774..aecba71 100644 --- a/docs/source/acknowledgements.rst +++ b/docs/source/acknowledgements.rst @@ -2,5 +2,5 @@ Acknowledgements ================ .. mdinclude:: ../../README.md - :start-line: 1176 - :end-line: 1196 + :start-line: 1178 + :end-line: 1198 diff --git a/docs/source/available_methods.rst b/docs/source/available_methods.rst index 31305c3..7ab6366 100644 --- a/docs/source/available_methods.rst +++ b/docs/source/available_methods.rst @@ -2,8 +2,8 @@ Available inference methods ================ .. mdinclude:: ../../README.md - :start-line: 325 - :end-line: 368 + :start-line: 327 + :end-line: 370 .. note:: Have a new method to add? Please let us know by creating a pull request. We would be happy to work with you to integrate new methodology into this benchmark! diff --git a/docs/source/bonus.rst b/docs/source/bonus.rst index 13deacd..a8e3e33 100644 --- a/docs/source/bonus.rst +++ b/docs/source/bonus.rst @@ -2,8 +2,8 @@ Bonus ================ .. mdinclude:: ../../README.md - :start-line: 1214 - :end-line: 1216 + :start-line: 1216 + :end-line: 1218 .. image:: ./_static/WorkBench.jpeg :alt: My brain after building PoseBench diff --git a/docs/source/citing_this_work.rst b/docs/source/citing_this_work.rst index 375b9d5..c27d0e3 100644 --- a/docs/source/citing_this_work.rst +++ b/docs/source/citing_this_work.rst @@ -2,5 +2,5 @@ Citing this work ================ .. mdinclude:: ../../README.md - :start-line: 1198 - :end-line: 1210 + :start-line: 1200 + :end-line: 1212 diff --git a/docs/source/comparative_plots.rst b/docs/source/comparative_plots.rst index 48d657b..17a2904 100644 --- a/docs/source/comparative_plots.rst +++ b/docs/source/comparative_plots.rst @@ -2,5 +2,5 @@ How to create comparative plots of inference results ================ .. mdinclude:: ../../README.md - :start-line: 1106 - :end-line: 1132 + :start-line: 1108 + :end-line: 1134 diff --git a/docs/source/data_preparation.rst b/docs/source/data_preparation.rst index 25bd523..0f220b8 100644 --- a/docs/source/data_preparation.rst +++ b/docs/source/data_preparation.rst @@ -2,8 +2,8 @@ How to prepare `PoseBench` data ================ .. mdinclude:: ../../README.md - :start-line: 169 - :end-line: 317 + :start-line: 171 + :end-line: 319 .. note:: The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (available via Zenodo at https://doi.org/10.5281/zenodo.14629652) provide pre-holo-aligned protein structures predicted by AlphaFold 3 (and alternatively MIT-licensed ESMFold) for these respective datasets. Accordingly, users must ensure their usage of such predicted protein structures from AlphaFold 3 aligns with AlphaFold 3's Terms of Use at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. diff --git a/docs/source/ensemble_inference.rst b/docs/source/ensemble_inference.rst index a4215a1..ba61e7d 100644 --- a/docs/source/ensemble_inference.rst +++ b/docs/source/ensemble_inference.rst @@ -2,8 +2,8 @@ How to run inference with a method ensemble ================ .. mdinclude:: ../../README.md - :start-line: 1047 - :end-line: 1098 + :start-line: 1049 + :end-line: 1100 .. note:: In addition to having `consensus` as an available value for `ensemble_ranking_method`, one can also set `ensemble_ranking_method=ff` to have the method ensemble's top-ranked predictions selected using the criterion of "minimum (molecular dynamics) force field energy" (albeit while incurring a very large runtime complexity). diff --git a/docs/source/for_developers.rst b/docs/source/for_developers.rst index 871e126..4f96d33 100644 --- a/docs/source/for_developers.rst +++ b/docs/source/for_developers.rst @@ -2,5 +2,5 @@ For developers ================ .. mdinclude:: ../../README.md - :start-line: 1138 - :end-line: 1172 + :start-line: 1140 + :end-line: 1174 diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 4c149a7..3fcab2a 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -3,4 +3,4 @@ Installation .. mdinclude:: ../../README.md :start-line: 42 - :end-line: 151 + :end-line: 153 diff --git a/docs/source/method_inference.rst b/docs/source/method_inference.rst index 65cc94e..56f6a8e 100644 --- a/docs/source/method_inference.rst +++ b/docs/source/method_inference.rst @@ -2,5 +2,5 @@ How to run inference with individual methods ================ .. mdinclude:: ../../README.md - :start-line: 396 - :end-line: 1041 + :start-line: 398 + :end-line: 1043 diff --git a/docs/source/sweep_inference.rst b/docs/source/sweep_inference.rst index c176038..04119a9 100644 --- a/docs/source/sweep_inference.rst +++ b/docs/source/sweep_inference.rst @@ -2,8 +2,8 @@ How to run a sweep of benchmarking experiments ================ .. mdinclude:: ../../README.md - :start-line: 376 - :end-line: 388 + :start-line: 378 + :end-line: 390 .. note:: See the config file `configs/scripts/build_inference_script.yaml` for more details. diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst index f42dc80..a82875a 100644 --- a/docs/source/tutorials.rst +++ b/docs/source/tutorials.rst @@ -2,5 +2,5 @@ Tutorials ================ .. mdinclude:: ../../README.md - :start-line: 157 - :end-line: 163 + :start-line: 159 + :end-line: 165