boltz-vsynthes 1.0.0__py3-none-any.whl

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Files changed (112) hide show
  1. boltz/__init__.py +7 -0
  2. boltz/data/__init__.py +0 -0
  3. boltz/data/const.py +1184 -0
  4. boltz/data/crop/__init__.py +0 -0
  5. boltz/data/crop/affinity.py +164 -0
  6. boltz/data/crop/boltz.py +296 -0
  7. boltz/data/crop/cropper.py +45 -0
  8. boltz/data/feature/__init__.py +0 -0
  9. boltz/data/feature/featurizer.py +1230 -0
  10. boltz/data/feature/featurizerv2.py +2208 -0
  11. boltz/data/feature/symmetry.py +602 -0
  12. boltz/data/filter/__init__.py +0 -0
  13. boltz/data/filter/dynamic/__init__.py +0 -0
  14. boltz/data/filter/dynamic/date.py +76 -0
  15. boltz/data/filter/dynamic/filter.py +24 -0
  16. boltz/data/filter/dynamic/max_residues.py +37 -0
  17. boltz/data/filter/dynamic/resolution.py +34 -0
  18. boltz/data/filter/dynamic/size.py +38 -0
  19. boltz/data/filter/dynamic/subset.py +42 -0
  20. boltz/data/filter/static/__init__.py +0 -0
  21. boltz/data/filter/static/filter.py +26 -0
  22. boltz/data/filter/static/ligand.py +37 -0
  23. boltz/data/filter/static/polymer.py +299 -0
  24. boltz/data/module/__init__.py +0 -0
  25. boltz/data/module/inference.py +307 -0
  26. boltz/data/module/inferencev2.py +429 -0
  27. boltz/data/module/training.py +684 -0
  28. boltz/data/module/trainingv2.py +660 -0
  29. boltz/data/mol.py +900 -0
  30. boltz/data/msa/__init__.py +0 -0
  31. boltz/data/msa/mmseqs2.py +235 -0
  32. boltz/data/pad.py +84 -0
  33. boltz/data/parse/__init__.py +0 -0
  34. boltz/data/parse/a3m.py +134 -0
  35. boltz/data/parse/csv.py +100 -0
  36. boltz/data/parse/fasta.py +138 -0
  37. boltz/data/parse/mmcif.py +1239 -0
  38. boltz/data/parse/mmcif_with_constraints.py +1607 -0
  39. boltz/data/parse/schema.py +1851 -0
  40. boltz/data/parse/yaml.py +68 -0
  41. boltz/data/sample/__init__.py +0 -0
  42. boltz/data/sample/cluster.py +283 -0
  43. boltz/data/sample/distillation.py +57 -0
  44. boltz/data/sample/random.py +39 -0
  45. boltz/data/sample/sampler.py +49 -0
  46. boltz/data/tokenize/__init__.py +0 -0
  47. boltz/data/tokenize/boltz.py +195 -0
  48. boltz/data/tokenize/boltz2.py +396 -0
  49. boltz/data/tokenize/tokenizer.py +24 -0
  50. boltz/data/types.py +777 -0
  51. boltz/data/write/__init__.py +0 -0
  52. boltz/data/write/mmcif.py +305 -0
  53. boltz/data/write/pdb.py +171 -0
  54. boltz/data/write/utils.py +23 -0
  55. boltz/data/write/writer.py +330 -0
  56. boltz/main.py +1292 -0
  57. boltz/model/__init__.py +0 -0
  58. boltz/model/layers/__init__.py +0 -0
  59. boltz/model/layers/attention.py +132 -0
  60. boltz/model/layers/attentionv2.py +111 -0
  61. boltz/model/layers/confidence_utils.py +231 -0
  62. boltz/model/layers/dropout.py +34 -0
  63. boltz/model/layers/initialize.py +100 -0
  64. boltz/model/layers/outer_product_mean.py +98 -0
  65. boltz/model/layers/pair_averaging.py +135 -0
  66. boltz/model/layers/pairformer.py +337 -0
  67. boltz/model/layers/relative.py +58 -0
  68. boltz/model/layers/transition.py +78 -0
  69. boltz/model/layers/triangular_attention/__init__.py +0 -0
  70. boltz/model/layers/triangular_attention/attention.py +189 -0
  71. boltz/model/layers/triangular_attention/primitives.py +409 -0
  72. boltz/model/layers/triangular_attention/utils.py +380 -0
  73. boltz/model/layers/triangular_mult.py +212 -0
  74. boltz/model/loss/__init__.py +0 -0
  75. boltz/model/loss/bfactor.py +49 -0
  76. boltz/model/loss/confidence.py +590 -0
  77. boltz/model/loss/confidencev2.py +621 -0
  78. boltz/model/loss/diffusion.py +171 -0
  79. boltz/model/loss/diffusionv2.py +134 -0
  80. boltz/model/loss/distogram.py +48 -0
  81. boltz/model/loss/distogramv2.py +105 -0
  82. boltz/model/loss/validation.py +1025 -0
  83. boltz/model/models/__init__.py +0 -0
  84. boltz/model/models/boltz1.py +1286 -0
  85. boltz/model/models/boltz2.py +1249 -0
  86. boltz/model/modules/__init__.py +0 -0
  87. boltz/model/modules/affinity.py +223 -0
  88. boltz/model/modules/confidence.py +481 -0
  89. boltz/model/modules/confidence_utils.py +181 -0
  90. boltz/model/modules/confidencev2.py +495 -0
  91. boltz/model/modules/diffusion.py +844 -0
  92. boltz/model/modules/diffusion_conditioning.py +116 -0
  93. boltz/model/modules/diffusionv2.py +677 -0
  94. boltz/model/modules/encoders.py +639 -0
  95. boltz/model/modules/encodersv2.py +565 -0
  96. boltz/model/modules/transformers.py +322 -0
  97. boltz/model/modules/transformersv2.py +261 -0
  98. boltz/model/modules/trunk.py +688 -0
  99. boltz/model/modules/trunkv2.py +828 -0
  100. boltz/model/modules/utils.py +303 -0
  101. boltz/model/optim/__init__.py +0 -0
  102. boltz/model/optim/ema.py +389 -0
  103. boltz/model/optim/scheduler.py +99 -0
  104. boltz/model/potentials/__init__.py +0 -0
  105. boltz/model/potentials/potentials.py +497 -0
  106. boltz/model/potentials/schedules.py +32 -0
  107. boltz_vsynthes-1.0.0.dist-info/METADATA +151 -0
  108. boltz_vsynthes-1.0.0.dist-info/RECORD +112 -0
  109. boltz_vsynthes-1.0.0.dist-info/WHEEL +5 -0
  110. boltz_vsynthes-1.0.0.dist-info/entry_points.txt +2 -0
  111. boltz_vsynthes-1.0.0.dist-info/licenses/LICENSE +21 -0
  112. boltz_vsynthes-1.0.0.dist-info/top_level.txt +1 -0
boltz/__init__.py ADDED
@@ -0,0 +1,7 @@
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+ from importlib.metadata import PackageNotFoundError, version
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+
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+ try: # noqa: SIM105
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+ __version__ = version("boltz")
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+ except PackageNotFoundError:
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+ # package is not installed
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+ pass
boltz/data/__init__.py ADDED
File without changes