├── .github └── workflows │ ├── deploy-mkdocs.yml │ ├── publish-python-package.yml │ └── test-python-package.yml ├── .gitignore ├── Dockerfile ├── LICENSE.md ├── Makefile ├── README.md ├── SSDraw.ipynb ├── docs ├── commands │ ├── multi.md │ └── single.md ├── getting-started.md ├── index.md └── troubleshooting.md ├── examples ├── 1ndd.fasta ├── 1ndd.pdb ├── 2kdl.fasta ├── 2kdl.pdb ├── 2kdl_scoring.txt ├── 2n1v.fasta ├── 2n1v.pdb ├── 2n1v_nscores.txt ├── aligned.fasta ├── example_run.txt └── run_examples.sh ├── figures ├── GA-GB │ ├── input │ │ ├── 2kdl.pdb │ │ ├── 2kdm.pdb │ │ ├── 2lhc.pdb │ │ ├── 2lhd.pdb │ │ ├── 2lhe.pdb │ │ ├── 2lhg.pdb │ │ ├── rcsb_pdb_2KDL.fasta │ │ ├── rcsb_pdb_2KDM.fasta │ │ ├── rcsb_pdb_2LHC.fasta │ │ ├── rcsb_pdb_2LHD.fasta │ │ ├── rcsb_pdb_2LHE.fasta │ │ ├── rcsb_pdb_2LHG.fasta │ │ └── scoring_files │ │ │ ├── 2kdl_scoring.txt │ │ │ ├── 2kdm_scoring.txt │ │ │ ├── 2lhc_scoring.txt │ │ │ ├── 2lhd_scoring.txt │ │ │ ├── 2lhd_scoring.txt~ │ │ │ ├── 2lhe_scoring.txt │ │ │ ├── 2lhg_scoring.txt │ │ │ └── 2lhg_scoring.txt~ │ └── run_ssdraw.sh ├── NusG │ ├── 5ond.fasta │ ├── 5ond.pdb │ ├── 5ond_gaps.fasta │ ├── 5ond_gaps.fasta~ │ ├── 6ztj.cif │ ├── NusG.horiz │ ├── NusG.horiz~ │ ├── NusG.pdb │ ├── RfaH_NusG_align.pse │ ├── RfaH_alignment.fasta │ ├── RfaH_alignment.fasta~ │ ├── make_figure3.sh │ └── make_figure3.sh~ ├── Response_regulators │ ├── 1p2f.fasta │ ├── 1p2f_bfac.pdb │ ├── 4kfc.fasta │ ├── 4kfc_bfac.pdb │ ├── 4kfc_score.txt │ ├── 5XSO_4KFC_alignment.fa │ ├── 5xso.fasta │ ├── 5xso.fasta~ │ ├── 5xso_bfac.pdb │ ├── 5xso_score.txt │ ├── make_fig1.sh │ ├── make_fig1.sh~ │ ├── make_scoring_file.py │ ├── make_scoring_file.py~ │ └── unique_RR_structures_aligned_072122.fasta ├── draw_all_figures.sh ├── ubiquitin │ ├── input │ │ ├── 1ndd.pdb │ │ ├── 1oqy.pdb │ │ ├── 1p1a.pdb │ │ ├── 1ubq.pdb │ │ ├── 1vcb.pdb │ │ ├── 1wh3.pdb │ │ ├── 1wx9.pdb │ │ ├── 1yqb.pdb │ │ ├── 1z2m.pdb │ │ ├── 2bwf.pdb │ │ ├── 2dzi.pdb │ │ ├── 2l7r.pdb │ │ ├── 2n1v.pdb │ │ ├── 4k95.pdb │ │ └── aligned.fasta │ └── run_ssdraw.sh └── workflow │ ├── input │ ├── 2n1v.pdb │ └── aligned.fasta │ └── run_ssdraw.sh ├── imgs ├── 1ndd_bfactor.png ├── 1ndd_conservation.png ├── 1ndd_out.png ├── 2kdl_out.png └── 2n1v_consurf.png ├── mkdocs.yml ├── pyproject.toml ├── requirements.txt ├── scripts └── generate_docs.py ├── site ├── 404.html ├── commands │ ├── multi │ │ └── index.html │ └── single │ │ └── index.html ├── css │ ├── fonts │ │ ├── Roboto-Slab-Bold.woff │ │ ├── Roboto-Slab-Bold.woff2 │ │ ├── Roboto-Slab-Regular.woff │ │ ├── Roboto-Slab-Regular.woff2 │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ ├── lato-bold-italic.woff │ │ ├── lato-bold-italic.woff2 │ │ ├── lato-bold.woff │ │ ├── lato-bold.woff2 │ │ ├── lato-normal-italic.woff │ │ ├── lato-normal-italic.woff2 │ │ ├── lato-normal.woff │ │ └── lato-normal.woff2 │ ├── theme.css │ └── theme_extra.css ├── getting-started │ └── 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