.gitignore
CHANGELOG.md
CITATION.cff
LICENSE
README.md
TRAINING.md
main_finetune_ted.py
main_linprobe_ted.py
main_pretrain.py
main_test_ted.py
pyproject.toml
requirements.txt
.github/workflows/ci.yml
.github/workflows/publish.yml
TEDBench.egg-info/PKG-INFO
TEDBench.egg-info/SOURCES.txt
TEDBench.egg-info/dependency_links.txt
TEDBench.egg-info/requires.txt
TEDBench.egg-info/top_level.txt
baselines/esm2_finetune_ted.py
baselines/esm2_linprobe_ted.py
baselines/esm2_test_ted.py
baselines/proteinmpnn_linprobe_ted.py
baselines/saprot_finetune_ted.py
baselines/saprot_linprobe_ted.py
baselines/saprot_test_ted.py
baselines/configs/esm2_finetune_ted.yaml
baselines/configs/esm2_linprobe_ted.yaml
baselines/configs/proteinmpnn_linprobe_ted.yaml
baselines/configs/saprot_finetune_ted.yaml
baselines/configs/saprot_linprobe_ted.yaml
baselines/configs/datamodule/afdbfs_ted.yaml
baselines/models/esm2_classifier.py
baselines/models/proteinmpnn_utils.py
baselines/models/saprot_classifier.py
baselines/models/structure_models.py
baselines/saprot/LICENSE
baselines/saprot/README.md
baselines/saprot/__init__.py
baselines/saprot/model/abstract_model.py
baselines/saprot/model/saprot/base.py
baselines/saprot/utils/__init__.py
baselines/saprot/utils/constants.py
baselines/saprot/utils/esm_loader.py
baselines/saprot/utils/foldseek_util.py
baselines/saprot/utils/lr_scheduler.py
configs/finetune_ted.yaml
configs/linprobe_ted.yaml
configs/pretrain.yaml
configs/test_ted.yaml
configs/datamodule/afdbfs.yaml
configs/datamodule/afdbfs_stream.yaml
configs/datamodule/afdbfs_ted.yaml
configs/datamodule/cath_test.yaml
configs/datamodule/hf_afdbfs.yaml
configs/datamodule/hf_cath_test.yaml
configs/datamodule/hf_ted.yaml
configs/experiment/finetune_ted_base.yaml
configs/experiment/finetune_ted_base_n1g8.yaml
configs/experiment/scratch_ted_base.yaml
configs/experiment/scratch_ted_base_n1g8.yaml
configs/experiment/tedbench_base.yaml
configs/experiment/tedbench_base_n4g8.yaml
configs/mode/debug.yaml
configs/mode/default.yaml
minesm/__init__.py
minesm/layers/__init__.py
minesm/layers/attention.py
minesm/layers/blocks.py
minesm/layers/geom_attention.py
minesm/layers/geometric_attn.py
minesm/layers/rotary.py
minesm/layers/structure_proj.py
minesm/layers/transformer_stack.py
minesm/models/__init__.py
minesm/models/vqvae.py
minesm/tokenization/__init__.py
minesm/tokenization/sequence_tokenizer.py
minesm/tokenization/tokenizer_base.py
minesm/utils/__init__.py
minesm/utils/misc.py
minesm/utils/residue_constants.py
minesm/utils/types.py
minesm/utils/constants/__init__.py
minesm/utils/constants/esm3.py
minesm/utils/constants/physics.py
minesm/utils/structure/__init__.py
minesm/utils/structure/affine3d.py
minesm/utils/structure/aligner.py
minesm/utils/structure/metrics.py
minesm/utils/structure/normalize_coordinates.py
minesm/utils/structure/protein_chain.py
minesm/utils/structure/protein_structure.py
resources/tedbench_logo.png
resources/tedbench_logo_transp.png
tedbench/__init__.py
tedbench/_version.py
tedbench/lr_schedulers.py
tedbench/py.typed
tedbench/data/__init__.py
tedbench/data/abstract.py
tedbench/data/afdb.py
tedbench/data/afdb_ted.py
tedbench/data/cath_test.py
tedbench/data/datasets.py
tedbench/data/hf_datasets.py
tedbench/data/transform.py
tedbench/layer/__init__.py
tedbench/layer/head.py
tedbench/layer/pos_embed.py
tedbench/model/__init__.py
tedbench/model/encoder.py
tedbench/model/fot.py
tedbench/model/loss.py
tedbench/model/mae.py
tedbench/model/metrics.py
tedbench/model/pl_engine.py
tedbench/utils/__init__.py
tedbench/utils/io.py
tedbench/utils/lars.py
tedbench/utils/linear_clf.py
tedbench/utils/tensor_utils.py