atomworks 2.1.2__tar.gz → 2.2.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (137) hide show
  1. {atomworks-2.1.2 → atomworks-2.2.0}/PKG-INFO +1 -1
  2. {atomworks-2.1.2 → atomworks-2.2.0}/pyproject.toml +1 -1
  3. {atomworks-2.1.2 → atomworks-2.2.0}/.gitignore +0 -0
  4. {atomworks-2.1.2 → atomworks-2.2.0}/LICENSE.md +0 -0
  5. {atomworks-2.1.2 → atomworks-2.2.0}/README.md +0 -0
  6. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/__init__.py +0 -0
  7. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/biotite_patch.py +0 -0
  8. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/common.py +0 -0
  9. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/constants.py +0 -0
  10. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/enums.py +0 -0
  11. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/__init__.py +0 -0
  12. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/parser.py +0 -0
  13. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/template.py +0 -0
  14. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/tools/chembl_transformations.smirks +0 -0
  15. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/tools/fasta.py +0 -0
  16. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/tools/inference.py +0 -0
  17. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/tools/rdkit.py +0 -0
  18. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/transforms/atom_array.py +0 -0
  19. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/transforms/categories.py +0 -0
  20. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/__init__.py +0 -0
  21. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/assembly.py +0 -0
  22. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/atom_array.py +0 -0
  23. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/atom_array_plus.py +0 -0
  24. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/bonds.py +0 -0
  25. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/ccd.py +0 -0
  26. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/chain.py +0 -0
  27. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/compression.py +0 -0
  28. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/error.py +0 -0
  29. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/io_utils.py +0 -0
  30. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/non_rcsb.py +0 -0
  31. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/query.py +0 -0
  32. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/scatter.py +0 -0
  33. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/selection.py +0 -0
  34. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/sequence.py +0 -0
  35. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/testing.py +0 -0
  36. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/io/utils/visualize.py +0 -0
  37. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/__init__.py +0 -0
  38. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/conditions/__init__.py +0 -0
  39. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/conditions/annotator.py +0 -0
  40. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/conditions/base.py +0 -0
  41. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/conditions/conditions.py +0 -0
  42. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/README.md +0 -0
  43. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/__init__.py +0 -0
  44. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/base.py +0 -0
  45. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/concat_dataset.py +0 -0
  46. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/file_dataset.py +0 -0
  47. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/loaders/__init__.py +0 -0
  48. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/loaders/base.py +0 -0
  49. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/loaders/cif.py +0 -0
  50. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/pandas_dataset.py +0 -0
  51. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/parsers/__init__.py +0 -0
  52. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/parsers/base.py +0 -0
  53. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/parsers/custom_metadata_row_parsers.py +0 -0
  54. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/datasets/parsers/default_metadata_row_parsers.py +0 -0
  55. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/encoding_definitions.py +0 -0
  56. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/example_id.py +0 -0
  57. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/executables/__init__.py +0 -0
  58. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/executables/hbplus.py +0 -0
  59. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/executables/hhfilter.py +0 -0
  60. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/executables/mmseqs2.py +0 -0
  61. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/executables/x3dna.py +0 -0
  62. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/pipelines/__init__.py +0 -0
  63. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/pipelines/af3.py +0 -0
  64. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/pipelines/rf2aa.py +0 -0
  65. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/__init__.py +0 -0
  66. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/constants.py +0 -0
  67. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/get_pn_unit_data_from_structure.py +0 -0
  68. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/msa/filtering.py +0 -0
  69. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/msa/finding.py +0 -0
  70. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/msa/generating.py +0 -0
  71. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/msa/organizing.py +0 -0
  72. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/utils/fasta.py +0 -0
  73. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/preprocessing/utils/structure_utils.py +0 -0
  74. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/samplers.py +0 -0
  75. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/_checks.py +0 -0
  76. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/af3_reference_molecule.py +0 -0
  77. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/atom_array.py +0 -0
  78. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/atom_frames.py +0 -0
  79. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/atom_level_embeddings.py +0 -0
  80. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/atomize.py +0 -0
  81. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/base.py +0 -0
  82. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/bfactor_conditioned_transforms.py +0 -0
  83. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/bonds.py +0 -0
  84. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/cached_residue_data.py +0 -0
  85. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/center_random_augmentation.py +0 -0
  86. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/chirals.py +0 -0
  87. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/covalent_modifications.py +0 -0
  88. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/crop.py +0 -0
  89. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/design_task.py +0 -0
  90. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/diffusion/batch_structures.py +0 -0
  91. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/diffusion/edm.py +0 -0
  92. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/dna/pad_dna.py +0 -0
  93. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/encoding.py +0 -0
  94. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/feature_aggregation/af3.py +0 -0
  95. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/feature_aggregation/confidence.py +0 -0
  96. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/feature_aggregation/rf2aa.py +0 -0
  97. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/featurize_unresolved_residues.py +0 -0
  98. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/filters.py +0 -0
  99. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/mask_generator.py +0 -0
  100. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/masks.py +0 -0
  101. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/mirror_transform.py +0 -0
  102. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/msa/_msa_constants.py +0 -0
  103. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/msa/_msa_featurizing_utils.py +0 -0
  104. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/msa/_msa_loading_utils.py +0 -0
  105. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/msa/_msa_pairing_utils.py +0 -0
  106. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/msa/msa.py +0 -0
  107. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/openbabel_utils.py +0 -0
  108. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/random_atomize_residues.py +0 -0
  109. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/rdkit_utils.py +0 -0
  110. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/rf2aa_assumptions.py +0 -0
  111. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/sasa.py +0 -0
  112. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/symmetry.py +0 -0
  113. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/transforms/template.py +0 -0
  114. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/__init__.py +0 -0
  115. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/condition.py +0 -0
  116. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/debug.py +0 -0
  117. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/error.py +0 -0
  118. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/geometry.py +0 -0
  119. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/io.py +0 -0
  120. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/misc.py +0 -0
  121. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/nested_dict.py +0 -0
  122. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/numpy.py +0 -0
  123. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/rng.py +0 -0
  124. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/testing.py +0 -0
  125. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/timer.py +0 -0
  126. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/ml/utils/token.py +0 -0
  127. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks/py.typed +0 -0
  128. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/__main__.py +0 -0
  129. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/ccd.py +0 -0
  130. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/common.py +0 -0
  131. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/filter.py +0 -0
  132. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/find.py +0 -0
  133. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/generate.py +0 -0
  134. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/msa.py +0 -0
  135. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/organize.py +0 -0
  136. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/pdb.py +0 -0
  137. {atomworks-2.1.2 → atomworks-2.2.0}/atomworks_cli/setup.py +0 -0
{atomworks-2.1.2 → atomworks-2.2.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: atomworks
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- Version: 2.1.2
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+ Version: 2.2.0
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  Summary: A research-oriented data toolkit for training biomolecular deep-learning foundation models
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  Project-URL: homepage, https://rosettacommons.github.io/atomworks/latest/index.html
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  Project-URL: repository, https://github.com/RosettaCommons/atomworks
{atomworks-2.1.2 → atomworks-2.2.0}/pyproject.toml RENAMED
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  [project]
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  name = "atomworks"
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- version = "2.1.2"
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+ version = "2.2.0"
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  description = "A research-oriented data toolkit for training biomolecular deep-learning foundation models"
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  readme = "README.md"
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  requires-python = ">=3.11"
{atomworks-2.1.2 → atomworks-2.2.0}/.gitignore RENAMED
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{atomworks-2.1.2 → atomworks-2.2.0}/LICENSE.md RENAMED
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{atomworks-2.1.2 → atomworks-2.2.0}/README.md RENAMED
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{atomworks-2.1.2 → atomworks-2.2.0}/atomworks/common.py RENAMED
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{atomworks-2.1.2 → atomworks-2.2.0}/atomworks/enums.py RENAMED
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{atomworks-2.1.2 → atomworks-2.2.0}/atomworks/py.typed RENAMED
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