MANIFEST.in
README.md
requirements.txt
setup.py
settmhc/MHC_pseudo.dat
settmhc/__init__.py
settmhc/cnn_model.py
settmhc/fusion_model.py
settmhc/hparams.yaml
settmhc/preprocess.py
settmhc/pshm.py
settmhc/rnn_model.py
settmhc/settmhc_main.py
settmhc/structure_modeling.py
settmhc/supported_alleles.txt
settmhc/templates.txt
settmhc/utils.py
settmhc.egg-info/PKG-INFO
settmhc.egg-info/SOURCES.txt
settmhc.egg-info/dependency_links.txt
settmhc.egg-info/entry_points.txt
settmhc.egg-info/requires.txt
settmhc.egg-info/top_level.txt
settmhc/APE-Gen/APE_Gen.py
settmhc/APE-Gen/APE_Gen_IO.py
settmhc/APE-Gen/README.md
settmhc/APE-Gen/__init__.py
settmhc/APE-Gen/align.py
settmhc/APE-Gen/dunbrack.bin
settmhc/APE-Gen/example.ipynb
settmhc/APE-Gen/flex_res.txt
settmhc/APE-Gen/flex_res.txt.orig
settmhc/APE-Gen/get_pMHC_pdb.py
settmhc/APE-Gen/loco.score
settmhc/APE-Gen/minimize.py
settmhc/APE-Gen/model_receptor.py
settmhc/APE-Gen/mutate.py
settmhc/APE-Gen/n-mer-templates.txt
settmhc/APE-Gen/receptor-class-templates.backup.txt
settmhc/APE-Gen/receptor-class-templates.txt
settmhc/APE-Gen/rename_atoms.py
settmhc/APE-Gen/supertype_templates.csv
settmhc/APE-Gen/templates/1DUZ.pdb
settmhc/APE-Gen/templates/1LP9.pdb
settmhc/APE-Gen/templates/1N2R.pdb
settmhc/APE-Gen/templates/1i4f.pdb
settmhc/APE-Gen/templates/1xh3.pdb
settmhc/APE-Gen/templates/2RFX.pdb
settmhc/APE-Gen/templates/2XPG.pdb
settmhc/APE-Gen/templates/2YPL.pdb
settmhc/APE-Gen/templates/2ak4.pdb
settmhc/APE-Gen/templates/2nw3.pdb
settmhc/APE-Gen/templates/2vaa.pdb
settmhc/APE-Gen/templates/3BO8.pdb
settmhc/APE-Gen/templates/3I6L.pdb
settmhc/APE-Gen/templates/3OX8.pdb
settmhc/APE-Gen/templates/3OXS.pdb
settmhc/APE-Gen/templates/3WL9.pdb
settmhc/APE-Gen/templates/3bw9.pdb
settmhc/APE-Gen/templates/3vfv.pdb
settmhc/APE-Gen/templates/4MJI.pdb
settmhc/APE-Gen/templates/4NT6.pdb
settmhc/APE-Gen/templates/4no0.pdb
settmhc/APE-Gen/templates/4u6y.pdb
settmhc/APE-Gen/templates/5BRZ.pdb
settmhc/APE-Gen/templates/5WJN.pdb
settmhc/APE-Gen/templates/5XOT.pdb
settmhc/APE-Gen/templates/5XOV.pdb
settmhc/APE-Gen/templates/5ddh.pdb
settmhc/APE-Gen/templates/5wwi.pdb
settmhc/APE-Gen/templates/A0101.pdb
settmhc/APE-Gen/templates/A0201-from3I6L.pdb
settmhc/APE-Gen/templates/A0201.pdb
settmhc/APE-Gen/templates/A0202.pdb
settmhc/APE-Gen/templates/A0203.pdb
settmhc/APE-Gen/templates/A0205.pdb
settmhc/APE-Gen/templates/A0206.pdb
settmhc/APE-Gen/templates/A0301.pdb
settmhc/APE-Gen/templates/A1101.pdb
settmhc/APE-Gen/templates/A1102.pdb
settmhc/APE-Gen/templates/A2301.pdb
settmhc/APE-Gen/templates/A2402-from1DUZ.pdb
settmhc/APE-Gen/templates/A2402.pdb
settmhc/APE-Gen/templates/A2403.pdb
settmhc/APE-Gen/templates/A2501.pdb
settmhc/APE-Gen/templates/A2601.pdb
settmhc/APE-Gen/templates/A2901-from1DUZ.pdb
settmhc/APE-Gen/templates/A2901.pdb
settmhc/APE-Gen/templates/A2902.pdb
settmhc/APE-Gen/templates/A3001.pdb
settmhc/APE-Gen/templates/A3002.pdb
settmhc/APE-Gen/templates/A3101.pdb
settmhc/APE-Gen/templates/A3201.pdb
settmhc/APE-Gen/templates/A3301.pdb
settmhc/APE-Gen/templates/A3303-from1DUZ.pdb
settmhc/APE-Gen/templates/A3303.pdb
settmhc/APE-Gen/templates/A3401.pdb
settmhc/APE-Gen/templates/A3402.pdb
settmhc/APE-Gen/templates/A3601.pdb
settmhc/APE-Gen/templates/A4301.pdb
settmhc/APE-Gen/templates/A6601.pdb
settmhc/APE-Gen/templates/A6602.pdb
settmhc/APE-Gen/templates/A6801.pdb
settmhc/APE-Gen/templates/A6802.pdb
settmhc/APE-Gen/templates/A6901.pdb
settmhc/APE-Gen/templates/A7401.pdb
settmhc/APE-Gen/templates/A8001.pdb
settmhc/APE-Gen/templates/B0702.pdb
settmhc/APE-Gen/templates/B0703.pdb
settmhc/APE-Gen/templates/B0801.pdb
settmhc/APE-Gen/templates/B1301.pdb
settmhc/APE-Gen/templates/B1302.pdb
settmhc/APE-Gen/templates/B1401.pdb
settmhc/APE-Gen/templates/B1402.pdb
settmhc/APE-Gen/templates/B1501.pdb
settmhc/APE-Gen/templates/B1502.pdb
settmhc/APE-Gen/templates/B1503.pdb
settmhc/APE-Gen/templates/B1508-from5XOT.pdb
settmhc/APE-Gen/templates/B1510-from5XOT.pdb
settmhc/APE-Gen/templates/B1510.pdb
settmhc/APE-Gen/templates/B1511.pdb
settmhc/APE-Gen/templates/B1512.pdb
settmhc/APE-Gen/templates/B1513.pdb
settmhc/APE-Gen/templates/B1516-from5XOT.pdb
settmhc/APE-Gen/templates/B1516.pdb
settmhc/APE-Gen/templates/B1518.pdb
settmhc/APE-Gen/templates/B1801.pdb
settmhc/APE-Gen/templates/B2703.pdb
settmhc/APE-Gen/templates/B2705.pdb
settmhc/APE-Gen/templates/B2708.pdb
settmhc/APE-Gen/templates/B3501.pdb
settmhc/APE-Gen/templates/B3508.pdb
settmhc/APE-Gen/templates/B3701.pdb
settmhc/APE-Gen/templates/B3801.pdb
settmhc/APE-Gen/templates/B3901.pdb
settmhc/APE-Gen/templates/B4001.pdb
settmhc/APE-Gen/templates/B4002.pdb
settmhc/APE-Gen/templates/B4006.pdb
settmhc/APE-Gen/templates/B4101.pdb
settmhc/APE-Gen/templates/B4201.pdb
settmhc/APE-Gen/templates/B4402.pdb
settmhc/APE-Gen/templates/B4403.pdb
settmhc/APE-Gen/templates/B4405-from5XOT.pdb
settmhc/APE-Gen/templates/B4501.pdb
settmhc/APE-Gen/templates/B4601.pdb
settmhc/APE-Gen/templates/B4701.pdb
settmhc/APE-Gen/templates/B4801.pdb
settmhc/APE-Gen/templates/B4901.pdb
settmhc/APE-Gen/templates/B5001.pdb
settmhc/APE-Gen/templates/B5101.pdb
settmhc/APE-Gen/templates/B5102.pdb
settmhc/APE-Gen/templates/B5201.pdb
settmhc/APE-Gen/templates/B5301.pdb
settmhc/APE-Gen/templates/B5401.pdb
settmhc/APE-Gen/templates/B5501.pdb
settmhc/APE-Gen/templates/B5502-from5XOT.pdb
settmhc/APE-Gen/templates/B5601.pdb
settmhc/APE-Gen/templates/B5701.pdb
settmhc/APE-Gen/templates/B5703.pdb
settmhc/APE-Gen/templates/B5801.pdb
settmhc/APE-Gen/templates/B5901.pdb
settmhc/APE-Gen/templates/B6701.pdb
settmhc/APE-Gen/templates/B7301.pdb
settmhc/APE-Gen/templates/B7801.pdb
settmhc/APE-Gen/templates/B8101.pdb
settmhc/APE-Gen/templates/B8201.pdb
settmhc/APE-Gen/templates/C0102.pdb
settmhc/APE-Gen/templates/C0202.pdb
settmhc/APE-Gen/templates/C0302.pdb
settmhc/APE-Gen/templates/C0303.pdb
settmhc/APE-Gen/templates/C0304.pdb
settmhc/APE-Gen/templates/C0401.pdb
settmhc/APE-Gen/templates/C0403.pdb
settmhc/APE-Gen/templates/C0501.pdb
settmhc/APE-Gen/templates/C0602.pdb
settmhc/APE-Gen/templates/C0702.pdb
settmhc/APE-Gen/templates/C0801.pdb
settmhc/APE-Gen/templates/C0802.pdb
settmhc/APE-Gen/templates/C1202.pdb
settmhc/APE-Gen/templates/C1203.pdb
settmhc/APE-Gen/templates/C1402.pdb
settmhc/APE-Gen/templates/C1502.pdb
settmhc/APE-Gen/templates/C1601.pdb
settmhc/APE-Gen/templates/C1701.pdb
settmhc/APE-Gen/templates/C1802.pdb
settmhc/APE-Gen/templates/best_model.pdb
settmhc/mhc-pep-threader/README.md
settmhc/mhc-pep-threader/__init__.py
settmhc/mhc-pep-threader/compute_rmsd_ia.py
settmhc/mhc-pep-threader/main.py
settmhc/mhc-pep-threader/model.py
settmhc/mhc-pep-threader/production.RosettaMHC.job
settmhc/mhc-pep-threader/submit_jobs.sh
settmhc/mhc-pep-threader/__pycache__/model.cpython-38.pyc
settmhc/mhc-pep-threader/alignment/align.py
settmhc/mhc-pep-threader/alignment/grishin.py
settmhc/mhc-pep-threader/alignment/substitution_matrix.py
settmhc/mhc-pep-threader/alignment/__pycache__/align.cpython-38.pyc
settmhc/mhc-pep-threader/alignment/__pycache__/grishin.cpython-38.pyc
settmhc/mhc-pep-threader/alignment/__pycache__/substitution_matrix.cpython-38.pyc
settmhc/mhc-pep-threader/covid_scripts/identify_common_cold_peps.py
settmhc/mhc-pep-threader/covid_scripts/simple_sliding_window_epitope_creator.py
settmhc/mhc-pep-threader/database/HLA_sequences_180.py
settmhc/mhc-pep-threader/database/HLA_sequences_complex.py
settmhc/mhc-pep-threader/database/beta2m_sequences.py
settmhc/mhc-pep-threader/database/chaperone_sequences.py
settmhc/mhc-pep-threader/database/__pycache__/HLA_sequences_180.cpython-38.pyc
settmhc/mhc-pep-threader/database/__pycache__/HLA_sequences_complex.cpython-38.pyc
settmhc/mhc-pep-threader/database/__pycache__/beta2m_sequences.cpython-38.pyc
settmhc/mhc-pep-threader/database/__pycache__/chaperone_sequences.cpython-38.pyc
settmhc/mhc-pep-threader/ia/call_ia.py
settmhc/mhc-pep-threader/ia/chain_split.py
settmhc/mhc-pep-threader/ia/interface_analyzer.py
settmhc/mhc-pep-threader/ia/__pycache__/chain_split.cpython-38.pyc
settmhc/mhc-pep-threader/ia/__pycache__/interface_analyzer.cpython-38.pyc
settmhc/mhc-pep-threader/idealize_relax/create_movemap.py
settmhc/mhc-pep-threader/idealize_relax/idealize.py
settmhc/mhc-pep-threader/idealize_relax/movemap.py
settmhc/mhc-pep-threader/idealize_relax/relax.py
settmhc/mhc-pep-threader/idealize_relax/__pycache__/idealize.cpython-38.pyc
settmhc/mhc-pep-threader/idealize_relax/__pycache__/movemap.cpython-38.pyc
settmhc/mhc-pep-threader/idealize_relax/__pycache__/relax.cpython-38.pyc
settmhc/mhc-pep-threader/input_output/input/argparser.py
settmhc/mhc-pep-threader/input_output/input/beta2m.py
settmhc/mhc-pep-threader/input_output/input/chaperone.py
settmhc/mhc-pep-threader/input_output/input/header_readers.py
settmhc/mhc-pep-threader/input_output/input/mhc.py
settmhc/mhc-pep-threader/input_output/input/peptides.py
settmhc/mhc-pep-threader/input_output/input/tcr.py
settmhc/mhc-pep-threader/input_output/input/__pycache__/argparser.cpython-38.pyc
settmhc/mhc-pep-threader/input_output/input/__pycache__/beta2m.cpython-38.pyc
settmhc/mhc-pep-threader/input_output/input/__pycache__/chaperone.cpython-38.pyc
settmhc/mhc-pep-threader/input_output/input/__pycache__/header_readers.cpython-38.pyc
settmhc/mhc-pep-threader/input_output/input/__pycache__/mhc.cpython-38.pyc
settmhc/mhc-pep-threader/input_output/input/__pycache__/peptides.cpython-38.pyc
settmhc/mhc-pep-threader/input_output/input/__pycache__/tcr.cpython-38.pyc
settmhc/mhc-pep-threader/input_output/output/output_interface_energies.py
settmhc/mhc-pep-threader/input_output/output/__pycache__/output_interface_energies.cpython-38.pyc
settmhc/mhc-pep-threader/jd/job_distributor.py
settmhc/mhc-pep-threader/jd/__pycache__/job_distributor.cpython-38.pyc
settmhc/mhc-pep-threader/scoring/compute_rmsds.py
settmhc/mhc-pep-threader/scoring/rmsd.py
settmhc/mhc-pep-threader/scoring/__pycache__/rmsd.cpython-38.pyc
settmhc/mhc-pep-threader/thread/fasta.py
settmhc/mhc-pep-threader/thread/post_thread.py
settmhc/mhc-pep-threader/thread/pre_thread.py
settmhc/mhc-pep-threader/thread/template.py
settmhc/mhc-pep-threader/thread/thread.py
settmhc/mhc-pep-threader/thread/__pycache__/fasta.cpython-38.pyc
settmhc/mhc-pep-threader/thread/__pycache__/post_thread.cpython-38.pyc
settmhc/mhc-pep-threader/thread/__pycache__/pre_thread.cpython-38.pyc
settmhc/mhc-pep-threader/thread/__pycache__/template.cpython-38.pyc
settmhc/mhc-pep-threader/thread/__pycache__/thread.cpython-38.pyc
settmhc/mhc-pep-threader/util/custom_pdb.py
settmhc/mhc-pep-threader/util/__pycache__/custom_pdb.cpython-38.pyc