rc-foundry 0.1.4__tar.gz → 0.1.6__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.
- rc_foundry-0.1.6/.git +1 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/PKG-INFO +1 -1
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/cli.py +10 -4
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rfd3/src/rfd3/run_inference.py +3 -7
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/pyproject.toml +4 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/src/foundry/version.py +2 -2
- rc_foundry-0.1.4/.git +0 -1
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/.github/workflows/lint_trunk.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/.gitignore +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/.gitmodules +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/.pre-commit-config.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/.project-root +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/LICENSE.md +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/Makefile +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/README.md +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/3en2_from_file.cif +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/3en2_from_json_with_msa.json +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/5hkn_from_file.cif +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/7o1r_from_json.json +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/7xli_template_antigen_and_framework.json +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/9dfn.cif +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/9dfn_template_ligand_and_protein.json +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/ligands/HEM.sdf +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/ligands/NAG.cif +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/msas/3en2_A.a3m.gz +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/msas/7o1r_A.a3m.gz +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/msas/8cdz_A.a3m.gz +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/multiple_examples_from_json.json +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/templates/7xli_chain_A.cif +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rf3/examples/templates/7xli_chain_B.cif +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/docs/releases/rfd3/examples/README.md +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/examples/all.ipynb +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/examples/enzymes.ipynb +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/README.md +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/__init__.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/collate/feature_collator.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/inference.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/inference_engines/mpnn.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/loss/nll_loss.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/metrics/nll.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/metrics/sequence_recovery.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/layers/graph_embeddings.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/layers/message_passing.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/layers/position_wise_feed_forward.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/layers/positional_encoding.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/model/mpnn.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/pipelines/mpnn.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/samplers/samplers.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/train.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/trainers/mpnn.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/feature_aggregation/mpnn.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/feature_aggregation/polymer_ligand_interface.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/feature_aggregation/token_encodings.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/feature_aggregation/user_settings.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/transforms/polymer_ligand_interface.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/utils/inference.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/utils/probability.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/src/mpnn/utils/weights.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/conftest.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_feature_collator.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_inference_engine.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_inference_utils.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_integration.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_loss.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_metrics.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_model.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_pipeline.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_polymer_ligand_interface.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_samplers.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/mpnn/tests/test_utils.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/README.md +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/callbacks/default.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/callbacks/dump_validation_structures.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/callbacks/metrics_logging.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/callbacks/train_logging.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/dataloader/default.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/base.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/pdb_and_distillation.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/pdb_only.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/disorder_distillation.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/domain_distillation.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/monomer_distillation.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/na_complex_distillation.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/af3_weighted_sampling.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/base.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/plinder.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/train_interface.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/pdb/train_pn_unit.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/train/rna_monomer_distillation.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/val/af3_ab_set.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/val/af3_validation.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/val/base.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/datasets/val/runs_and_poses.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/debug/default.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/debug/train_specific_examples.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/experiment/pretrained/rf3.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/experiment/pretrained/rf3_with_confidence.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/experiment/quick-rf3-with-confidence.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/experiment/quick-rf3.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/hydra/default.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/hydra/no_logging.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/inference.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/inference_engine/base.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/inference_engine/rf3.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/logger/csv.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/logger/default.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/logger/wandb.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/model/components/ema.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/model/components/rf3_net.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/model/components/rf3_net_with_confidence_head.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/model/optimizers/adam.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/model/rf3.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/model/rf3_with_confidence.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/model/schedulers/af3.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/paths/data/default.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/paths/default.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/train.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/cpu.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/ddp.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/losses/confidence_loss.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/losses/diffusion_loss.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/losses/distogram_loss.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/structure_prediction.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/loss/structure_prediction_with_confidence.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/metrics/structure_prediction.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/rf3.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/trainer/rf3_with_confidence.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/configs/validate.yaml +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/__init__.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/_version.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/alignment.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/callbacks/dump_validation_structures.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/callbacks/metrics_logging.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/chemical.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/cli.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/cyclic_transform.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/extra_xforms.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/ground_truth_template.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/paired_msa.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/pipeline_utils.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/data/pipelines.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/diffusion_samplers/inference_sampler.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/inference.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/inference_engines/__init__.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/inference_engines/rf3.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/kinematics.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/loss/af3_confidence_loss.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/loss/af3_losses.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/loss/loss.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/chiral.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/clashing_chains.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/distogram.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/lddt.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/metadata.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/metric_utils.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/predicted_error.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/rasa.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/metrics/selected_distances.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/RF3.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/RF3_blocks.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/RF3_structure.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/af3_auxiliary_heads.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/af3_diffusion_transformer.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/attention.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/layer_utils.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/mlff.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/outer_product.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/pairformer_layers.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/model/layers/structure_bias.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/scoring.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/symmetry/resolve.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/train.py +0 -0
- {rc_foundry-0.1.4 → rc_foundry-0.1.6}/models/rf3/src/rf3/trainers/rf3.py +0 -0
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