rc-foundry 0.1.5__py3-none-any.whl → 0.1.7__py3-none-any.whl

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 (152) hide show
  1. foundry/inference_engines/checkpoint_registry.py +58 -11
  2. foundry/utils/alignment.py +10 -2
  3. foundry/version.py +2 -2
  4. foundry_cli/download_checkpoints.py +66 -66
  5. {rc_foundry-0.1.5.dist-info → rc_foundry-0.1.7.dist-info}/METADATA +25 -20
  6. rc_foundry-0.1.7.dist-info/RECORD +311 -0
  7. rf3/configs/callbacks/default.yaml +5 -0
  8. rf3/configs/callbacks/dump_validation_structures.yaml +6 -0
  9. rf3/configs/callbacks/metrics_logging.yaml +10 -0
  10. rf3/configs/callbacks/train_logging.yaml +16 -0
  11. rf3/configs/dataloader/default.yaml +15 -0
  12. rf3/configs/datasets/base.yaml +31 -0
  13. rf3/configs/datasets/pdb_and_distillation.yaml +58 -0
  14. rf3/configs/datasets/pdb_only.yaml +17 -0
  15. rf3/configs/datasets/train/disorder_distillation.yaml +48 -0
  16. rf3/configs/datasets/train/domain_distillation.yaml +50 -0
  17. rf3/configs/datasets/train/monomer_distillation.yaml +49 -0
  18. rf3/configs/datasets/train/na_complex_distillation.yaml +50 -0
  19. rf3/configs/datasets/train/pdb/af3_weighted_sampling.yaml +8 -0
  20. rf3/configs/datasets/train/pdb/base.yaml +32 -0
  21. rf3/configs/datasets/train/pdb/plinder.yaml +54 -0
  22. rf3/configs/datasets/train/pdb/train_interface.yaml +51 -0
  23. rf3/configs/datasets/train/pdb/train_pn_unit.yaml +46 -0
  24. rf3/configs/datasets/train/rna_monomer_distillation.yaml +56 -0
  25. rf3/configs/datasets/val/af3_ab_set.yaml +11 -0
  26. rf3/configs/datasets/val/af3_validation.yaml +11 -0
  27. rf3/configs/datasets/val/base.yaml +32 -0
  28. rf3/configs/datasets/val/runs_and_poses.yaml +12 -0
  29. rf3/configs/debug/default.yaml +66 -0
  30. rf3/configs/debug/train_specific_examples.yaml +21 -0
  31. rf3/configs/experiment/pretrained/rf3.yaml +50 -0
  32. rf3/configs/experiment/pretrained/rf3_with_confidence.yaml +13 -0
  33. rf3/configs/experiment/quick-rf3-with-confidence.yaml +15 -0
  34. rf3/configs/experiment/quick-rf3.yaml +61 -0
  35. rf3/configs/hydra/default.yaml +18 -0
  36. rf3/configs/hydra/no_logging.yaml +7 -0
  37. rf3/configs/inference.yaml +7 -0
  38. rf3/configs/inference_engine/base.yaml +23 -0
  39. rf3/configs/inference_engine/rf3.yaml +33 -0
  40. rf3/configs/logger/csv.yaml +6 -0
  41. rf3/configs/logger/default.yaml +3 -0
  42. rf3/configs/logger/wandb.yaml +15 -0
  43. rf3/configs/model/components/ema.yaml +1 -0
  44. rf3/configs/model/components/rf3_net.yaml +177 -0
  45. rf3/configs/model/components/rf3_net_with_confidence_head.yaml +45 -0
  46. rf3/configs/model/optimizers/adam.yaml +5 -0
  47. rf3/configs/model/rf3.yaml +43 -0
  48. rf3/configs/model/rf3_with_confidence.yaml +7 -0
  49. rf3/configs/model/schedulers/af3.yaml +6 -0
  50. rf3/configs/paths/data/default.yaml +43 -0
  51. rf3/configs/paths/default.yaml +21 -0
  52. rf3/configs/train.yaml +42 -0
  53. rf3/configs/trainer/cpu.yaml +6 -0
  54. rf3/configs/trainer/ddp.yaml +5 -0
  55. rf3/configs/trainer/loss/losses/confidence_loss.yaml +29 -0
  56. rf3/configs/trainer/loss/losses/diffusion_loss.yaml +9 -0
  57. rf3/configs/trainer/loss/losses/distogram_loss.yaml +2 -0
  58. rf3/configs/trainer/loss/structure_prediction.yaml +4 -0
  59. rf3/configs/trainer/loss/structure_prediction_with_confidence.yaml +2 -0
  60. rf3/configs/trainer/metrics/structure_prediction.yaml +14 -0
  61. rf3/configs/trainer/rf3.yaml +20 -0
  62. rf3/configs/trainer/rf3_with_confidence.yaml +13 -0
  63. rf3/configs/validate.yaml +45 -0
  64. rfd3/cli.py +10 -4
  65. rfd3/configs/__init__.py +0 -0
  66. rfd3/configs/callbacks/design_callbacks.yaml +10 -0
  67. rfd3/configs/callbacks/metrics_logging.yaml +20 -0
  68. rfd3/configs/callbacks/train_logging.yaml +24 -0
  69. rfd3/configs/dataloader/default.yaml +15 -0
  70. rfd3/configs/dataloader/fast.yaml +11 -0
  71. rfd3/configs/datasets/conditions/dna_condition.yaml +3 -0
  72. rfd3/configs/datasets/conditions/island.yaml +28 -0
  73. rfd3/configs/datasets/conditions/ppi.yaml +2 -0
  74. rfd3/configs/datasets/conditions/sequence_design.yaml +17 -0
  75. rfd3/configs/datasets/conditions/tipatom.yaml +28 -0
  76. rfd3/configs/datasets/conditions/unconditional.yaml +21 -0
  77. rfd3/configs/datasets/design_base.yaml +97 -0
  78. rfd3/configs/datasets/train/pdb/af3_train_interface.yaml +46 -0
  79. rfd3/configs/datasets/train/pdb/af3_train_pn_unit.yaml +42 -0
  80. rfd3/configs/datasets/train/pdb/base.yaml +14 -0
  81. rfd3/configs/datasets/train/pdb/base_no_weights.yaml +19 -0
  82. rfd3/configs/datasets/train/pdb/base_transform_args.yaml +59 -0
  83. rfd3/configs/datasets/train/pdb/na_complex_distillation.yaml +20 -0
  84. rfd3/configs/datasets/train/pdb/pdb_base.yaml +11 -0
  85. rfd3/configs/datasets/train/pdb/rfd3_train_interface.yaml +22 -0
  86. rfd3/configs/datasets/train/pdb/rfd3_train_pn_unit.yaml +23 -0
  87. rfd3/configs/datasets/train/rfd3_monomer_distillation.yaml +38 -0
  88. rfd3/configs/datasets/val/bcov_ppi_easy_medium.yaml +9 -0
  89. rfd3/configs/datasets/val/design_validation_base.yaml +40 -0
  90. rfd3/configs/datasets/val/dna_binder_design5.yaml +9 -0
  91. rfd3/configs/datasets/val/dna_binder_long.yaml +13 -0
  92. rfd3/configs/datasets/val/dna_binder_short.yaml +13 -0
  93. rfd3/configs/datasets/val/indexed.yaml +9 -0
  94. rfd3/configs/datasets/val/mcsa_41.yaml +9 -0
  95. rfd3/configs/datasets/val/mcsa_41_short_rigid.yaml +10 -0
  96. rfd3/configs/datasets/val/ppi_inference.yaml +7 -0
  97. rfd3/configs/datasets/val/sm_binder_hbonds.yaml +13 -0
  98. rfd3/configs/datasets/val/sm_binder_hbonds_short.yaml +15 -0
  99. rfd3/configs/datasets/val/unconditional.yaml +9 -0
  100. rfd3/configs/datasets/val/unconditional_deep.yaml +9 -0
  101. rfd3/configs/datasets/val/unindexed.yaml +8 -0
  102. rfd3/configs/datasets/val/val_examples/bcov_ppi_easy_medium_with_ori.yaml +151 -0
  103. rfd3/configs/datasets/val/val_examples/bcov_ppi_easy_medium_with_ori_spoof_helical_bundle.yaml +7 -0
  104. rfd3/configs/datasets/val/val_examples/bcov_ppi_easy_medium_with_ori_varying_lengths.yaml +28 -0
  105. rfd3/configs/datasets/val/val_examples/bpem_ori_hb.yaml +212 -0
  106. rfd3/configs/debug/default.yaml +64 -0
  107. rfd3/configs/debug/train_specific_examples.yaml +21 -0
  108. rfd3/configs/dev.yaml +9 -0
  109. rfd3/configs/experiment/debug.yaml +14 -0
  110. rfd3/configs/experiment/pretrain.yaml +31 -0
  111. rfd3/configs/experiment/test-uncond.yaml +10 -0
  112. rfd3/configs/experiment/test-unindexed.yaml +21 -0
  113. rfd3/configs/hydra/default.yaml +18 -0
  114. rfd3/configs/hydra/no_logging.yaml +7 -0
  115. rfd3/configs/inference.yaml +9 -0
  116. rfd3/configs/inference_engine/base.yaml +15 -0
  117. rfd3/configs/inference_engine/dev.yaml +20 -0
  118. rfd3/configs/inference_engine/rfdiffusion3.yaml +65 -0
  119. rfd3/configs/logger/csv.yaml +6 -0
  120. rfd3/configs/logger/default.yaml +2 -0
  121. rfd3/configs/logger/wandb.yaml +15 -0
  122. rfd3/configs/model/components/ema.yaml +1 -0
  123. rfd3/configs/model/components/rfd3_net.yaml +131 -0
  124. rfd3/configs/model/optimizers/adam.yaml +5 -0
  125. rfd3/configs/model/rfd3_base.yaml +8 -0
  126. rfd3/configs/model/samplers/edm.yaml +21 -0
  127. rfd3/configs/model/samplers/symmetry.yaml +10 -0
  128. rfd3/configs/model/schedulers/af3.yaml +6 -0
  129. rfd3/configs/paths/data/default.yaml +18 -0
  130. rfd3/configs/paths/default.yaml +22 -0
  131. rfd3/configs/train.yaml +28 -0
  132. rfd3/configs/trainer/cpu.yaml +6 -0
  133. rfd3/configs/trainer/ddp.yaml +5 -0
  134. rfd3/configs/trainer/loss/losses/diffusion_loss.yaml +12 -0
  135. rfd3/configs/trainer/loss/losses/sequence_loss.yaml +3 -0
  136. rfd3/configs/trainer/metrics/design_metrics.yaml +22 -0
  137. rfd3/configs/trainer/rfd3_base.yaml +35 -0
  138. rfd3/configs/validate.yaml +34 -0
  139. rfd3/engine.py +19 -11
  140. rfd3/inference/input_parsing.py +1 -1
  141. rfd3/inference/legacy_input_parsing.py +17 -1
  142. rfd3/inference/parsing.py +1 -0
  143. rfd3/inference/symmetry/atom_array.py +1 -5
  144. rfd3/inference/symmetry/checks.py +53 -28
  145. rfd3/inference/symmetry/frames.py +8 -5
  146. rfd3/inference/symmetry/symmetry_utils.py +38 -60
  147. rfd3/run_inference.py +3 -1
  148. rfd3/utils/inference.py +23 -0
  149. rc_foundry-0.1.5.dist-info/RECORD +0 -180
  150. {rc_foundry-0.1.5.dist-info → rc_foundry-0.1.7.dist-info}/WHEEL +0 -0
  151. {rc_foundry-0.1.5.dist-info → rc_foundry-0.1.7.dist-info}/entry_points.txt +0 -0
  152. {rc_foundry-0.1.5.dist-info → rc_foundry-0.1.7.dist-info}/licenses/LICENSE.md +0 -0
rc_foundry-0.1.5.dist-info/RECORD DELETED
@@ -1,180 +0,0 @@
1
- foundry/__init__.py,sha256=H8S1nl5v6YeW8ggn1jKy4GdtH7c-FGS-j7CqUCAEnAU,1926
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- foundry/common.py,sha256=Aur8mH-CNmcUqSsw7VgaCQSW5sH1Bqf8Da91jzxPV1Y,3035
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- foundry/constants.py,sha256=0n1wBKCvNuw3QaQehSbmsHYkIdaGn3tLeRFItBrdeHY,913
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- foundry/version.py,sha256=rdxBMYpwzYxiWk08QbPLHSAxHoDfeKWwyaJIAM0lSic,704
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- foundry/callbacks/__init__.py,sha256=VsRT1e4sqlJHPcTCsfupMEx82Iz-LoOAGPpwvf_OJeE,126
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- foundry/callbacks/callback.py,sha256=xZBo_suP4bLrP6gl5uJPbaXm00DXigePa6dMeDxucgg,3890
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- foundry/callbacks/health_logging.py,sha256=tEtkByOlaAA7nnelxb7PbM9_dcIgOsdbxCdQY3K5pMc,16664
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- foundry/callbacks/metrics_logging.py,sha256=Vekzs831d-HE7TfLJZnQ45iPeG9ziQWLQaMBGaymfQM,8696
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- foundry/callbacks/timing_logging.py,sha256=u-r0hKp7fWOY3mLk7CcuIwHgZbhte13m5M09xNgatZA,2343
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- foundry/callbacks/train_logging.py,sha256=Xs3tmZA88qLxmdSOwt-x8YKN4NKb1kVm59uptNXl4Qo,10399
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- foundry/hydra/resolvers.py,sha256=xyJzo6OeWAc_LOu8RiHhX7_CRNoLZ22626AvYHXYl4U,2186
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- foundry/inference_engines/base.py,sha256=ZHdlmGUqH4-p3v4RdrLH-Ps8_zalr7j5mQ4x-S53N4M,8375
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- foundry/inference_engines/checkpoint_registry.py,sha256=kt2Z1JhrAjoOiEpkIIQ0sLttie1ceL8OgXUBmmyA6iw,2544
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- foundry/metrics/__init__.py,sha256=qL4wwaiQ7EtR30pmZ9MCknqx909BJcNvHVmNJUaz_WM,236
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- foundry/metrics/losses.py,sha256=2CLUmf7oCdFUCvgJukdNkff0FVG3BlATI-NI60TtpVY,903
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- foundry/metrics/metric.py,sha256=23pKh_Ra0EcHGo5cSzYQQrUGr5zWRxeufKSJ58tfXXo,12687
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- foundry/model/layers/blocks.py,sha256=ihbbP_1fOlrkrcrQSk9thCrNWjK8mtxD3WxcBng9Htk,1403
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- foundry/testing/__init__.py,sha256=BnrU7fZ4l0Dm1vrGcNPQYTAw83PW4DGYz7TGhGqgrfQ,223
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- foundry/testing/fixtures.py,sha256=j27a8CAonygjlWsUjZ-95M5MF4Rjp9nw7JskqiZlweI,486
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- foundry/testing/pytest_hooks.py,sha256=5Ebw1GXYO2XqS9Jvpzty7g3gCXIdXu16jqg53XcuUx4,450
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- foundry/trainers/fabric.py,sha256=cjaTHbGuJEQwaGBvIAXD_il4bHtY-crsTY14Xn77uXA,40401
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- foundry/training/EMA.py,sha256=3OWA9Pz7XuDr-SRxbz24tZf55DmhSa2fKy9r5v2IXqA,2651
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- foundry/training/checkpoint.py,sha256=mUiObg-qcF3tvMfVu77sD9m3yVRp71czv07ccliU7qQ,1791
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- foundry/training/schedulers.py,sha256=StmXegPfIdLAv31FreCTrDh9dsOvNUfzG4YGa61Y4oE,3647
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- foundry/utils/alignment.py,sha256=OAN7H2TqraGxP1uMXUpwLO7g0qS0cxUVjuV33pY16z0,2316
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- foundry/utils/components.py,sha256=Piw2TfQF26uuxC3hXG3iv_4rgud1lVO-cv6N-p05EDY,15200
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- foundry/utils/datasets.py,sha256=pLBxVezm-TSrYuC5gFnJZdGnNWV7aPH2QiWIVE2hkdQ,16629
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- foundry/utils/ddp.py,sha256=ydHrO6peGbRnWAwgH5rmpHuQd55g2gFzzoZJYypn7GU,3970
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- foundry/utils/instantiators.py,sha256=oGCp6hrmY-QPPPEjxKxe5uVFL125fH1RaLxjMKWCD_8,2169
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- foundry/utils/logging.py,sha256=jrDgiB_56q_hWDc0jkBFekvqnNWcowJBt4B-S-ipJmM,9312
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- foundry/utils/rigid.py,sha256=_Z1pmitb6xgxyguLj_TukKscUBJjQsU4bsBD24GVS84,44444
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- foundry/utils/rotation_augmentation.py,sha256=7q1WEX2iJ0i7-2aV-M97nEaEdpqexDTaZn5JquYpkUk,1927
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- foundry/utils/squashfs.py,sha256=QlcwuJyVe-QVfIOS7o1QfLhaCQPNzzox7ln4n8dcYEg,5234
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- foundry/utils/torch.py,sha256=OLsqoxw4CTXbGzWUHernLUT7uQjLu0tVPtD8h8747DI,11211
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- foundry/utils/weights.py,sha256=btz4S02xff2vgiq4xMfiXuhK1ERafqQPtmimo1DmoWY,10381
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- foundry_cli/__init__.py,sha256=0BxY2RUKJLaMXUGgypPCwlTskTEFdVnkhTR4C4ft2Kw,52
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- foundry_cli/download_checkpoints.py,sha256=UCNdy4VZyJe1PH_lnVLqy-VSMuTu875mGGd99ma7fTQ,8426
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- mpnn/__init__.py,sha256=hgQcXFaCbAxFrhydVAy0xj8yC7UJF-GCCFhqD0sZ7I4,57
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- mpnn/inference.py,sha256=wPtGR325eVRVeesXoWtBK6b_-VcU8BZae5IfQN3-mvA,1669
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- mpnn/train.py,sha256=9eQGBd3rdNF5Zr2w8oUgETbqxBavNBajtA6Vbc5zESE,10239
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- mpnn/collate/feature_collator.py,sha256=LpzAFWo1VMa06dJLmfUWZsKe4xvLZjHbx4RICg2lgbQ,10510
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- mpnn/inference_engines/mpnn.py,sha256=PmDEsIFipdk2fY57FA-vCp4evoU83DVVuUVmlViUtWk,21725
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- mpnn/loss/nll_loss.py,sha256=KmdNe-BCzGYtijjappzBArQcT1gHVlJnKdY1PYQ4mhU,5947
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- mpnn/metrics/nll.py,sha256=T6oMeUOEeHZzOMTH8NHFtsH9vUwLAsHQDPszzj4YKXI,15299
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- mpnn/metrics/sequence_recovery.py,sha256=YDw_LmH-a3ajBYWK0mucJEQvw0_VEyxvrBN7da4vX8Q,19034
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- mpnn/model/mpnn.py,sha256=vhkair2tYoId_akRP2qEq5O0IMZv6wsv9Q-V9plKgV8,131144
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- mpnn/model/layers/graph_embeddings.py,sha256=aEtd7iorMh8DxNH0eZVrK_zOo8HDLM5FRJyIJ8Cfz6k,99795
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- mpnn/model/layers/message_passing.py,sha256=TUkG9pXuo4Rtz5Bcij-OB7T4gSKmLt1KgxNmjJYPcMY,13051
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- mpnn/model/layers/position_wise_feed_forward.py,sha256=FATM8oveWy2XW-PDaaF9XLPIiWbehOHxG715E60n_8g,1602
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- mpnn/model/layers/positional_encoding.py,sha256=f-YpH1xvPGFC75U2-sOHrK13XtA9ZAWxjxxH1GrDt1M,4876
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- mpnn/pipelines/mpnn.py,sha256=SukwxEcAzaCgUZKcA1_KusodvcCg3_buN1dAZU-Udas,6185
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- mpnn/samplers/samplers.py,sha256=LDpetPMVklMboj1tucgnNvSHRUaQuehBmR2jFl4VWIE,6129
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- mpnn/trainers/mpnn.py,sha256=waXLQ-7pFD8MJRlnK37mHWcvqD6uOjTXVP6910tB6cw,6586
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- mpnn/transforms/polymer_ligand_interface.py,sha256=lipKDt_NFrpM-GiOXtvnTAvMpISOO4eHwilCgxnISJU,6106
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- mpnn/transforms/feature_aggregation/mpnn.py,sha256=jkhyMCqJipKQ2PvjqPkvvClhoiXx_I8e03lnDeH9__M,6324
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- mpnn/transforms/feature_aggregation/polymer_ligand_interface.py,sha256=gDdt9RZd0PO0YJdouNr0qsHFZV1i-5ewU6XuJrwPY54,2870
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- mpnn/transforms/feature_aggregation/token_encodings.py,sha256=qVlUky4HcDSU5drrZpZBnUvTSGdT6C7MN8f_owa81Bw,2227
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- mpnn/transforms/feature_aggregation/user_settings.py,sha256=uKyIDXz-QG0-KWQO1kqPlMj6i7RoVM6yH4iGNXFStoU,15007
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- mpnn/utils/inference.py,sha256=QLeukqLpedMNmvjbYgvLwDS5k7Q__NWILDSEbETkoCI,96539
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- mpnn/utils/probability.py,sha256=EYisliXNGXjuSPbzZwcIKjlhyINikGsqQndGBEbQoPI,990
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- mpnn/utils/weights.py,sha256=VsaIcOWTv8G-WJ9denxLRm3FQ9l6L66AVQN08E9BMSg,16411
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- rf3/__init__.py,sha256=XBb5hF2RqBPHODGRmjiRbfTXgOGfOzdY91GbS4Vex00,70
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- rf3/_version.py,sha256=fCfpbI5aeA6yHqjo3tK78-l2dPGxhp-AyKSoCXp34Nc,739
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- rf3/alignment.py,sha256=BvvwMqQGCVxV20xIsTighD1kXMadXXL2SkckLjTerx0,2102
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- rf3/chemical.py,sha256=VECnRPgVm-icXbZeUG4svcENzdUiIupP6dhka_8zCrg,26572
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- rf3/cli.py,sha256=dPKJFRHYoV2XS6xc_ZmdLTz6frqa6HZg4qgZU5oJcXU,2356
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- rf3/inference.py,sha256=_AAJ07AfSeU3xTM2_KH9n_H12EK4qZ23IJuyauOrMaQ,2466
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- rf3/kinematics.py,sha256=V3yjalPupu1X2FEp7l3XZR-qzLKrhWLZyECk6RgIkcs,10901
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- rf3/scoring.py,sha256=dTllswE-6Fgli2eLiNzLFc2Rhz4ouDT4WL-sVbvLTGU,41541
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- rf3/train.py,sha256=V4nqCC_1JKLI3WQ-nErNa8sqFpvb1mFhXSe6ZPpEheM,7945
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- rf3/util_module.py,sha256=ltc7QXJDb5Z184wxYQuT_-Z68YWXuPmOEBMLSzS6Pes,1428
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- rf3/validate.py,sha256=wXZLTWiOdTsCKiKK2_Dfnj5PInDiv5KxojOZwaUJjuo,5832
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- rf3/callbacks/dump_validation_structures.py,sha256=j_pDfPETyI10ZtsUlvf16-zpJdaUcC5w8TEYCk--Xbo,3909
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