update: adjust line references in documentation includes for consistency, and update PoseBench image

Author: amorehead

docs/source/_static/PoseBench.png

@@ -2,5 +2,5 @@ Acknowledgements
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1309
-    :end-line: 1332
+    :start-line: 1311
+    :end-line: 1334

docs/source/acknowledgements.rst

@@ -2,8 +2,8 @@ Available inference methods
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 367
-    :end-line: 412
+    :start-line: 369
+    :end-line: 414
 
 .. 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/available_methods.rst

@@ -2,8 +2,8 @@ Bonus
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1350
-    :end-line: 1352
+    :start-line: 1352
+    :end-line: 1354
 
 .. image:: ./_static/WorkBench.jpeg
   :alt: My brain after building PoseBench

docs/source/bonus.rst

@@ -2,5 +2,5 @@ Citing this work
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1334
-    :end-line: 1346
+    :start-line: 1336
+    :end-line: 1348

docs/source/citing_this_work.rst

@@ -2,5 +2,5 @@ How to create comparative plots of inference results
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1237
-    :end-line: 1265
+    :start-line: 1239
+    :end-line: 1267

docs/source/comparative_plots.rst

@@ -2,8 +2,8 @@ How to prepare `PoseBench` data
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 207
-    :end-line: 359
+    :start-line: 209
+    :end-line: 361
 
 .. note::
     The preprocessed Astex Diverse, PoseBusters Benchmark, DockGen, and CASP15 data (available via Zenodo at https://doi.org/10.5281/zenodo.19138652) 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/data_preparation.rst

@@ -2,8 +2,8 @@ How to run inference with a method ensemble
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1178
-    :end-line: 1229
+    :start-line: 1180
+    :end-line: 1231
 
 .. 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/ensemble_inference.rst

@@ -2,5 +2,5 @@ For developers
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 1271
-    :end-line: 1305
+    :start-line: 1273
+    :end-line: 1307

docs/source/for_developers.rst

@@ -20,6 +20,10 @@ Welcome to PoseBench's documentation!
     :start-line: 20
     :end-line: 22
 
+.. mdinclude:: ../../README.md
+    :start-line: 24
+    :end-line: 26
+
 
 .. toctree::
    :maxdepth: 2