README.md
pyproject.toml
src/foldeverything/__init__.py
src/foldeverything.egg-info/PKG-INFO
src/foldeverything.egg-info/SOURCES.txt
src/foldeverything.egg-info/dependency_links.txt
src/foldeverything.egg-info/requires.txt
src/foldeverything.egg-info/top_level.txt
src/foldeverything/data/__init__.py
src/foldeverything/data/bond_analyze.py
src/foldeverything/data/bond_inference.py
src/foldeverything/data/conformers_smile_new.py
src/foldeverything/data/const.py
src/foldeverything/data/data.py
src/foldeverything/data/loading_utils.py
src/foldeverything/data/mol.py
src/foldeverything/data/pad.py
src/foldeverything/data/rmsd_computation.py
src/foldeverything/data/crop/__init__.py
src/foldeverything/data/crop/affinity.py
src/foldeverything/data/crop/cropper.py
src/foldeverything/data/crop/monomer.py
src/foldeverything/data/crop/multimer.py
src/foldeverything/data/decoy/decoy.py
src/foldeverything/data/feature/__init__.py
src/foldeverything/data/feature/af3.py
src/foldeverything/data/feature/featurizer.py
src/foldeverything/data/filter/__init__.py
src/foldeverything/data/filter/dynamic/MD.py
src/foldeverything/data/filter/dynamic/__init__.py
src/foldeverything/data/filter/dynamic/confidence.py
src/foldeverything/data/filter/dynamic/date.py
src/foldeverything/data/filter/dynamic/decoys.py
src/foldeverything/data/filter/dynamic/error.py
src/foldeverything/data/filter/dynamic/filter.py
src/foldeverything/data/filter/dynamic/filter_id.py
src/foldeverything/data/filter/dynamic/id_filter.py
src/foldeverything/data/filter/dynamic/ligand.py
src/foldeverything/data/filter/dynamic/max_residues.py
src/foldeverything/data/filter/dynamic/method.py
src/foldeverything/data/filter/dynamic/min_protein_residues.py
src/foldeverything/data/filter/dynamic/mol_size.py
src/foldeverything/data/filter/dynamic/pdb_id_txtfile.py
src/foldeverything/data/filter/dynamic/protein.py
src/foldeverything/data/filter/dynamic/protein_cluster.py
src/foldeverything/data/filter/dynamic/resolution.py
src/foldeverything/data/filter/dynamic/size.py
src/foldeverything/data/filter/dynamic/subset.py
src/foldeverything/data/filter/static/__init__.py
src/foldeverything/data/filter/static/filter.py
src/foldeverything/data/filter/static/ligand.py
src/foldeverything/data/filter/static/polymer.py
src/foldeverything/data/md_sampling/md_sampler.py
src/foldeverything/data/md_sampling/msm.py
src/foldeverything/data/md_sampling/uniform.py
src/foldeverything/data/parse/IDRome.py
src/foldeverything/data/parse/MemProtMD.py
src/foldeverything/data/parse/__init__.py
src/foldeverything/data/parse/a3m.py
src/foldeverything/data/parse/affinity.py
src/foldeverything/data/parse/atlas.py
src/foldeverything/data/parse/dynamicPDB.py
src/foldeverything/data/parse/fasta.py
src/foldeverything/data/parse/hhr.py
src/foldeverything/data/parse/md.py
src/foldeverything/data/parse/mdCATH.py
src/foldeverything/data/parse/misato.py
src/foldeverything/data/parse/mmcif.py
src/foldeverything/data/parse/openfold.py
src/foldeverything/data/parse/pdb_parser.py
src/foldeverything/data/parse/pfam.py
src/foldeverything/data/parse/schema.py
src/foldeverything/data/parse/schema_old.py
src/foldeverything/data/parse/yaml.py
src/foldeverything/data/sample/__init__.py
src/foldeverything/data/sample/affinity.py
src/foldeverything/data/sample/affinity_consecutive.py
src/foldeverything/data/sample/affinity_difference.py
src/foldeverything/data/sample/affinity_difference_K.py
src/foldeverything/data/sample/affinity_difference_neg.py
src/foldeverything/data/sample/affinity_difference_type.py
src/foldeverything/data/sample/affinity_difference_type_cluster.py
src/foldeverything/data/sample/cluster.py
src/foldeverything/data/sample/distillation.py
src/foldeverything/data/sample/sampler.py
src/foldeverything/data/sample_new/affinity.py
src/foldeverything/data/sample_new/affinity_cliffs.py
src/foldeverything/data/sample_new/affinity_decoy_id.py
src/foldeverything/data/sample_new/sampler.py
src/foldeverything/data/sample_new/sampler_wrapper.py
src/foldeverything/data/sample_new/sampler_wrapper_val.py
src/foldeverything/data/select/__init__.py
src/foldeverything/data/select/ligand_selector.py
src/foldeverything/data/select/protein.py
src/foldeverything/data/select/protein_new.py
src/foldeverything/data/select/selector.py
src/foldeverything/data/template/__init__.py
src/foldeverything/data/template/features.py
src/foldeverything/data/tokenize/__init__.py
src/foldeverything/data/tokenize/af3.py
src/foldeverything/data/tokenize/tokenizer.py
src/foldeverything/data/write/__init__.py
src/foldeverything/data/write/mmcif.py
src/foldeverything/data/write/mmcif_modelcif.py
src/foldeverything/data/write/pdb.py
src/foldeverything/data/write/utils.py
src/foldeverything/model/__init__.py
src/foldeverything/model/kernels/__init__.py
src/foldeverything/model/kernels/transition.py
src/foldeverything/model/layers/__init__.py
src/foldeverything/model/layers/attention.py
src/foldeverything/model/layers/axial.py
src/foldeverything/model/layers/axial_samples.py
src/foldeverything/model/layers/confidence_utils.py
src/foldeverything/model/layers/dropout.py
src/foldeverything/model/layers/initialize.py
src/foldeverything/model/layers/memory_utils.py
src/foldeverything/model/layers/miniformer.py
src/foldeverything/model/layers/outer_product_mean.py
src/foldeverything/model/layers/pair_averaging.py
src/foldeverything/model/layers/pairformer.py
src/foldeverything/model/layers/relative.py
src/foldeverything/model/layers/transition.py
src/foldeverything/model/layers/triangular.py
src/foldeverything/model/loss/__init__.py
src/foldeverything/model/loss/affinity.py
src/foldeverything/model/loss/alphaflow.py
src/foldeverything/model/loss/atom_type.py
src/foldeverything/model/loss/bfactor.py
src/foldeverything/model/loss/bond_len.py
src/foldeverything/model/loss/bond_type.py
src/foldeverything/model/loss/confidence.py
src/foldeverything/model/loss/diffusion.py
src/foldeverything/model/loss/distogram.py
src/foldeverything/model/loss/focal.py
src/foldeverything/model/loss/inference.py
src/foldeverything/model/loss/metrics.py
src/foldeverything/model/loss/pairtoken.py
src/foldeverything/model/loss/res_type.py
src/foldeverything/model/loss/tistogram.py
src/foldeverything/model/loss/validation.py
src/foldeverything/model/models/__init__.py
src/foldeverything/model/models/boltz.py
src/foldeverything/model/modules/__init__.py
src/foldeverything/model/modules/affinity.py
src/foldeverything/model/modules/affinity_jeremy_baseline.py
src/foldeverything/model/modules/affinity_ligand.py
src/foldeverything/model/modules/affinity_pair_inter.py
src/foldeverything/model/modules/affinity_pair_single.py
src/foldeverything/model/modules/affinity_pair_single_confidence.py
src/foldeverything/model/modules/affinity_pair_single_confidence_multiple.py
src/foldeverything/model/modules/affinity_single.py
src/foldeverything/model/modules/affinity_single_atom.py
src/foldeverything/model/modules/confidence.py
src/foldeverything/model/modules/diffusion.py
src/foldeverything/model/modules/diffusion_conditioning.py
src/foldeverything/model/modules/encoders.py
src/foldeverything/model/modules/inverse_fold.py
src/foldeverything/model/modules/masker.py
src/foldeverything/model/modules/transformers.py
src/foldeverything/model/modules/trunk.py
src/foldeverything/model/modules/utils.py
src/foldeverything/model/openfold/__init__.py
src/foldeverything/model/openfold/fast_primitives.py
src/foldeverything/model/openfold/fast_triangular_attention.py
src/foldeverything/model/openfold/openfold_utils.py
src/foldeverything/model/openfold/primitives.py
src/foldeverything/model/openfold/triangular_attention.py
src/foldeverything/model/optim/__init__.py
src/foldeverything/model/optim/ema.py
src/foldeverything/model/optim/scheduler.py
src/foldeverything/model/potentials/potentials.py
src/foldeverything/model/potentials/schedules.py
src/foldeverything/model/validation/affinity.py
src/foldeverything/model/validation/design.py
src/foldeverything/model/validation/md.py
src/foldeverything/model/validation/monomer_design.py
src/foldeverything/model/validation/rcsb.py
src/foldeverything/model/validation/validator.py
src/foldeverything/task/__init__.py
src/foldeverything/task/task.py
src/foldeverything/task/analyze/analyze.py
src/foldeverything/task/eval/__init__.py
src/foldeverything/task/eval/eval.py
src/foldeverything/task/eval/eval_folding.py
src/foldeverything/task/eval/archive/affinity.py
src/foldeverything/task/eval/archive/evaluate.py
src/foldeverything/task/eval/archive/qcp.py
src/foldeverything/task/eval/archive/utils.py
src/foldeverything/task/eval/archive/data/__init__.py
src/foldeverything/task/eval/archive/data/cameo.py
src/foldeverything/task/eval/archive/data/casp14.py
src/foldeverything/task/eval/archive/data/casp15.py
src/foldeverything/task/eval/archive/data/dataset.py
src/foldeverything/task/eval/archive/data/long.py
src/foldeverything/task/eval/archive/data/posebusters.py
src/foldeverything/task/eval/archive/metrics/__init__.py
src/foldeverything/task/eval/archive/metrics/codm.py
src/foldeverything/task/eval/archive/metrics/gdt.py
src/foldeverything/task/eval/archive/metrics/lddt.py
src/foldeverything/task/eval/archive/metrics/metric.py
src/foldeverything/task/eval/archive/metrics/plddt.py
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src/foldeverything/task/eval/archive/metrics/rna.py
src/foldeverything/task/eval/archive/metrics/tmscore.py
src/foldeverything/task/eval/archive/models/__init__.py
src/foldeverything/task/eval/archive/models/af2.py
src/foldeverything/task/eval/archive/models/model.py
src/foldeverything/task/eval/archive/models/omega.py
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src/foldeverything/task/eval/models/esm.py
src/foldeverything/task/filter/__init__.py
src/foldeverything/task/filter/filter.py
src/foldeverything/task/filter/seqplot_utils.py
src/foldeverything/task/hallucination/__init__.py
src/foldeverything/task/hallucination/binder_hallucinator.py
src/foldeverything/task/hallucination/coordinate_trajectory.py
src/foldeverything/task/hallucination/hallucination_task.py
src/foldeverything/task/hallucination/loss.py
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src/foldeverything/task/predict/__init__.py
src/foldeverything/task/predict/data.py
src/foldeverything/task/predict/data_affinity.py
src/foldeverything/task/predict/data_eval.py
src/foldeverything/task/predict/data_folding.py
src/foldeverything/task/predict/data_from_new_yaml.py
src/foldeverything/task/predict/data_from_yaml.py
src/foldeverything/task/predict/data_ligands.py
src/foldeverything/task/predict/data_peppc.py
src/foldeverything/task/predict/data_protein_binder.py
src/foldeverything/task/predict/data_scaffold_lab.py
src/foldeverything/task/predict/data_scaffolding.py
src/foldeverything/task/predict/data_unconditional.py
src/foldeverything/task/predict/predict.py
src/foldeverything/task/predict/writer.py
src/foldeverything/task/process/__init__.py
src/foldeverything/task/process/process.py
src/foldeverything/task/process/msa/IDRome.py
src/foldeverything/task/process/msa/__init__.py
src/foldeverything/task/process/msa/afdb.py
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src/foldeverything/task/process/msa/openfold.py
src/foldeverything/task/process/msa/pubchem.py
src/foldeverything/task/process/msa/rcsb.py
src/foldeverything/task/process/sequences/sequences.py
src/foldeverything/task/process/targets/__init__.py
src/foldeverything/task/process/targets/afdb.py
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src/foldeverything/task/process/targets/broad.py
src/foldeverything/task/process/targets/casp15.py
src/foldeverything/task/process/targets/casp15_seqs.py
src/foldeverything/task/process/targets/casp16_affinity.py
src/foldeverything/task/process/targets/fepp.py
src/foldeverything/task/process/targets/ligands.py
src/foldeverything/task/process/targets/manifest.py
src/foldeverything/task/process/targets/mcpcba.py
src/foldeverything/task/process/targets/openfold.py
src/foldeverything/task/process/targets/posebusters.py
src/foldeverything/task/process/targets/proteins.py
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src/foldeverything/task/process/targets/rcsb.py
src/foldeverything/task/process/targets/target.py
src/foldeverything/task/process/targets/test.py
src/foldeverything/task/process/targets/yamls.py
src/foldeverything/task/process/targets/MD/IDRome.py
src/foldeverything/task/process/targets/MD/MemProtMD.py
src/foldeverything/task/process/targets/MD/__init__.py
src/foldeverything/task/process/targets/MD/atlas.py
src/foldeverything/task/process/targets/MD/dynamicPDB.py
src/foldeverything/task/process/targets/MD/mdCATH.py
src/foldeverything/task/process/targets/MD/misato.py
src/foldeverything/task/process/templates/__init__.py
src/foldeverything/task/process/templates/template.py
src/foldeverything/task/process/templates/templatev2.py
src/foldeverything/task/train/__init__.py
src/foldeverything/task/train/data.py
src/foldeverything/task/train/train.py
src/foldeverything/utils/__init__.py
src/foldeverything/utils/iterator.py
src/foldeverything/utils/sasa_npy.py
src/foldeverything/utils/script.py
tests/test_axial.py
tests/test_ddp.py
tests/test_eval.py
tests/test_hallucination.py
tests/test_lr.py
tests/test_random.py
tests/test_speed.py
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tests/test_utils.py