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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: f21dcf8b8d69e165e6fbab9dfd760aa4
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/acknowledgements.doctree b/.doctrees/acknowledgements.doctree
diff --git a/.doctrees/available_methods.doctree b/.doctrees/available_methods.doctree
diff --git a/.doctrees/bonus.doctree b/.doctrees/bonus.doctree
diff --git a/.doctrees/citing_this_work.doctree b/.doctrees/citing_this_work.doctree
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+{
+  "acknowledgements": [],
+  "available_methods": [],
+  "bonus": [],
+  "citing_this_work": [],
+  "comparative_plots": [],
+  "configs/analysis": [],
+  "configs/data": [],
+  "configs/model": [],
+  "data_preparation": [],
+  "ensemble_inference": [],
+  "for_developers": [],
+  "index": [],
+  "installation": [],
+  "method_inference": [],
+  "modules/src.complex_alignment": [],
+  "modules/src.data_utils": [],
+  "modules/src.ensemble_generation": [],
+  "modules/src.inference_relaxation": [],
+  "modules/src.minimize_energy": [],
+  "modules/src.model_utils": [],
+  "modules/src.resolvers": [],
+  "modules/src.utils": [],
+  "tutorials": []
+}
diff --git a/.doctrees/comparative_plots.doctree b/.doctrees/comparative_plots.doctree
diff --git a/.doctrees/configs/analysis.doctree b/.doctrees/configs/analysis.doctree
diff --git a/.doctrees/configs/data.doctree b/.doctrees/configs/data.doctree
diff --git a/.doctrees/configs/model.doctree b/.doctrees/configs/model.doctree
diff --git a/.doctrees/data_preparation.doctree b/.doctrees/data_preparation.doctree
diff --git a/.doctrees/ensemble_inference.doctree b/.doctrees/ensemble_inference.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/for_developers.doctree b/.doctrees/for_developers.doctree
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diff --git a/.doctrees/modules/src.complex_alignment.doctree b/.doctrees/modules/src.complex_alignment.doctree
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diff --git a/.doctrees/modules/src.ensemble_generation.doctree b/.doctrees/modules/src.ensemble_generation.doctree
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diff --git a/.doctrees/tutorials.doctree b/.doctrees/tutorials.doctree
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diff --git a/_modules/index.html b/_modules/index.html
diff --git a/_modules/src/__init__.html b/_modules/src/__init__.html
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diff --git a/_sources/acknowledgements.rst.txt b/_sources/acknowledgements.rst.txt
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+Acknowledgements
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 806
+    :end-line: 822
diff --git a/_sources/available_methods.rst.txt b/_sources/available_methods.rst.txt
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+Available inference methods
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 271
+    :end-line: 308
+
+.. 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/_sources/bonus.rst.txt b/_sources/bonus.rst.txt
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+Bonus
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 838
+    :end-line: 840
+
+.. image:: ./_static/WorkBench.jpeg
+  :alt: My brain after building PoseBench
+  :align: center
+  :width: 400
diff --git a/_sources/citing_this_work.rst.txt b/_sources/citing_this_work.rst.txt
@@ -0,0 +1,6 @@
+Citing this work
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 824
+    :end-line: 834
diff --git a/_sources/comparative_plots.rst.txt b/_sources/comparative_plots.rst.txt
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+How to create comparative plots of inference results
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 755
+    :end-line: 762
diff --git a/_sources/configs/analysis.rst.txt b/_sources/configs/analysis.rst.txt
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+Analysis
+==============
+
+This section describes the configurations for various analysis-related scripts.
+
+Complex alignment
+--------------------------
+
+This config file is used to determine how a predicted protein-ligand complex structure is optimally aligned to a corresponding ground-truth protein-ligand complex.
+
+.. literalinclude:: ../../../configs/analysis/complex_alignment.yaml
+    :language: yaml
+    :caption: :file:`analysis/complex_alignment.yaml`
+
+
+Inference analysis (PoseBusters and Astex)
+--------------------------
+
+This config file is used to determine how to score a predicted protein-ligand complex from the PoseBusters Benchmark or Astex Diverse datasets.
+
+.. literalinclude:: ../../../configs/analysis/inference_analysis.yaml
+    :language: yaml
+    :caption: :file:`analysis/inference_analysis.yaml`
+
+
+Inference analysis (CASP)
+--------------------------
+
+This config file is used to determine how to score a predicted protein-ligand complex from the CASP15 dataset.
+
+.. literalinclude:: ../../../configs/analysis/inference_analysis_casp.yaml
+    :language: yaml
+    :caption: :file:`analysis/inference_analysis_casp.yaml`
diff --git a/_sources/configs/data.rst.txt b/_sources/configs/data.rst.txt
@@ -0,0 +1,76 @@
+Data
+==============
+
+This section describes the configurations for various data-related scripts.
+
+
+Input data components
+------------------------
+
+These data component configurations are used to modify how the input (apo) protein structures are predicted or aligned.
+
+ESMFold apo-to-holo alignment
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/components/esmfold_apo_to_holo_alignment.yaml
+    :language: yaml
+    :caption: :file:`data/components/esmfold_apo_to_holo_alignment.yaml`
+
+ESMFold FASTA preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/components/esmfold_fasta_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/components/esmfold_fasta_preparation.yaml`
+
+ESMFold sequence preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/components/esmfold_sequence_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/components/esmfold_sequence_preparation.yaml`
+
+
+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).
+
+DiffDock input preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/diffdock_input_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/diffdock_input_preparation.yaml`
+
+FABind input preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/fabind_input_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/fabind_input_preparation.yaml`
+
+DynamicBind input preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/dynamicbind_input_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/dynamicbind_input_preparation.yaml`
+
+NeuralPLexer input preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/neuralplexer_input_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/neuralplexer_input_preparation.yaml`
+
+RoseTTAFold-All-Atom input preparation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/rfaa_input_preparation.yaml
+    :language: yaml
+    :caption: :file:`data/rfaa_input_preparation.yaml`
+
+RoseTTAFold-All-Atom output extraction
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/rfaa_output_extraction.yaml
+    :language: yaml
+    :caption: :file:`data/rfaa_output_extraction.yaml`
+
+TULIP output extraction
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/data/tulip_output_extraction.yaml
+    :language: yaml
+    :caption: :file:`data/tulip_output_extraction.yaml`
diff --git a/_sources/configs/model.rst.txt b/_sources/configs/model.rst.txt
@@ -0,0 +1,83 @@
+Model
+==============
+
+This section describes the configurations for various method-related scripts.
+
+
+Method inference
+------------------------
+
+These configurations are used to specify how inference is performed with each method.
+
+DiffDock inference
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/diffdock_inference.yaml
+    :language: yaml
+    :caption: :file:`model/diffdock_inference.yaml`
+
+FABind inference
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/fabind_inference.yaml
+    :language: yaml
+    :caption: :file:`model/fabind_inference.yaml`
+
+DynamicBind inference
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/dynamicbind_inference.yaml
+    :language: yaml
+    :caption: :file:`model/dynamicbind_inference.yaml`
+
+NeuralPLexer inference
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/neuralplexer_inference.yaml
+    :language: yaml
+    :caption: :file:`model/neuralplexer_inference.yaml`
+
+RoseTTAFold-All-Atom inference
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/rfaa_inference.yaml
+    :language: yaml
+    :caption: :file:`model/rfaa_inference.yaml`
+
+Vina inference
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/vina_inference.yaml
+    :language: yaml
+    :caption: :file:`model/vina_inference.yaml`
+
+
+Ensemble inference
+------------------------
+
+This configuration is used to specify how inference is performed with a method ensemble (e.g., via `consensus` ranking).
+
+.. note::
+    This script not only enables inference with a method ensemble, but it also provides a unified wrapper with which one
+    can relax and structure a method's predictions in a CASP-compliant file format for scoring.
+
+Ensemble generation
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/ensemble_generation.yaml
+    :language: yaml
+    :caption: :file:`model/ensemble_generation.yaml`
+
+
+Structure relaxation
+------------------------
+
+These configurations are used to specify how relaxation is (optionally) applied to a predicted protein-ligand complex structure using molecular dynamics (i.e., `OpenMM <https://openmm.org>`_).
+
+.. note::
+    The `inference_relaxation` configuration describes the behavior of the script that serves as an entry point for the relaxation process. The `minimize_energy` configuration is a multi-ligand generalization of the main energy minimization script originally implemented for the `PoseBusters <https://github.com/maabuu/posebusters_em>`_ software suite.
+
+Inference relaxation (entry point)
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/inference_relaxation.yaml
+    :language: yaml
+    :caption: :file:`model/inference_relaxation.yaml`
+
+Minimize energy (relaxation engine)
+^^^^^^^^^^^^^^^^^^^^^^^^
+.. literalinclude:: ../../../configs/model/minimize_energy.yaml
+    :language: yaml
+    :caption: :file:`model/minimize_energy.yaml`
diff --git a/_sources/data_preparation.rst.txt b/_sources/data_preparation.rst.txt
@@ -0,0 +1,6 @@
+How to prepare `PoseBench` data
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 130
+    :end-line: 265
diff --git a/_sources/ensemble_inference.rst.txt b/_sources/ensemble_inference.rst.txt
@@ -0,0 +1,9 @@
+How to run inference with a method ensemble
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 703
+    :end-line: 747
+
+.. 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/_sources/for_developers.rst.txt b/_sources/for_developers.rst.txt
@@ -0,0 +1,6 @@
+For developers
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 768
+    :end-line: 802
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -0,0 +1,70 @@
+.. PoseBench documentation master file, created by
+   sphinx-quickstart on Sun May 12 14:49:07 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to PoseBench's documentation!
+============================================
+
+
+.. mdinclude:: ../../README.md
+    :start-line: 4
+    :end-line: 12
+
+.. image:: ./_static/PoseBench.png
+  :alt: Overview of PoseBench
+  :align: center
+  :width: 600
+
+.. mdinclude:: ../../README.md
+    :start-line: 18
+    :end-line: 20
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   tutorials
+   data_preparation
+   available_methods
+   method_inference
+   ensemble_inference
+   comparative_plots
+   for_developers
+   acknowledgements
+   citing_this_work
+   bonus
+
+.. toctree::
+   :glob:
+   :maxdepth: 2
+   :hidden:
+   :caption: Default Configs
+
+   configs/analysis
+   configs/data
+   configs/model
+
+.. toctree::
+   :glob:
+   :maxdepth: 1
+   :hidden:
+   :caption: API Reference
+
+   modules/src.complex_alignment
+   modules/src.inference_relaxation
+   modules/src.minimize_energy
+   modules/src.ensemble_generation
+   modules/src.data_utils
+   modules/src.model_utils
+   modules/src.utils
+   modules/src.resolvers
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt
@@ -0,0 +1,6 @@
+Installation
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 40
+    :end-line: 112
diff --git a/_sources/method_inference.rst.txt b/_sources/method_inference.rst.txt
@@ -0,0 +1,6 @@
+How to run inference with individual methods
+================
+
+.. mdinclude:: ../../README.md
+    :start-line: 316
+    :end-line: 697
diff --git a/_sources/modules/src.complex_alignment.rst.txt b/_sources/modules/src.complex_alignment.rst.txt
@@ -0,0 +1,4 @@
+Complex alignment
+==============
+.. automodule:: src.analysis.complex_alignment
+   :members:
diff --git a/_sources/modules/src.data_utils.rst.txt b/_sources/modules/src.data_utils.rst.txt
@@ -0,0 +1,4 @@
+Data utilities
+==============
+.. automodule:: src.utils.data_utils
+   :members:
diff --git a/_sources/modules/src.ensemble_generation.rst.txt b/_sources/modules/src.ensemble_generation.rst.txt
@@ -0,0 +1,4 @@
+Ensemble generation
+==============
+.. automodule:: src.models.ensemble_generation
+   :members:
diff --git a/_sources/modules/src.inference_relaxation.rst.txt b/_sources/modules/src.inference_relaxation.rst.txt
@@ -0,0 +1,4 @@
+Inference relaxation
+==============
+.. automodule:: src.models.inference_relaxation
+   :members: