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BioinfoMachineLearning · Sep 24, 2024 · 296f81a · 296f81a
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diff --git a/docs/source/acknowledgements.rst b/docs/source/acknowledgements.rst
@@ -2,5 +2,5 @@ Acknowledgements
 ================
 
 .. mdinclude:: ../../README.md
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diff --git a/docs/source/available_methods.rst b/docs/source/available_methods.rst
@@ -2,8 +2,8 @@ Available inference methods
 ================
 
 .. mdinclude:: ../../README.md
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+    :start-line: 295
+    :end-line: 334
 
 .. 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
@@ -2,8 +2,8 @@ Bonus
 ================
 
 .. mdinclude:: ../../README.md
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 .. 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
@@ -2,5 +2,5 @@ Citing this work
 ================
 
 .. mdinclude:: ../../README.md
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diff --git 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
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diff --git a/docs/source/configs/data.rst b/docs/source/configs/data.rst
@@ -75,6 +75,18 @@ RoseTTAFold-All-Atom output extraction
     :language: yaml
     :caption: :file:`data/rfaa_output_extraction.yaml`
 
+Chai-1 input preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/chai_input_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/chai_input_preparation.yaml`
+
+Chai-1 output extraction
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/chai_output_extraction.yaml
+    :language: yaml
+    :caption: :file:`data/chai_output_extraction.yaml`
+
 TULIP output extraction
 ^^^^^^^^^^^^^^^^^^^^^^^^
 .. literalinclude:: ../../../configs/data/tulip_output_extraction.yaml

diff --git a/docs/source/configs/model.rst b/docs/source/configs/model.rst
@@ -39,6 +39,12 @@ RoseTTAFold-All-Atom inference
     :language: yaml
     :caption: :file:`model/rfaa_inference.yaml`
 
+Chai-1 inference
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/chai_inference.yaml
+    :language: yaml
+    :caption: :file:`model/chai_inference.yaml`
+
 Vina inference
 ^^^^^^^^^^^^^^^^^^^^^^^^
 .. literalinclude:: ../../../configs/model/vina_inference.yaml

diff --git a/docs/source/data_preparation.rst b/docs/source/data_preparation.rst
@@ -2,5 +2,5 @@ How to prepare `PoseBench` data
 ================
 
 .. mdinclude:: ../../README.md
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+    :end-line: 289
diff --git 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
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+    :end-line: 904
 
 .. 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
@@ -2,5 +2,5 @@ For developers
 ================
 
 .. mdinclude:: ../../README.md
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diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -3,4 +3,4 @@ Installation
 
 .. mdinclude:: ../../README.md
     :start-line: 42
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+    :end-line: 134
diff --git 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
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diff --git a/docs/source/sweep_inference.rst b/docs/source/sweep_inference.rst
@@ -2,5 +2,5 @@ How to run a sweep of benchmarking experiments
 ================
 
 .. mdinclude:: ../../README.md
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diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
@@ -2,5 +2,5 @@ Tutorials
 ================
 
 .. mdinclude:: ../../README.md
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