rc-foundry 0.1.4__tar.gz → 0.1.5__tar.gz

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Files changed (416) hide show
  1. rc_foundry-0.1.5/.git +1 -0
  2. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/PKG-INFO +1 -1
  3. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/run_inference.py +3 -7
  4. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/src/foundry/version.py +2 -2
  5. rc_foundry-0.1.4/.git +0 -1
  6. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/.github/workflows/lint_trunk.yaml +0 -0
  7. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/.gitignore +0 -0
  8. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/.gitmodules +0 -0
  9. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/.pre-commit-config.yaml +0 -0
  10. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/.project-root +0 -0
  11. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/LICENSE.md +0 -0
  12. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/Makefile +0 -0
  13. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/README.md +0 -0
  14. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/3en2_from_file.cif +0 -0
  15. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/3en2_from_json_with_msa.json +0 -0
  16. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/5hkn_from_file.cif +0 -0
  17. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/7o1r_from_json.json +0 -0
  18. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/7xli_template_antigen_and_framework.json +0 -0
  19. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/9dfn.cif +0 -0
  20. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/9dfn_template_ligand_and_protein.json +0 -0
  21. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/ligands/HEM.sdf +0 -0
  22. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/ligands/NAG.cif +0 -0
  23. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/msas/3en2_A.a3m.gz +0 -0
  24. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/msas/7o1r_A.a3m.gz +0 -0
  25. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/msas/8cdz_A.a3m.gz +0 -0
  26. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/multiple_examples_from_json.json +0 -0
  27. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/templates/7xli_chain_A.cif +0 -0
  28. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rf3/examples/templates/7xli_chain_B.cif +0 -0
  29. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/docs/releases/rfd3/examples/README.md +0 -0
  30. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/examples/all.ipynb +0 -0
  31. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/examples/enzymes.ipynb +0 -0
  32. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/README.md +0 -0
  33. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/__init__.py +0 -0
  34. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/collate/feature_collator.py +0 -0
  35. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/inference.py +0 -0
  36. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/inference_engines/mpnn.py +0 -0
  37. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/loss/nll_loss.py +0 -0
  38. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/metrics/nll.py +0 -0
  39. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/metrics/sequence_recovery.py +0 -0
  40. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/model/layers/graph_embeddings.py +0 -0
  41. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/model/layers/message_passing.py +0 -0
  42. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/model/layers/position_wise_feed_forward.py +0 -0
  43. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/model/layers/positional_encoding.py +0 -0
  44. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/model/mpnn.py +0 -0
  45. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/pipelines/mpnn.py +0 -0
  46. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/samplers/samplers.py +0 -0
  47. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/train.py +0 -0
  48. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/trainers/mpnn.py +0 -0
  49. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/transforms/feature_aggregation/mpnn.py +0 -0
  50. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/transforms/feature_aggregation/polymer_ligand_interface.py +0 -0
  51. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/transforms/feature_aggregation/token_encodings.py +0 -0
  52. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/transforms/feature_aggregation/user_settings.py +0 -0
  53. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/transforms/polymer_ligand_interface.py +0 -0
  54. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/utils/inference.py +0 -0
  55. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/utils/probability.py +0 -0
  56. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/src/mpnn/utils/weights.py +0 -0
  57. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/conftest.py +0 -0
  58. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_feature_collator.py +0 -0
  59. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_inference_engine.py +0 -0
  60. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_inference_utils.py +0 -0
  61. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_integration.py +0 -0
  62. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_loss.py +0 -0
  63. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_metrics.py +0 -0
  64. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_model.py +0 -0
  65. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_pipeline.py +0 -0
  66. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_polymer_ligand_interface.py +0 -0
  67. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_samplers.py +0 -0
  68. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/mpnn/tests/test_utils.py +0 -0
  69. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/README.md +0 -0
  70. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/callbacks/default.yaml +0 -0
  71. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/callbacks/dump_validation_structures.yaml +0 -0
  72. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/callbacks/metrics_logging.yaml +0 -0
  73. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/callbacks/train_logging.yaml +0 -0
  74. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/dataloader/default.yaml +0 -0
  75. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/base.yaml +0 -0
  76. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/pdb_and_distillation.yaml +0 -0
  77. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/pdb_only.yaml +0 -0
  78. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/disorder_distillation.yaml +0 -0
  79. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/domain_distillation.yaml +0 -0
  80. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/monomer_distillation.yaml +0 -0
  81. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/na_complex_distillation.yaml +0 -0
  82. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/pdb/af3_weighted_sampling.yaml +0 -0
  83. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/pdb/base.yaml +0 -0
  84. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/pdb/plinder.yaml +0 -0
  85. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/pdb/train_interface.yaml +0 -0
  86. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/pdb/train_pn_unit.yaml +0 -0
  87. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/train/rna_monomer_distillation.yaml +0 -0
  88. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/val/af3_ab_set.yaml +0 -0
  89. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/val/af3_validation.yaml +0 -0
  90. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/val/base.yaml +0 -0
  91. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/datasets/val/runs_and_poses.yaml +0 -0
  92. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/debug/default.yaml +0 -0
  93. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/debug/train_specific_examples.yaml +0 -0
  94. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/experiment/pretrained/rf3.yaml +0 -0
  95. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/experiment/pretrained/rf3_with_confidence.yaml +0 -0
  96. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/experiment/quick-rf3-with-confidence.yaml +0 -0
  97. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/experiment/quick-rf3.yaml +0 -0
  98. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/hydra/default.yaml +0 -0
  99. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/hydra/no_logging.yaml +0 -0
  100. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/inference.yaml +0 -0
  101. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/inference_engine/base.yaml +0 -0
  102. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/inference_engine/rf3.yaml +0 -0
  103. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/logger/csv.yaml +0 -0
  104. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/logger/default.yaml +0 -0
  105. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/logger/wandb.yaml +0 -0
  106. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/model/components/ema.yaml +0 -0
  107. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/model/components/rf3_net.yaml +0 -0
  108. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/model/components/rf3_net_with_confidence_head.yaml +0 -0
  109. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/model/optimizers/adam.yaml +0 -0
  110. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/model/rf3.yaml +0 -0
  111. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/model/rf3_with_confidence.yaml +0 -0
  112. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/model/schedulers/af3.yaml +0 -0
  113. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/paths/data/default.yaml +0 -0
  114. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/paths/default.yaml +0 -0
  115. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/train.yaml +0 -0
  116. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/cpu.yaml +0 -0
  117. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/ddp.yaml +0 -0
  118. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/loss/losses/confidence_loss.yaml +0 -0
  119. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/loss/losses/diffusion_loss.yaml +0 -0
  120. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/loss/losses/distogram_loss.yaml +0 -0
  121. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/loss/structure_prediction.yaml +0 -0
  122. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/loss/structure_prediction_with_confidence.yaml +0 -0
  123. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/metrics/structure_prediction.yaml +0 -0
  124. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/rf3.yaml +0 -0
  125. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/trainer/rf3_with_confidence.yaml +0 -0
  126. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/configs/validate.yaml +0 -0
  127. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/__init__.py +0 -0
  128. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/_version.py +0 -0
  129. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/alignment.py +0 -0
  130. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/callbacks/dump_validation_structures.py +0 -0
  131. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/callbacks/metrics_logging.py +0 -0
  132. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/chemical.py +0 -0
  133. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/cli.py +0 -0
  134. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/data/cyclic_transform.py +0 -0
  135. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/data/extra_xforms.py +0 -0
  136. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/data/ground_truth_template.py +0 -0
  137. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/data/paired_msa.py +0 -0
  138. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/data/pipeline_utils.py +0 -0
  139. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/data/pipelines.py +0 -0
  140. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/diffusion_samplers/inference_sampler.py +0 -0
  141. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/inference.py +0 -0
  142. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/inference_engines/__init__.py +0 -0
  143. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/inference_engines/rf3.py +0 -0
  144. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/kinematics.py +0 -0
  145. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/loss/af3_confidence_loss.py +0 -0
  146. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/loss/af3_losses.py +0 -0
  147. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/loss/loss.py +0 -0
  148. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/chiral.py +0 -0
  149. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/clashing_chains.py +0 -0
  150. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/distogram.py +0 -0
  151. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/lddt.py +0 -0
  152. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/metadata.py +0 -0
  153. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/metric_utils.py +0 -0
  154. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/predicted_error.py +0 -0
  155. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/rasa.py +0 -0
  156. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/metrics/selected_distances.py +0 -0
  157. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/RF3.py +0 -0
  158. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/RF3_blocks.py +0 -0
  159. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/RF3_structure.py +0 -0
  160. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/layers/af3_auxiliary_heads.py +0 -0
  161. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/layers/af3_diffusion_transformer.py +0 -0
  162. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/layers/attention.py +0 -0
  163. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/layers/layer_utils.py +0 -0
  164. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/layers/mlff.py +0 -0
  165. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rf3/src/rf3/model/layers/outer_product.py +0 -0
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  337. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/trainer/fabric_trainer.py +0 -0
  338. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/trainer/recycling.py +0 -0
  339. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/trainer/rfd3.py +0 -0
  340. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/trainer/trainer_utils.py +0 -0
  341. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/transforms/conditioning_base.py +0 -0
  342. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/transforms/conditioning_utils.py +0 -0
  343. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/transforms/design_transforms.py +0 -0
  344. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/transforms/dna_crop.py +0 -0
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  368. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/tests/test_tokenization.py +0 -0
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  370. {rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/tests/transforms/regression_test_data/1p5d_0_inference_pretrain.pkl +0 -0
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rc_foundry-0.1.5/.git ADDED
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+ gitdir: /home/rohith/modelhub/.git/worktrees/release
{rc_foundry-0.1.4 → rc_foundry-0.1.5}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: rc-foundry
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- Version: 0.1.4
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+ Version: 0.1.5
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  Summary: Shared utilities and training infrastructure for biomolecular structure prediction models.
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  Author-email: Institute for Protein Design <contact@ipd.uw.edu>
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  License: BSD 3-Clause License
{rc_foundry-0.1.4 → rc_foundry-0.1.5}/models/rfd3/src/rfd3/run_inference.py RENAMED
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  import os
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  import hydra
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- import rootutils
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  from dotenv import load_dotenv
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  from omegaconf import DictConfig, OmegaConf
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  from rfd3.engine import RFD3InferenceConfig, RFD3InferenceEngine
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- # Setup root dir and environment variables (more info: https://github.com/ashleve/rootutils)
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- # NOTE: Sets the `PROJECT_ROOT` environment variable to the root directory of the project (where `.project-root` is located)
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- # If the user has set `PROJECT_PATH`, use it to build the config path; otherwise, fall back to `PROJECT_ROOT`
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- _config_path = os.path.join(os.environ["PROJECT_ROOT"], "models/rfd3/configs")
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+ # For pip-installed package, configs should be relative to this file
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+ # Adjust this path based on where configs are bundled in the package
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+ _config_path = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(__file__))), "configs")
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  @hydra.main(
{rc_foundry-0.1.4 → rc_foundry-0.1.5}/src/foundry/version.py RENAMED
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+ __version__ = version = '0.1.5'
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rc_foundry-0.1.4/.git DELETED
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- gitdir: /home/ncorley/projects/modelhub/modelhub.git/worktrees/modelworks
{rc_foundry-0.1.4 → rc_foundry-0.1.5}/.gitignore RENAMED
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