├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── THIRD_PARTY_LICENSES ├── alignment ├── AlignSubPeptides.py ├── AlignUtils.py ├── ApiUtils.py ├── PyHELM_simple.py ├── ROCS ├── __init__.py ├── api.py ├── mafft │ ├── bin │ │ ├── einsi │ │ ├── fftns │ │ ├── fftnsi │ │ ├── ginsi │ │ ├── linsi │ │ ├── mafft │ │ ├── mafft-distance │ │ ├── mafft-einsi │ │ ├── mafft-fftns │ │ ├── mafft-fftnsi │ │ ├── mafft-ginsi │ │ ├── mafft-homologs.rb │ │ ├── mafft-linsi │ │ ├── mafft-nwns │ │ ├── mafft-nwnsi │ │ ├── mafft-profile │ │ ├── mafft-qinsi │ │ ├── mafft-sparsecore.rb │ │ ├── mafft-xinsi │ │ ├── nwns │ │ └── nwnsi │ ├── libexec │ │ └── mafft │ │ │ ├── addsingle │ │ │ ├── contrafoldwrap │ │ │ ├── countlen │ │ │ ├── disttbfast │ │ │ ├── dndblast │ │ │ ├── dndfast7 │ │ │ ├── dndpre │ │ │ ├── dvtditr │ │ │ ├── f2cl │ │ │ ├── getlag │ │ │ ├── hex2maffttext │ │ │ ├── mafft-distance │ │ │ ├── mafft-homologs.1 │ │ │ ├── mafft-profile │ │ │ ├── mafft.1 │ │ │ ├── mafftash_premafft.pl │ │ │ ├── maffttext2hex │ │ │ ├── makedirectionlist │ │ │ ├── mccaskillwrap │ │ │ ├── multi2hat3s │ │ │ ├── nodepair │ │ │ ├── pairash │ │ │ ├── pairlocalalign │ │ │ ├── regtable2seq │ │ │ ├── replaceu │ │ │ ├── restoreu │ │ │ ├── score │ │ │ ├── seekquencer_premafft.pl │ │ │ ├── seq2regtable │ │ │ ├── setcore │ │ │ ├── setdirection │ │ │ ├── sextet5 │ │ │ ├── splittbfast │ │ │ ├── tbfast │ │ │ └── version │ └── share │ │ └── man │ │ └── man1 │ │ ├── mafft-homologs.1 │ │ └── mafft.1 ├── mafft_manpage.txt ├── models.py ├── monomers_map.txt └── scoring │ ├── SCORING.md │ └── ScoringUtils.py ├── local.env ├── requirements.txt └── tests ├── .flake8 ├── .pylintrc └── unit_tests ├── environment.yml ├── resources ├── test_AlignSubPeptides │ ├── PEPTIDE1_SCORE_matrix.txt │ ├── ROCS │ ├── align_input.txt │ ├── align_output.json │ ├── for_scoring.txt │ ├── monomers_map.txt │ ├── new_sequences.txt │ ├── realign_output.json │ └── test_split_sub_peptides │ │ ├── example_PEPTIDE1_only_output.json │ │ ├── example_PEPTIDE2_only_output.json │ │ ├── example_all_peptides_output.json │ │ ├── example_input.txt │ │ ├── for_alignment1_CHEM1_only_output.json │ │ ├── for_alignment1_PEPTIDE1_only_output.json │ │ ├── for_alignment1_all_peptides_output.json │ │ ├── for_alignment1_input.txt │ │ ├── for_alignment2_PEPTIDE1_only_output.json │ │ ├── for_alignment2_all_peptides_output.json │ │ ├── for_alignment2_input.txt │ │ ├── for_alignment3_PEPTIDE1_only_output.json │ │ ├── for_alignment3_all_peptides_output.json │ │ ├── for_alignment3_input.txt │ │ ├── for_alignment_without_nh2_CHEM1_only_output.json │ │ ├── for_alignment_without_nh2_PEPTIDE1_only_output.json │ │ ├── for_alignment_without_nh2_all_peptides_output.json │ │ ├── for_alignment_without_nh2_input.txt │ │ ├── helmtest_CHEM1_only_output.json │ │ ├── helmtest_PEPTIDE1_only_output.json │ │ ├── helmtest_all_peptides_output.json │ │ ├── helmtest_input.txt │ │ ├── input_data_PEPTIDE1_only_output.json │ │ ├── input_data_all_peptides_output.json │ │ ├── input_data_input.txt │ │ ├── multi_chain_peps_PEPTIDE1_only_output.json │ │ ├── multi_chain_peps_PEPTIDE2_only_output.json │ │ ├── multi_chain_peps_PEPTIDE3_only_output.json │ │ ├── multi_chain_peps_all_peptides_output.json │ │ ├── multi_chain_peps_input.txt │ │ ├── multi_pep_chem_CHEM1_only_output.json │ │ ├── multi_pep_chem_CHEM2_only_output.json │ │ ├── multi_pep_chem_CHEM3_only_output.json │ │ ├── multi_pep_chem_PEPTIDE1_only_output.json │ │ ├── multi_pep_chem_PEPTIDE2_only_output.json │ │ ├── multi_pep_chem_all_peptides_output.json │ │ ├── multi_pep_chem_input.txt │ │ ├── test_data_PEPTIDE1_only_output.json │ │ ├── test_data_all_peptides_output.json │ │ └── test_data_input.txt ├── test_AlignUtils │ ├── CHEM1_EXPECTED_matrix.txt │ ├── CHEM1_TEST_mafft.txt │ ├── PEPTIDE1_EXPECTED_matrix.txt │ ├── PEPTIDE1_TEST_mafft.txt │ ├── PEPTIDE1_mafft_aligned.txt │ ├── ROCS │ ├── artificial_seqs.json │ ├── decode.json │ ├── input.json │ └── monomers_map.txt ├── test_ApiUtils │ ├── 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