Add official support for DockGen and pocket-only PoseBusters Benchmark experiments

Author: amorehead

README.md

@@ -2,5 +2,5 @@ Acknowledgements
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 806
-    :end-line: 822
+    :start-line: 871
+    :end-line: 887

data/test_cases/dockgen/ensemble_inputs.csv

@@ -2,8 +2,8 @@ Available inference methods
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 271
-    :end-line: 308
+    :start-line: 282
+    :end-line: 319
 
 .. 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/acknowledgements.rst

@@ -2,8 +2,8 @@ Bonus
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 838
-    :end-line: 840
+    :start-line: 903
+    :end-line: 905
 
 .. image:: ./_static/WorkBench.jpeg
   :alt: My brain after building PoseBench

docs/source/available_methods.rst

@@ -2,5 +2,5 @@ Citing this work
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 824
-    :end-line: 834
+    :start-line: 889
+    :end-line: 899

docs/source/bonus.rst

@@ -2,5 +2,5 @@ How to create comparative plots of inference results
 ================
 
 .. mdinclude:: ../../README.md
-    :start-line: 755
-    :end-line: 762
+    :start-line: 818
+    :end-line: 827

docs/source/citing_this_work.rst

@@ -13,10 +13,10 @@ This config file is used to determine how a predicted protein-ligand complex str
     :caption: :file:`analysis/complex_alignment.yaml`
 
 
-Inference analysis (PoseBusters and Astex)
+Inference analysis (PoseBusters, Astex, and DockGen)
 --------------------------
 
-This config file is used to determine how to score a predicted protein-ligand complex from the PoseBusters Benchmark or Astex Diverse datasets.
+This config file is used to determine how to score a predicted protein-ligand complex from the PoseBusters Benchmark, Astex Diverse, or DockGen datasets.
 
 .. literalinclude:: ../../../configs/analysis/inference_analysis.yaml
     :language: yaml

docs/source/comparative_plots.rst

@@ -33,6 +33,12 @@ Method data parsers
 
 These data parser configurations are used to modify how the input (output) protein-ligand complex structures of each method are prepared (extracted).
 
+Binding site crop preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/binding_site_crop_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/binding_site_crop_preparation.yaml`
+
 DiffDock input preparation
 ^^^^^^^^^^^^^^^^^^^^^^^^
 .. literalinclude:: ../../../configs/data/diffdock_input_preparation.yaml

docs/source/configs/analysis.rst

@@ -3,4 +3,4 @@ How to prepare `PoseBench` data
 
 .. mdinclude:: ../../README.md
     :start-line: 130
-    :end-line: 265
+    :end-line: 276