.gitignore

.DS_Store
.idea/

# Python cache
__pycache__/
*.py[cod]
.ipynb_checkpoints/

# Generated figures and reports
*.png
*.pdf
!docs/assets/readme/*.png

# Local result/features/model artifacts
/Results/
/esm2_t36_3B_UR50D_embeddings_ptm/
/data/*
!/data/README.md
!/data/*.tar.gz
/mutation_result_reclip*/
/mutation_result_mint_global_embed/
/mutation_result_mint_pair_embed/
/peptide_result_reclip/
/peptide_result_mint_cross_attn/
/peptide_result_mint_pair_embed/
/ptm_result_reclip/
/classI_result_reclip/
/swing-github-code/
/mint/
/analyse/
/ukbb/

# Local data/model assets not included in the repo
/data/ClassI_Model/
/data/ClassII_Model/
/data/MixedClass_Model/
/data/__MACOSX/
/data/manuscript_files/
/data/four_classes_mutation/alpha_missense_data/
/data/mutation_data/
/data/mutation_data.zip
/data/ptm/_label_fix_backups/
/data/ptm/PrimateAI/
/data/ptm/alpha_missense_data/

# Local Codex workspace artifacts
/.codex
/.codex_backups/

# Runtime outputs under scripts
scripts/**/__pycache__/
scripts/**/logs/
scripts/**/snapshots/
scripts/**/output/
scripts/**/outputs/
scripts/**/figures/
scripts/**/figures2/
scripts/**/figures3/
scripts/**/checkpoints/
scripts/**/_tmp*
scripts/**/*.model
scripts/**/*.npy
scripts/**/*.npz
scripts/**/*.pkl
scripts/**/*.pt
scripts/**/*.pth
scripts/**/*.ckpt
scripts/**/*.bin
scripts/**/*.arrow
scripts/**/*.log
scripts/**/*.pid
scripts/**/*status.json
scripts/**/notebook_outputs/
scripts/**/outputs_prelabelfix/

# Manuscript task benchmark plotting bundles withheld during revision
/scripts/four_classes_mutation/figure_plot/
/scripts/ptm/figure_plot/
/scripts/peptide/figure_plot/
/scripts/ablation/data/
/scripts/ablation/notebooks/
/scripts/ablation/outputs/
/scripts/ablation/runs/
scripts/four_classes_mutation/ReCLIP/results/
scripts/ptm/ReCLIP/results/
scripts/peptide/ReCLIP/results/

# Local exploratory code/results not intended for release
scripts/ptm/self_attention/
scripts/*/per_head_attention/
scripts/*/SWING/ablation/
scripts/ptm/mint_partner_feature/
scripts/suppplement_figure/
scripts/four_classes_mutation/figure_plot/binary classification/
scripts/peptide/*.sh

# Local experiment notes not intended for release
/PTM_RANDOM_TOPK_AND_EMBEDDING_SIMILARITY_CONTEXT.md
/PTM_VALIDATION_EXPERIMENTS_README.md

# BERT run artifacts
scripts/peptide/bert/BERTiLM/BERTiLM/peptide_bert_runs/

# Baseline raw data kept locally
scripts/*/PrimateAI/*.csv

# Large local new_analyse data files
/new_analyse/allset_self_attn_3d_distances_out.tsv
/new_analyse/allset_self_attn_same_interval_domain_visual_new_method/sample_stats.tsv
/new_analyse/functional_site_3d_top5_mutated_vs_random5_new_method/position_level.tsv
/new_analyse/reclip_results/mutation_reclip_mintpartnerL32_L32_hall_flatten_context_ln_k5_self_attention_rank_table.tsv
/new_analyse/reclip_results/mutation_reclip_mintpartnerL32_L32_hall_flatten_context_ln_k5_self_attention_rank_table_only_our_right_no_0_subset.tsv
analysis/