Clarify CASP15 environment install, and update docs after changing README

Author: amorehead

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

docs/source/acknowledgements.rst

@@ -2,5 +2,5 @@ Acknowledgements
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1176
-    :end-line: 1196
+    :start-line: 1178
+    :end-line: 1198

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!

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

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

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

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.

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).

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

docs/source/installation.rst

@@ -3,4 +3,4 @@ Installation
 
 .. mdinclude:: ../../README.md
     :start-line: 42
-    :end-line: 151
+    :end-line: 153