Update docs

Author: amorehead

docs/source/acknowledgements.rst

@@ -2,5 +2,5 @@ Acknowledgements
 ================
 
 .. mdinclude:: ../../README.md
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docs/source/available_methods.rst

@@ -2,8 +2,8 @@ Available inference methods
 ================
 
 .. mdinclude:: ../../README.md
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 .. 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!

docs/source/bonus.rst

@@ -2,8 +2,8 @@ Bonus
 ================
 
 .. mdinclude:: ../../README.md
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 .. image:: ./_static/WorkBench.jpeg
   :alt: My brain after building PoseBench

docs/source/citing_this_work.rst

@@ -2,5 +2,5 @@ Citing this work
 ================
 
 .. mdinclude:: ../../README.md
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docs/source/comparative_plots.rst

@@ -2,5 +2,5 @@ How to create comparative plots of inference results
 ================
 
 .. mdinclude:: ../../README.md
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docs/source/data_preparation.rst

@@ -3,4 +3,7 @@ How to prepare `PoseBench` data
 
 .. mdinclude:: ../../README.md
     :start-line: 169
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+
+.. 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.

docs/source/ensemble_inference.rst

@@ -2,8 +2,8 @@ How to run inference with a method ensemble
 ================
 
 .. mdinclude:: ../../README.md
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 .. 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).

docs/source/for_developers.rst

@@ -2,5 +2,5 @@ For developers
 ================
 
 .. mdinclude:: ../../README.md
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docs/source/method_inference.rst

@@ -2,5 +2,5 @@ How to run inference with individual methods
 ================
 
 .. mdinclude:: ../../README.md
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docs/source/sweep_inference.rst

@@ -2,5 +2,8 @@ How to run a sweep of benchmarking experiments
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 372
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+    :start-line: 376
+    :end-line: 388
+
+.. note::
+    See the config file `configs/scripts/build_inference_script.yaml` for more details.