.gitignore
LICENSE
README.md
pyproject.toml
run_igloo.py
train.py
trainer.py
utils.py
assets/igloo_logo.png
evals/eval_clusters.py
evals/eval_clusters.sh
example/igloolm_training_data_sample.parquet
example/sample_igloo_input.jsonl
example/sample_igloo_input.parquet
example/sample_igloo_input_sequence_only.csv
example/sample_igloo_sequences.csv
example/my_pdbs/10091.pdb
example/my_pdbs/11227.pdb
example/my_pdbs/11270.pdb
example/my_pdbs/1263.pdb
example/my_pdbs/18451.pdb
example/my_pdbs/18627.pdb
example/my_pdbs/4632.pdb
example/my_pdbs/580.pdb
example/my_pdbs/9649.pdb
example/my_pdbs/9661.pdb
finetune_igbert/README.md
finetune_igbert/__init__.py
finetune_igbert/add_loops_to_data.py
finetune_igbert/constants.py
finetune_igbert/custom_data_collator.py
finetune_igbert/embedding_model.py
finetune_igbert/eval_masking.py
finetune_igbert/inference.py
finetune_igbert/process_data.py
finetune_igbert/sample_cdrs.py
finetune_igbert/train.py
finetune_igbert/train_igbert.py
finetune_igbert/train_with_hf_trainer.py
finetune_igbert/__pycache__/custom_data_collator.cpython-311.pyc
finetune_igbert/__pycache__/model.cpython-311.pyc
finetune_igbert/__pycache__/models.cpython-311.pyc
finetune_igbert/__pycache__/process_data.cpython-311.pyc
model/__init__.py
model/align_loops.py
model/dataset.py
model/metrics.py
model/modules.py
model/multihead_attention.py
model/rotary_embedding.py
model/transformer_stack.py
model/vqvae.py
model/vqvae_length_dependent.py
paper_analyses/0_baselines/run_ablang2.py
paper_analyses/0_baselines/run_ablang2_subsequence.py
paper_analyses/0_baselines/run_aminoaseed.py
paper_analyses/0_baselines/run_baselines.py
paper_analyses/0_baselines/run_esm2.py
paper_analyses/0_baselines/run_esm2_subsequence.py
paper_analyses/0_baselines/run_esmc.py
paper_analyses/0_baselines/run_foldseek3di.py
paper_analyses/0_baselines/run_igbert.py
paper_analyses/0_baselines/run_prostt5.py
paper_analyses/0_baselines/run_prostt5_subsequence.py
paper_analyses/0_baselines/run_saprot.py
paper_analyses/0_baselines/run_saprot_subsequence.py
paper_analyses/1_recovery_of_canonical_clusters/recovery_of_canonical_clusters.ipynb
paper_analyses/1_recovery_of_canonical_clusters/recovery_of_canonical_clusters_test_set.ipynb
paper_analyses/1_recovery_of_canonical_clusters/visualize_loops.ipynb
paper_analyses/2_retrieve_similar_loops/sabdab_test_set.ipynb
paper_analyses/3_abbibench/AbiBench.ipynb
paper_analyses/3_abbibench/ridge_regression_task.py
paper_analyses/3_abbibench/run_abbibench.py
paper_analyses/4_sampled_cdrs/analyse_sampled_cdrs.ipynb
paper_analyses/4_sampled_cdrs/run_rmsd_calculation.py
paper_analyses/5_umap/plot_umap.ipynb
paper_analyses/5_umap/plot_umap.py
paper_analyses/5_umap/umap_20_0.5_canonical_cluster.png
paper_analyses/5_umap/umap_20_0.5_loop_length.png
paper_analyses/5_umap/umap_20_0.5_loop_type.png
prescient_igloo.egg-info/PKG-INFO
prescient_igloo.egg-info/SOURCES.txt
prescient_igloo.egg-info/dependency_links.txt
prescient_igloo.egg-info/requires.txt
prescient_igloo.egg-info/top_level.txt
process_data/0_process_annotate_sabdab_data.py
process_data/1_load_extract_loops.py
process_data/2_extract_chains.py
process_data/3_assign_canonical_Kelow_cluster.py
process_data/4a_prepare_mmseq.py
process_data/4b_prepare_mmseq_cdr_only.py
process_data/5_split_data.py
process_data/Kelow_cluster_center_dihedrals.parquet
process_data/biotoolkit.py
process_data/process_dihedrals.py
process_data/process_sabdab.sh