Transforms
=========

This module contains various transformation classes and utilities for processing molecular data.

Core Transform Classes
--------------------

.. automodule:: atomworks.ml.transforms.base
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.. automodule:: atomworks.ml.transforms.af3_reference_molecule
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.. automodule:: atomworks.ml.transforms.atom_array
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.. automodule:: atomworks.ml.transforms.atom_frames
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.. automodule:: atomworks.ml.transforms.atomize
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.. automodule:: atomworks.ml.transforms.bonds
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.. automodule:: atomworks.ml.transforms.chirals
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.. automodule:: atomworks.ml.transforms.covalent_modifications
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.. automodule:: atomworks.ml.transforms.crop
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.. automodule:: atomworks.ml.transforms.encoding
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.. automodule:: atomworks.ml.transforms.featurize_unresolved_residues
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.. automodule:: atomworks.ml.transforms.filters
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.. automodule:: atomworks.ml.transforms.masks
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.. automodule:: atomworks.ml.transforms.sasa
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.. automodule:: atomworks.ml.transforms.symmetry
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.. automodule:: atomworks.ml.transforms.template
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Utility Modules
-------------

.. automodule:: atomworks.ml.transforms._checks
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.. automodule:: atomworks.ml.transforms.center_random_augmentation
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.. automodule:: atomworks.ml.transforms.openbabel_utils
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.. automodule:: atomworks.ml.transforms.rdkit_utils
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.. automodule:: atomworks.ml.transforms.rf2aa_assumptions
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Submodules
---------

DNA Transforms
~~~~~~~~~~~~

.. automodule:: atomworks.ml.transforms.dna
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Diffusion Transforms
~~~~~~~~~~~~~~~~~

.. automodule:: atomworks.ml.transforms.diffusion
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ESM Transforms
~~~~~~~~~~~~

.. automodule:: atomworks.ml.transforms.esm
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Feature Aggregation Transforms
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: atomworks.ml.transforms.feature_aggregation
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MSA Transforms
~~~~~~~~~~~~

.. automodule:: atomworks.ml.transforms.msa
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