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Update docs and improve docking pipeline docs
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‎docs/api/alignment/index.rst‎

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Alignment Functions
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===================
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Functions for aligning molecules based on their interaction profiles.
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.. toctree::
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:maxdepth: 2
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main
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jax
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utilities

‎docs/api/alignment/jax.rst‎

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JAX Alignment
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=============
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.. automodule:: shepherd_score.alignment_jax
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:members:
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‎docs/api/alignment/main.rst‎

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Main Alignment Module
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=====================
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.. automodule:: shepherd_score.alignment
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:members:
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:undoc-members:
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:show-inheritance:

docs/api/alignment.rst renamed to docs/api/alignment/utilities.rst

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Alignment Functions
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===================
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Functions for aligning molecules based on their interaction profiles.
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Main Alignment Module
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---------------------
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.. automodule:: shepherd_score.alignment
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:members:
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:undoc-members:
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:show-inheritance:
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JAX Alignment
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-------------
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Alignment Utilities
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===================
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SE3 Transformations (PyTorch)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-----------------------------
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SE3 Transformations (NumPy)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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----------------------------
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SE3 Transformations (JAX)
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--------------------------
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PCA Utilities (PyTorch)
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PCA Utilities (NumPy)
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PCA Utilities (JAX)
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‎docs/api/evaluations.rst‎

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‎docs/api/evaluations/docking.rst‎

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Docking Evaluation
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==================
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Classes and pipelines for docking-based evaluation of generated molecules.
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Docking Classes
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---------------
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.. automodule:: shepherd_score.evaluations.docking.docking
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Docking Pipelines
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-----------------
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.. automodule:: shepherd_score.evaluations.docking.pipelines
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Docking Targets
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---------------
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.. automodule:: shepherd_score.evaluations.docking.targets
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Protein-Ligand Interactions
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---------------------------
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.. automodule:: shepherd_score.evaluations.docking.interactions
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‎docs/api/evaluations/evaluate.rst‎

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Evaluation
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==========
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Classes and pipelines for evaluating generated 3D conformers.
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Evaluation Classes
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------------------
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.. automodule:: shepherd_score.evaluations.evaluate.evals
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Evaluation Pipelines
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--------------------
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.. automodule:: shepherd_score.evaluations.evaluate.pipelines
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‎docs/api/evaluations/index.rst‎

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Evaluation Modules
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==================
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Modules for evaluating generated 3D conformers.
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.. toctree::
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:maxdepth: 2
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evaluate
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docking
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utilities

‎docs/api/evaluations/utilities.rst‎

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Evaluation Utilities
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====================
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Utility functions supporting the evaluation modules.
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Data Conversion
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---------------
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.. automodule:: shepherd_score.evaluations.utils.convert_data
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Protein & Ligand Preparation
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-----------------------------
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.. automodule:: shepherd_score.evaluations.utils.interactions
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‎docs/api/index.rst‎

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scoring
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scoring/index
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Alignment
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alignment
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alignment/index
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Evaluations
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evaluations
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evaluations/index
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Utilities
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