├── .codecov.yml ├── .gitattributes ├── .github ├── FUNDING.yml └── workflows │ └── main.yml ├── .gitignore ├── .readthedocs.yml ├── .scrutinizer.yml ├── .travis.yml ├── CHANGELOG.md ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.md ├── U6MolCell ├── Figure5b.r2r_results │ ├── u6-only.stk │ └── u6_R2R.pdf ├── Figure5f.energy_calculations │ ├── free-energies-used-for-the-plot.csv │ ├── group two introns free energies │ │ ├── gii_dv_mini-gii3shift-upper-loop-guaa-lower-loop-guaa-flanks-GC.csv │ │ ├── gii_dv_mini-gii3shift-upper-loop-guaa-lower-loop-guaa-flanks-GC.png │ │ └── gii_dv_mini.stk │ ├── src │ │ └── calc-energy2.py │ ├── u6 representatives free energies │ │ └── u6evo-seq-ss-groups-3x3-GC.csv │ └── yeast u6 mutants free energies │ │ ├── energies.csv │ │ ├── energies.txt │ │ └── seq-energies.txt ├── README.md ├── alignments │ ├── Intron_gpII_RF00029.stockholm.sto │ ├── U6_RF00026.stockholm.sto │ └── U6atac_minor_RF00619.stockholm.sto ├── example │ ├── A83g.fa │ ├── U64c+A83g.fa │ ├── U64c.fa │ └── wt.fa └── figure.png ├── __init__.py ├── docs ├── CONTRIBUTING.md ├── Gruntfile.js ├── LICENSE ├── Makefile ├── README.md ├── README.rst ├── bower.json ├── css │ ├── print │ │ ├── paper.css │ │ └── pdf.css │ ├── reveal.css │ ├── reveal.scss │ └── theme │ │ ├── README.md │ │ ├── beige.css │ │ ├── black.css │ │ ├── blood.css │ │ ├── league.css │ │ ├── moon.css │ │ ├── night.css │ │ ├── serif.css │ │ ├── simple.css │ │ ├── sky.css │ │ ├── solarized.css │ │ ├── source │ │ ├── beige.scss │ │ ├── black.scss │ │ ├── blood.scss │ │ ├── league.scss │ │ ├── moon.scss │ │ ├── night.scss │ │ ├── serif.scss │ │ ├── simple.scss │ │ ├── sky.scss │ │ ├── solarized.scss │ │ └── white.scss │ │ ├── template │ │ ├── mixins.scss │ │ ├── settings.scss │ │ └── theme.scss │ │ └── white.css ├── docs_requirements_py2.txt ├── env.yml ├── index.html ├── js │ └── reveal.js ├── lib │ ├── css │ │ └── zenburn.css │ ├── font │ │ ├── league-gothic │ │ │ ├── LICENSE │ │ │ ├── league-gothic.css │ │ │ ├── league-gothic.eot │ │ │ ├── league-gothic.ttf │ │ │ └── league-gothic.woff │ │ └── source-sans-pro │ │ │ ├── LICENSE │ │ │ ├── source-sans-pro-italic.eot │ │ │ ├── source-sans-pro-italic.ttf │ │ │ ├── source-sans-pro-italic.woff │ │ │ ├── source-sans-pro-regular.eot │ │ │ ├── source-sans-pro-regular.ttf │ │ │ ├── source-sans-pro-regular.woff │ │ │ ├── source-sans-pro-semibold.eot │ │ │ ├── source-sans-pro-semibold.ttf │ │ │ ├── source-sans-pro-semibold.woff │ │ │ ├── source-sans-pro-semibolditalic.eot │ │ │ ├── source-sans-pro-semibolditalic.ttf │ │ │ ├── source-sans-pro-semibolditalic.woff │ │ │ └── source-sans-pro.css │ └── js │ │ ├── classList.js │ │ ├── head.min.js │ │ └── html5shiv.js ├── package.json ├── pipify.sh ├── plugin │ ├── highlight │ │ └── highlight.js │ ├── markdown │ │ ├── example.html │ │ ├── example.md │ │ ├── markdown.js │ │ └── marked.js │ ├── math │ │ └── math.js │ ├── multiplex │ │ ├── client.js │ │ ├── index.js │ │ ├── master.js │ │ └── package.json │ ├── notes-server │ │ ├── client.js │ │ ├── index.js │ │ └── notes.html │ ├── notes │ │ ├── notes.html │ │ └── notes.js │ ├── print-pdf │ │ └── print-pdf.js │ ├── search │ │ └── search.js │ └── zoom-js │ │ └── zoom.js ├── pngs │ ├── 1duq.png │ ├── 276411138-236435ff-2944-4bec-ab75-dca0d1e3aacf.jpg │ ├── Git-Logo-1788C.png │ ├── XQxIC1CrCP.gif │ ├── align.png │ ├── dca.png │ ├── diffpdb_osx_diffmerge.png │ ├── docs.png │ ├── draw_circle.png │ ├── draw_dist.png │ ├── draw_vector.png │ ├── edges.png │ ├── edges2.png.jpeg │ ├── edges3.png │ ├── edit.png │ ├── emacs-rna-tools.png │ ├── favicon.png │ ├── find_core.png │ ├── fix_missing_bases.png │ ├── fix_missing_o_before_after.png │ ├── fix_missing_superposition.png │ ├── getdists.png │ ├── getseqcolor.png │ ├── git_everthing_is_local.png │ ├── gitgui.png │ ├── ipython-notebooks.png │ ├── mutate.png │ ├── op3.jpg │ ├── pdb_format_numbering.png │ ├── pymol_color_by_conserv.png │ ├── pymol_dists.png │ ├── pymol_inspect.jpeg │ ├── pymol_inspect2.jpeg │ ├── pymol_mutate.png │ ├── qKPVoPxDmq.gif │ ├── qrnas_0k.png │ ├── qrnas_10k.png │ ├── qrnas_20k.png │ ├── qrnas_3k.png │ ├── rchie.png │ ├── rebuild_op1op2_backbone.png │ ├── rmsd_transition.png │ ├── rna1.png │ ├── rna2.png │ ├── rna3.png │ ├── rna_cartoon.png │ ├── rna_cartoon_small.png │ ├── rp01_diffpdb.png │ ├── rp17A.png │ ├── rp17_AB.png │ ├── rp17_atoms.png │ ├── rp17_simrna.png │ ├── rp19.png │ ├── rpt_emacs.png │ ├── simrnatrajectory.png │ ├── species.png │ ├── ss_misgap.png │ ├── ss_misgap_ok.png │ ├── ss_misgap_wrong.png │ ├── ss_no_gu.png │ ├── ss_only_canonical.png │ ├── starit.png │ ├── torsions.jpg │ └── varna.png ├── requirements_for_docs.txt ├── source │ ├── conf.py │ ├── development.rst │ ├── emacs.rst │ ├── geekbook.rst │ ├── git.rst │ ├── index.rst │ ├── install-dev.rst │ ├── install.rst │ ├── main.rst │ ├── notebooks.rst │ ├── os.rst │ ├── pymol4rna.rst │ ├── rna-puzzles.rst │ ├── selection.rst │ ├── tips.rst │ ├── tools.rst │ ├── want.rst │ └── workflows.rst ├── test │ ├── examples │ │ ├── assets │ │ │ ├── image1.png │ │ │ └── image2.png │ │ ├── barebones.html │ │ ├── embedded-media.html │ │ ├── math.html │ │ ├── slide-backgrounds.html │ │ └── slide-transitions.html │ ├── qunit-1.12.0.css │ ├── qunit-1.12.0.js │ ├── test-markdown-element-attributes.html │ ├── test-markdown-element-attributes.js │ ├── test-markdown-slide-attributes.html │ ├── test-markdown-slide-attributes.js │ ├── test-markdown.html │ ├── test-markdown.js │ ├── test-pdf.html │ ├── test-pdf.js │ ├── test.html │ └── test.js └── tour-icon.png ├── notes ├── ENTRNA - a framework to predict RNA foldability.ipynb ├── Quickref.ipynb ├── SimRNA_and_SimRNAweb.md ├── SimRNA_and_SimRNAweb.py ├── dot2ct.md ├── fetch-rename-extract-chains.md ├── fig3-manuscript.ipynb ├── imgs │ ├── Screen Shot 2019-06-29 at 5.39.39 PM 2.png │ ├── Screen Shot 2019-06-29 at 5.39.39 PM.png │ ├── jupyter-rna.md │ ├── plot1.png │ └── plot2.png ├── jupyter-for-rna-code.md ├── jupyter-test-image.ipynb ├── migration-guide.md ├── mq.ipynb ├── na_align_find_seq_in_alignment.md ├── normalize-spl-structures.md ├── rna-get-chains-rna-only.md ├── rna-get-seq-compact-way.md ├── rna-get-seq-with-uniq.md ├── rna-pdb-tools.ipynb ├── rna-ss-with-mcfold-including-constraints-mask.md ├── rna_alignx.py ├── rna_ss_pred.md ├── rp18-191116.ipynb ├── rp18.ipynb ├── rp20 copy.ipynb ├── rp20.ipynb ├── rp21.ipynb ├── tutorial.md └── workshop.ipynb ├── pyproject.toml ├── requirements.txt ├── rna-tools-index.csv ├── rna_tools ├── BlastPDB.py ├── RfamSearch.py ├── SecondaryStructure.py ├── Seq.py ├── __init__.py ├── _version.py ├── data │ ├── 260c8ff6-f24e-4eff-9760-1831407fc770_ALL_thrs5.30A_clust01-000001_AA.pdb │ ├── A.pdb │ ├── ACGU.pdb │ ├── C.pdb │ ├── G.pdb │ ├── PO3_inner.pdb │ ├── U.pdb │ ├── o2prim.pdb │ ├── op4.pdb │ ├── pdb_ids.txt │ ├── rna_pdb_errors.csv │ └── shape.txt ├── input │ ├── 1I9V_A.pdb │ ├── 1I9V_YG_HETATM_ATOM.pdb │ ├── 1_das_1_rpr_fixed.pdb │ ├── 1a9l_NMR_1_2_models.pdb │ ├── 1a9l_NMR_1_2_models_0.pdb │ ├── 1a9l_NMR_1_2_models_1.pdb │ ├── 1f27.pdb │ ├── 1msy_A2672.pdb │ ├── 1msy_rnakbmd_decoy999_clx_noChain.pdb │ ├── 1nuj_clean_renumber.pdb │ ├── 1osw.pdb │ ├── 1osw_nt1-4_ChainRenamedToBC.pdb │ ├── 1xjr.pdb │ ├── 1xjr_A1-4.pdb │ ├── 1xjr_A3-4.pdb │ ├── 1xjr_A5-10.pdb │ ├── 1xjr_C10-11.pdb │ ├── 1xjr_GTP.pdb │ ├── 1xjr_ba.pdb │ ├── 1xjr_clx_charmm.pdb │ ├── 1xjr_clx_fChimera_noIncludeNumbers.mol2 │ ├── 1xjr_missing_atom.pdb │ ├── 1xjr_no_op3.pdb │ ├── 1xjr_no_op3_simrna_ready.pdb │ ├── 1xjr_onlyGTP.pdb │ ├── 1xjr_onlyGTP_X.pdb │ ├── 1xjr_rpr.pdb │ ├── 1ykq_clx.pdb │ ├── 205d_rmH2o.pdb │ ├── 205d_rmH2o_1chain.pdb │ ├── 20_Bujnicki_1.pdb │ ├── 20_Bujnicki_1_mini_2chains_on_TER.pdb │ ├── 23s_Tth_3I8I_triple.pdb │ ├── 2_bujnicki_1_rpr.pdb │ ├── 2_bujnicki_1_rpr_BA_chain_swap.pdb │ ├── 2_das_1_rpr.pdb │ ├── 2du3_prot_bound.mol2 │ ├── 377D.pdb │ ├── 3e5fA-nogtp_processed_zephyr.pdb │ ├── 3xmg-ANISOU.pdb │ ├── 3xmg-polim_ATL_LOC.pdb │ ├── 4GXY_3firstNt.pdb │ ├── 4GXY_min.pdb │ ├── 4GXY_min.pdb_2.pdb │ ├── 4GXY_min.pdb_3.pdb │ ├── 4W90_protein_rna.pdb │ ├── 4ts2.pdb │ ├── 5k7c.pdb │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb │ ├── 6_solution_0.pdb │ ├── 7_Chen_2_rpr.pdb │ ├── 7_Chen_7_rpr.pdb │ ├── 8_Chen_10_rpr_ChainB.pdb │ ├── ACGU_no_bases.pdb │ ├── A_YG_A.pdb │ ├── CCC.pdb │ ├── CG.pdb │ ├── CG_AA.pdb │ ├── CG_AB.pdb │ ├── K.pdb │ ├── RC-RC3_amberlike_RNAkb_decoys.pdb │ ├── RC5-RG_amberlike_RNAkb_decoys.pdb │ ├── RF02679_pistol_stockholm.txt │ ├── Triple_cWW_tSH_GCA_exemplar_rpr_alignedGAC.pdb │ ├── cif │ │ ├── 1xjr.cif │ │ ├── 1xjr.pdb │ │ ├── 6las.cif │ │ ├── 6las.pdb │ │ └── pdb2cif │ │ │ ├── 1xjr.cif │ │ │ ├── 1xjr.pdb │ │ │ ├── 6las.cif │ │ │ └── 6las.pdb │ ├── clarna_example_01.pdb │ ├── comparison │ │ ├── 4GXY_min.pdb │ │ ├── 4GXY_min_reconstruction.pdb │ │ ├── 4GXY_min_reconstruction_std.pdb │ │ └── 4GXY_min_std.pdb │ ├── comparison2 │ │ ├── 4GXY_min_std.pdb │ │ └── 4GXY_min_std_1P-52.pdb │ ├── cst.txt │ ├── cst2.ct │ ├── cst2.ss │ ├── cst2.ss.ct │ ├── decoy0165_amb.pdb │ ├── decoy0165_amb_out.pdb │ ├── dna_fconvpdb_charmm22.pdb │ ├── farna.pdb │ ├── gtp.pdb │ ├── image │ ├── image.png │ ├── image.png.zip │ ├── missing_o.pdb │ ├── missing_op1op2.pdb │ ├── missing_op1op2_r43OK.pdb │ ├── na_highAtomNum.pdb │ ├── na_solvet_old_format.pdb │ ├── openfoldrna.out │ ├── output.pdb │ ├── pistol_thrs0.50A_clust99-000001_AA.pdb │ ├── prot.pdb │ ├── qrna_config.txt │ ├── readme.md │ ├── remarks.pdb │ ├── rna-ru.pdb │ ├── rp03_solution.pdb │ ├── rp08 │ │ ├── 8_0_solution_4L81_rpr.pdb │ │ ├── 8_Adamiak_1_rpr.pdb │ │ ├── 8_Bujnicki_1_rpr.pdb │ │ ├── 8_Chen_1_rpr.pdb │ │ ├── 8_Das_1_rpr.pdb │ │ ├── 8_Ding_1_rpr.pdb │ │ └── 8_Dokholyan_1_rpr.pdb │ ├── rp13_Dokholyan_1_URI_CYT_ADE_GUA_hydrogens.pdb │ ├── rp17.out.1.pdb │ ├── rp17_seq_ss.fa │ ├── t2-4-ACA.pdb │ ├── t2-4-ACA_rpl.pdb │ ├── tetraloop.pdb │ ├── tetraloop_stem.pdb │ ├── to-replace.pdb │ ├── u2 │ │ ├── rnau2-63.fa │ │ ├── rnau2-a.fa │ │ └── rnau2-u32.fa │ ├── u6-duplex.pdb │ ├── u6_isl.fa │ └── ugly_rna.pdb ├── output │ ├── 1I9V_A_rpr.pdb │ ├── 1I9V_YG_HETATM_ATOM_rpr.pdb │ ├── 1_das_1_rpr_fixed.pdb │ ├── 1_das_1_rpr_inspect.txt │ ├── 1a9l_NMR_1_2_models_R1.pdb │ ├── 1a9l_NMR_1_2_models_lib.pdb │ ├── 1a9l_NMR_1_2_models_tool.pdb │ ├── 1msy_A1.pdb │ ├── 1msy_rnakbmd_decoy999_clx_noChain_Xchain.pdb │ ├── 1osw_NMR_1.pdb │ ├── 1osw_nt1-4_ChainRenamedToBC_dontRenameChains.pdb │ ├── 1osw_nt1-4_ChainRenamedToBC_toAB.pdb │ ├── 1xjr.pdb │ ├── 1xjr.rgyration │ ├── 1xjr.seq │ ├── 1xjr2.seq │ ├── 1xjr_A_clx.pdb │ ├── 1xjr_GTP.pdb │ ├── 1xjr_GTP_setChainC.pdb │ ├── 1xjr_clx.pdb │ ├── 1xjr_clx_charmm.pdb │ ├── 1xjr_clx_fChimera_noIncludeNumbers.mol2 │ ├── 1xjr_no_op3_simrna_ready.pdb │ ├── 1xjr_onlyGTP_rnapuzzle_ready.pdb │ ├── 1ykq_clx.seq │ ├── 1ykq_clx_A.pdb │ ├── 1ykq_clx_AB.pdb │ ├── 1ykq_clx_Apart.pdb │ ├── 205d_rmH2o_1chain_mutant.pdb │ ├── 205d_rmH2o_mutA1234-B1.pdb │ ├── 205d_rmH2o_mutA1234-B1_inplace.pdb │ ├── 205d_rmH2o_mutA1234.pdb │ ├── 20_Bujnicki_1_TER.pdb │ ├── 20_Bujnicki_1_mini_2chains_on_TER_swapped_chains.pdb │ ├── 20_Bujnicki_1_mini_2chains_on_TER_swapped_chains_B2B.pdb │ ├── 23s_Tth_3I8I_triple_backbone.pdb │ ├── 2_bujnicki_1_rpr.txt │ ├── 2_bujnicki_1_rpr_BA_chain_swap.txt │ ├── 2_das_1_rpr.org │ ├── 377D.txt │ ├── 3e5fA-nogtp_processed_zephyr.pdb │ ├── 3xmg-ANISOU.pdb │ ├── 3xmg-polim_ATL_LOC.pdb │ ├── 4GXY_3firstNt.pdb │ ├── 4W90_protein_rna_onlyRNA.pdb │ ├── 4gxy.fa │ ├── 4ts2_rpr.pdb │ ├── 4ts2_rpr_hta.pdb │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr.seq │ ├── 6_solution_0.seq │ ├── 7_Chen_2_rpr.pdb │ ├── 7_Chen_7_rpr.pdb │ ├── 7_Chen_7_rpr_inplacefix.pdb │ ├── 8_Chen_10_rpr_ChainA.pdb │ ├── ACGU_no_bases_fixed.pdb │ ├── A_YG_A.pdb │ ├── A_YG_A_norenumbered.pdb │ ├── A_YG_A_renumbered.pdb │ ├── CCC.pdb │ ├── CCC_empty.pdb │ ├── ClashScore.txt │ ├── Triple_cWW_tSH_GCA_exemplar_rpr_alignedGAC_basesOnly.pdb │ ├── Triple_cWW_tSH_GCA_exemplar_rpr_alignedGAC_noBackbone.pdb │ ├── decoy0165_amb_clx.pdb │ ├── demo.png │ ├── dna_fconvpdb_charmm22.pdb │ ├── farna.pdb │ ├── farna_clx.pdb │ ├── get_seq.txt │ ├── gtp.pdb │ ├── gtp_h2a.pdb │ ├── missing_o_fixed.pdb │ ├── na_highAtomNum.pdb │ ├── na_solvet_old_format.pdb │ ├── na_solvet_old_format__.pdb │ ├── openfoldrna.out │ ├── openfoldrna.pdb │ ├── pistol_compact.txt │ ├── pistol_thrs0.50A_clust99-000001_AA_A-2.pdb │ ├── pistol_thrs0.50A_clust99-000001_AA_srr.pdb │ ├── pistol_uniq.txt │ ├── rebuilt_missing_op.pdb │ ├── remarks_only.pdb │ ├── replaced.pdb │ ├── rna_calc_fenergy.txt │ ├── rp03_renumbered.pdb │ ├── rp03_solution_renumber.pdb │ ├── rp13_Dokholyan_1_URI_CYT_ADE_GUA_hydrogens_rpr.pdb │ ├── rp17_rmA10-60.pdb │ ├── run_clashscore.txt │ ├── secondary_structures.txt │ ├── tetraloop_a1-6_b200-204.pdb │ ├── tetraloop_a1-b200-204.pdb │ ├── tetraloop_a6_b200.pdb │ └── u6-duplex_mdr.pdb ├── pytest.ini ├── rchie.png ├── rna_calc_fenergy.py ├── rna_cif2pdb.py ├── rna_dot2ct.py ├── rna_pdb_fetch_header.py ├── rna_pdb_inspect.py ├── rna_pdb_replace.py ├── rna_pdb_seq.py ├── rna_pdb_tools.py ├── rna_secondary_structure_prediction.py ├── rna_simrnaweb_download_job.py ├── rna_standardize.py ├── rna_tools_config.py ├── rna_tools_lib.py ├── rna_tools_test_all.py ├── rna_torsions.py ├── shell_rc.sh ├── stats.py ├── test.sh ├── tests │ ├── test_eval.py │ ├── test_import_module │ │ ├── rchie.png │ │ ├── test_data │ │ │ └── RF00167.stockholm.sto │ │ └── test_import_rna_tools.py │ ├── test_rna_ss_pred.sh │ ├── test_rnafold.py │ ├── test_seq_cyclefold.py │ ├── test_seq_mcfold.py │ └── test_seq_mcfold2.py ├── tools │ ├── ClashCalc │ │ ├── .gitignore │ │ ├── ClashCalc.py │ │ ├── README.md │ │ ├── __init__.py │ │ └── test_data │ │ │ ├── no_clash.pdb │ │ │ ├── prot-na_2392.pdb │ │ │ └── super_clash.pdb │ ├── PyMOL4RNA │ │ ├── PyMOL4RNA.py │ │ ├── PyMOL4Spliceosome.py │ │ ├── README.md │ │ ├── Spliceosome_PyMOL-2020.ipynb │ │ ├── Spliceosome_PyMOL-2022.ipynb │ │ ├── Spliceosome_PyMOL.csv │ │ ├── Spliceosome_PyMOL.ipynb │ │ ├── Spliceosome_PyMOL.py │ │ ├── Spliceosome_PyMOL.xlsx │ │ ├── __init__.py │ │ ├── code_for_color_spl.py │ │ ├── code_for_spl.py │ │ ├── doc │ │ │ ├── clarna.png │ │ │ ├── ion.png │ │ │ ├── p.png │ │ │ ├── pdb.png │ │ │ ├── pucker.jpg │ │ │ ├── pymol4spliceosome.png │ │ │ ├── rna.png │ │ │ ├── rs.png │ │ │ ├── run.png │ │ │ ├── spl.png │ │ │ └── ss.png │ │ ├── external_flatten_object.py │ │ ├── libs │ │ │ ├── __init__.py │ │ │ ├── calc_gdt.py │ │ │ ├── colorbyrmsd.py │ │ │ ├── get_raw_distances.py │ │ │ ├── pucker.py │ │ │ └── show_contacts.py │ │ ├── rna_draw_edges.py │ │ ├── rnapuzzles.py │ │ └── test_data │ │ │ └── 5k7c_clean.pdb │ ├── __init__.py │ ├── clanstix │ │ ├── .gitignore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── __init__.py │ │ ├── colors.txt │ │ ├── doc │ │ │ ├── rna_clanstix.png │ │ │ ├── rp18_clanstix.png │ │ │ └── yndSrLTb7l.gif │ │ ├── rna_clanstix.py │ │ ├── test.sh │ │ ├── test2.sh │ │ ├── test3.sh │ │ └── test_data │ │ │ ├── gmp.clans │ │ │ ├── gmp_color_by_homolog.clans │ │ │ ├── gmp_color_by_homolog_shape_by_source.clans │ │ │ ├── gmp_ref_mapping_pk_refX.txt │ │ │ ├── matrix.txt │ │ │ ├── rp13_RNAevo_fragments_clans_raw.out │ │ │ ├── rp17_del │ │ │ ├── clans.input │ │ │ ├── rp17_clans.png │ │ │ ├── rp17_clans_process.png │ │ │ ├── rp17_rmsd.csv │ │ │ └── run.sh │ │ │ ├── rp18_rmsd.csv │ │ │ └── rp18_rmsd.in │ ├── clarna_app │ │ ├── __init__.py │ │ ├── data │ │ │ ├── cl.txt │ │ │ ├── cl_full.csv │ │ │ └── cl_short.csv │ │ ├── readme.md │ │ ├── rna_clarna2graph.py │ │ ├── rna_clarna_app.py │ │ ├── test.py │ │ └── test.sh │ ├── clarna_play │ │ ├── ClaRNAlib │ │ │ ├── .gitignore │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── cl_settings.py │ │ │ ├── cl_settings_global.py │ │ │ ├── clarna.py │ │ │ ├── descriptions-dict.json │ │ │ ├── distances.py │ │ │ ├── lib │ │ │ │ ├── classifier.base-phosphate.json.gz │ │ │ │ ├── classifier.base-ribose.json.gz │ │ │ │ ├── classifier.bp.json.gz │ │ │ │ ├── classifier.other.json.gz │ │ │ │ ├── classifier.other2.json.gz │ │ │ │ ├── classifier.other3.json.gz │ │ │ │ └── classifier.stacking.json.gz │ │ │ ├── normalize_pdb.py │ │ │ ├── structure_ciach.py │ │ │ └── utils.py │ │ ├── PDBSeq.py │ │ ├── __init__.py │ │ ├── docs │ │ │ └── clarna_run.png │ │ ├── lib │ │ │ ├── ClaRNAwd_to_vienaSS │ │ │ │ ├── ClaRNAwd_output_parser.cpp │ │ │ │ ├── ClaRNAwd_output_parser.h │ │ │ │ └── Makefile │ │ │ ├── __init__.py │ │ │ └── rna_pdb_tools │ │ │ │ ├── __init__.py │ │ │ │ ├── pdb_parser_lib.py │ │ │ │ └── rna-pdb-tools.py │ │ ├── readme.md │ │ ├── rna_clarna_compare.py │ │ ├── rna_clarna_run.py │ │ ├── test.sh │ │ ├── test_data │ │ │ ├── 1a51_00_A.pdb │ │ │ ├── 1kxk_00_A.pdb │ │ │ ├── 1q9a_00_A.pdb │ │ │ ├── 2a43_00_A.pdb │ │ │ ├── 3e5fA_M15_c.pdb │ │ │ ├── 3e5fA_M500_c.pdb │ │ │ ├── 5k7c.pdb │ │ │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr_AB.pdb │ │ │ └── ss.fa │ │ ├── test_output │ │ │ ├── 3e5fA_M15_c.pdb.outCR │ │ │ └── 3e5fA_M500_c.pdb.outCR │ │ └── tests │ │ │ ├── 1evv_00_A.pdb │ │ │ ├── 3e5fA_M15.pdb │ │ │ └── 3e5fA_M500.pdb │ ├── cluster_load │ │ ├── README.md │ │ ├── __init__.py │ │ ├── cluster_load.py │ │ ├── cluster_mini_free.py │ │ └── load │ ├── df │ │ ├── rna_df_concat.py │ │ ├── rna_df_csv_sort.py │ │ ├── rna_df_merge.py │ │ ├── rna_df_merge_on.py │ │ ├── rna_df_merge_two.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── cga_rmsd.csv │ │ │ ├── cgc_rmsd.csv │ │ │ ├── d3.csv │ │ │ ├── d8.csv │ │ │ ├── min_2.csv │ │ │ ├── min_3.csv │ │ │ ├── min_4.csv │ │ │ ├── rna_df_concat.py │ │ │ ├── rna_df_merge.csv │ │ │ └── rna_df_merge_on.csv │ ├── diffpdb │ │ ├── .gitignore │ │ ├── README.md │ │ ├── __init__.py │ │ ├── diffpdb.py │ │ ├── doc │ │ │ ├── atom-variants.png │ │ │ ├── diffpdb_osx_diffmerge.png │ │ │ ├── missing-atoms.png │ │ │ ├── missing-op3.png │ │ │ ├── screenshot.png │ │ │ └── screenshot2.png │ │ ├── lib │ │ │ └── diff2html.py │ │ ├── output │ │ │ └── 2_str1_vs_str2.html │ │ ├── test.sh │ │ └── test_data │ │ │ ├── 1 │ │ │ ├── 1kxkA.pdb │ │ │ └── 1kxkA_M1.pdb │ │ │ ├── 2 │ │ │ ├── str1.pdb │ │ │ └── str2.pdb │ │ │ ├── 4 │ │ │ ├── 1duq.pdb │ │ │ └── 1duq_decoy0171_amb_clx.pdb │ │ │ ├── 3.ident │ │ │ ├── str1.pdb │ │ │ └── str2.pdb │ │ │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb │ │ │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb.out │ │ │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr_min.pdb │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0.pdb │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0.pdb.out │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clx.pdb │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clx.pdb.out │ │ │ ├── pistol_thrs0.50A_clust272-000001_AA.pdb │ │ │ ├── pistol_thrs0.50A_clust272-000001_AA.pdb.out │ │ │ └── pistol_thrs0.50A_clust272-000001_AA_min.pdb │ ├── extra_functions │ │ ├── __init__.py │ │ ├── gen_numbering.py │ │ ├── numbering.txt │ │ └── select_fragment.py │ ├── md │ │ ├── .gitignore │ │ ├── README.md │ │ ├── __init__.py │ │ ├── data │ │ │ └── rnakb_all.txt │ │ ├── out.txt │ │ ├── rna_get_energy.py │ │ ├── rna_gromacs_ready.py │ │ ├── rna_md.py │ │ ├── rna_minimize.py │ │ ├── rna_traj_n.py │ │ ├── rna_traj_nohetm.py │ │ ├── rna_traj_range.py │ │ ├── rnakb_utils.py │ │ ├── test.py │ │ ├── test.sh │ │ ├── test_data │ │ │ ├── 1duq │ │ │ ├── 1duq.pdb │ │ │ ├── 1duq_rpr.pdb │ │ │ ├── 1msy_output4_01-000001_AA.pdb │ │ │ ├── 3nt.pdb │ │ │ ├── 3nt_edited.pdb │ │ │ ├── RA5_G.pdb │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clean_error_fx.pdb │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clean_error_fx_rmPO.pdb │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clean_noC.pdb │ │ │ ├── decoy0165_amb_clx.pdb │ │ │ ├── groups.txt │ │ │ └── temp.pdb │ │ └── test_output │ │ │ ├── 1duq_rnakb_ready.pdb │ │ │ ├── 1duq_rpr_rnakb_ready.pdb │ │ │ ├── 1msy_output4_01-000001_AA_rnakb_ready.pdb │ │ │ ├── 3nt_edited_rnakb_ready.pdb │ │ │ ├── RA5_G.pdb │ │ │ └── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clean_error_fx_rnakb_ready.pdb │ ├── mini_moderna3 │ │ ├── .coveragerc │ │ ├── .gitignore │ │ ├── .travis.yml │ │ ├── AUTHORS.rst │ │ ├── COPYING │ │ ├── MANIFEST.in │ │ ├── README.md │ │ ├── __init__.py │ │ └── moderna │ │ │ ├── CheckPdb.py │ │ │ ├── Constants.py │ │ │ ├── FragmentInsertion.py │ │ │ ├── Helix.py │ │ │ ├── ModelingRecipe.py │ │ │ ├── ModernaFragment.py │ │ │ ├── ModernaStructure.py │ │ │ ├── ModernaSuperimposer.py │ │ │ ├── PdbConverter.py │ │ │ ├── RNAChain.py │ │ │ ├── RNAModel.py │ │ │ ├── RNAResidue.py │ │ │ ├── Renumerator.py │ │ │ ├── Renumerator_new.py │ │ │ ├── Template.py │ │ │ ├── __init__.py │ │ │ ├── _version.py │ │ │ ├── analyze │ │ │ ├── BasePairCalculator.py │ │ │ ├── BaseRecognizer.py │ │ │ ├── ChainConnectivity.py │ │ │ ├── ClashRecognizer.py │ │ │ ├── Constants.py │ │ │ ├── GeometryAnalyzer.py │ │ │ ├── GeometryParameters.py │ │ │ ├── GeometryStatistics.py │ │ │ ├── HBondCalculator.py │ │ │ ├── MolGraphParser.py │ │ │ ├── MolParameters.py │ │ │ ├── MolTopologies.py │ │ │ ├── MolecularGraph.py │ │ │ ├── PuckerCalculator.py │ │ │ ├── RNASuites.py │ │ │ ├── StackingCalculator.py │ │ │ ├── __init__.py │ │ │ └── suites │ │ │ │ ├── SuiteCalculator.py │ │ │ │ ├── dihedral_bins.py │ │ │ │ ├── suite.py │ │ │ │ ├── suite2.py │ │ │ │ ├── suite_clusters.py │ │ │ │ ├── suitename.py │ │ │ │ ├── test_SuiteCalculator.py │ │ │ │ ├── test_data │ │ │ │ ├── 1JZC.pdb │ │ │ │ ├── 1WTS.pdb │ │ │ │ ├── ah0001Ha.pdb │ │ │ │ └── arhb90H.pdb │ │ │ │ ├── test_suite.py │ │ │ │ └── test_suitename.py │ │ │ ├── builder │ │ │ ├── BackboneBuilder.py │ │ │ ├── ChiRotator.py │ │ │ ├── Constants.py │ │ │ ├── CoordBuilder.py │ │ │ ├── FCCDLoopCloser.py │ │ │ ├── PhosphateBuilder.py │ │ │ └── __init__.py │ │ │ ├── commands.py │ │ │ ├── data │ │ │ ├── B_DNA.pdb │ │ │ ├── IsostericityMatrices.txt │ │ │ ├── all_atom_names │ │ │ ├── base_pairs │ │ │ │ ├── ----_GU.pdb │ │ │ │ ├── Rib_AG.pdb │ │ │ │ ├── Rib_GG.pdb │ │ │ │ ├── bif_AA.pdb │ │ │ │ ├── bif_AC.pdb │ │ │ │ ├── bif_CA.pdb │ │ │ │ ├── bif_CC.pdb │ │ │ │ ├── bif_GG.pdb │ │ │ │ ├── bif_GU.pdb │ │ │ │ ├── bifa_CA.pdb │ │ │ │ ├── bifa_CC.pdb │ │ │ │ ├── cHH_AG.pdb │ │ │ │ ├── cHH_CG.pdb │ │ │ │ ├── cHH_GA.pdb │ │ │ │ ├── cHH_GC.pdb │ │ │ │ ├── cHH_GG.pdb │ │ │ │ ├── cHS_AA.pdb │ │ │ │ ├── cHS_AC.pdb │ │ │ │ ├── cHS_AG.pdb │ │ │ │ ├── cHS_AU.pdb │ │ │ │ ├── cHS_CA.pdb │ │ │ │ ├── cHS_CC.pdb │ │ │ │ ├── cHS_CG.pdb │ │ │ │ ├── cHS_CU.pdb │ │ │ │ ├── cHS_GA.pdb │ │ │ │ ├── cHS_GG.pdb │ │ │ │ ├── cHS_UA.pdb │ │ │ │ ├── cHS_UC.pdb │ │ │ │ ├── cHS_UG.pdb │ │ │ │ ├── cHS_UU.pdb │ │ │ │ ├── cHSa_AG.pdb │ │ │ │ ├── cHSa_AU.pdb │ │ │ │ ├── cHSa_CU.pdb │ │ │ │ ├── cHSa_UG.pdb │ │ │ │ ├── cHSb_UG.pdb │ │ │ │ ├── cSS_AA.pdb │ │ │ │ ├── cSS_AC.pdb │ │ │ │ ├── cSS_AG.pdb │ │ │ │ ├── cSS_AU.pdb │ │ │ │ ├── cSS_CA.pdb │ │ │ │ ├── cSS_CC.pdb │ │ │ │ ├── cSS_CG.pdb │ │ │ │ ├── cSS_CU.pdb │ │ │ │ ├── cSS_GA.pdb │ │ │ │ ├── cSS_GC.pdb │ │ │ │ ├── cSS_GG.pdb │ │ │ │ ├── cSS_GU.pdb │ │ │ │ ├── cSS_UA.pdb │ │ │ │ ├── cSS_UC.pdb │ │ │ │ ├── cSS_UG.pdb │ │ │ │ ├── cSS_UU.pdb │ │ │ │ ├── cSSa_AC.pdb │ │ │ │ ├── cSSa_CA.pdb │ │ │ │ ├── cSSa_CG.pdb │ │ │ │ ├── cSSa_UG.pdb │ │ │ │ ├── cSSb_CA.pdb │ │ │ │ ├── cWH_AG.pdb │ │ │ │ ├── cWH_AU.pdb │ │ │ │ ├── cWH_CC.pdb │ │ │ │ ├── cWH_CG.pdb │ │ │ │ ├── cWH_CU.pdb │ │ │ │ ├── cWH_GA.pdb │ │ │ │ ├── cWH_GG.pdb │ │ │ │ ├── cWH_UA.pdb │ │ │ │ ├── cWH_UG.pdb │ │ │ │ ├── cWH_UU.pdb │ │ │ │ ├── cWHa_AG.pdb │ │ │ │ ├── cWHa_AU.pdb │ │ │ │ ├── cWHa_UA.pdb │ │ │ │ ├── cWS_AA.pdb │ │ │ │ ├── cWS_AC.pdb │ │ │ │ ├── cWS_AG.pdb │ │ │ │ ├── cWS_AU.pdb │ │ │ │ ├── cWS_CA.pdb │ │ │ │ ├── cWS_CC.pdb │ │ │ │ ├── cWS_CG.pdb │ │ │ │ ├── cWS_CU.pdb │ │ │ │ ├── cWS_GA.pdb │ │ │ │ ├── cWS_GC.pdb │ │ │ │ ├── cWS_GG.pdb │ │ │ │ ├── cWS_GU.pdb │ │ │ │ ├── cWS_UA.pdb │ │ │ │ ├── cWS_UC.pdb │ │ │ │ ├── cWS_UG.pdb │ │ │ │ ├── cWS_UU.pdb │ │ │ │ ├── cWSa_AC.pdb │ │ │ │ ├── cWSa_CC.pdb │ │ │ │ ├── cWSa_GU.pdb │ │ │ │ ├── cWSb_GU.pdb │ │ │ │ ├── cWW_AA.pdb │ │ │ │ ├── cWW_AC.pdb │ │ │ │ ├── cWW_AG.pdb │ │ │ │ ├── cWW_AU.pdb │ │ │ │ ├── cWW_CA.pdb │ │ │ │ ├── cWW_CC.pdb │ │ │ │ ├── cWW_CG.pdb │ │ │ │ ├── cWW_CU.pdb │ │ │ │ ├── cWW_GA.pdb │ │ │ │ ├── cWW_GC.pdb │ │ │ │ ├── cWW_GU.pdb │ │ │ │ ├── cWW_UA.pdb │ │ │ │ ├── cWW_UC.pdb │ │ │ │ ├── cWW_UG.pdb │ │ │ │ ├── cWW_UU.pdb │ │ │ │ ├── cWWa_AC.pdb │ │ │ │ ├── cWWa_AG.pdb │ │ │ │ ├── cWWa_CA.pdb │ │ │ │ ├── cWWa_CG.pdb │ │ │ │ ├── cWWa_CU.pdb │ │ │ │ ├── cWWa_GA.pdb │ │ │ │ ├── cWWa_GC.pdb │ │ │ │ ├── cWWa_GU.pdb │ │ │ │ ├── cWWa_UC.pdb │ │ │ │ ├── cWWa_UG.pdb │ │ │ │ ├── cWWb_AC.pdb │ │ │ │ ├── cWWb_AG.pdb │ │ │ │ ├── cWWb_CA.pdb │ │ │ │ ├── cWWb_CU.pdb │ │ │ │ ├── cWWb_GA.pdb │ │ │ │ ├── cWWb_GU.pdb │ │ │ │ ├── cWWb_UC.pdb │ │ │ │ ├── cWWb_UG.pdb │ │ │ │ ├── stacking │ │ │ │ │ ├── s33_AA.pdb │ │ │ │ │ ├── s33_AC.pdb │ │ │ │ │ ├── s33_AG.pdb │ │ │ │ │ ├── s33_AU.pdb │ │ │ │ │ ├── s33_CC.pdb │ │ │ │ │ ├── s33_CU.pdb │ │ │ │ │ ├── s33_GG.pdb │ │ │ │ │ ├── s33_GU.pdb │ │ │ │ │ ├── s33_UU.pdb │ │ │ │ │ ├── s35_AA.pdb │ │ │ │ │ ├── s35_AC.pdb │ │ │ │ │ ├── s35_AG.pdb │ │ │ │ │ ├── s35_AU.pdb │ │ │ │ │ ├── s35_CC.pdb │ │ │ │ │ ├── s35_CG.pdb │ │ │ │ │ ├── s35_CU.pdb │ │ │ │ │ ├── s35_GG.pdb │ │ │ │ │ ├── s35_GU.pdb │ │ │ │ │ ├── s35_UU.pdb │ │ │ │ │ ├── s55_AA.pdb │ │ │ │ │ ├── s55_AC.pdb │ │ │ │ │ ├── s55_AG.pdb │ │ │ │ │ ├── s55_AU.pdb │ │ │ │ │ ├── s55_CC.pdb │ │ │ │ │ ├── s55_CU.pdb │ │ │ │ │ ├── s55_GG.pdb │ │ │ │ │ ├── s55_GU.pdb │ │ │ │ │ └── s55_UU.pdb │ │ │ │ ├── tHH_AA.pdb │ │ │ │ ├── tHH_AC.pdb │ │ │ │ ├── tHH_AG.pdb │ │ │ │ ├── tHH_AU.pdb │ │ │ │ ├── tHH_CA.pdb │ │ │ │ ├── tHH_CG.pdb │ │ │ │ ├── tHH_CU.pdb │ │ │ │ ├── tHH_GA.pdb │ │ │ │ ├── tHH_GC.pdb │ │ │ │ ├── tHH_GG.pdb │ │ │ │ ├── tHH_UA.pdb │ │ │ │ ├── tHH_UC.pdb │ │ │ │ ├── tHHa_AU.pdb │ │ │ │ ├── tHHa_CG.pdb │ │ │ │ ├── tHHa_GC.pdb │ │ │ │ ├── tHHa_UA.pdb │ │ │ │ ├── tHHb_AU.pdb │ │ │ │ ├── tHHb_UA.pdb │ │ │ │ ├── tHS_AA.pdb │ │ │ │ ├── tHS_AC.pdb │ │ │ │ ├── tHS_AG.pdb │ │ │ │ ├── tHS_AU.pdb │ │ │ │ ├── tHS_CA.pdb │ │ │ │ ├── tHS_CC.pdb │ │ │ │ ├── tHS_CU.pdb │ │ │ │ ├── tHS_GG.pdb │ │ │ │ ├── tHS_UA.pdb │ │ │ │ ├── tHS_UG.pdb │ │ │ │ ├── tHSa_AG.pdb │ │ │ │ ├── tHSa_AU.pdb │ │ │ │ ├── tHSa_GG.pdb │ │ │ │ ├── tHSb_AG.pdb │ │ │ │ ├── tSS_AA.pdb │ │ │ │ ├── tSS_AC.pdb │ │ │ │ ├── tSS_AG.pdb │ │ │ │ ├── tSS_AU.pdb │ │ │ │ ├── tSS_GA.pdb │ │ │ │ ├── tSS_GC.pdb │ │ │ │ ├── tSS_GG.pdb │ │ │ │ ├── tSS_GU.pdb │ │ │ │ ├── tWH_AA.pdb │ │ │ │ ├── tWH_AG.pdb │ │ │ │ ├── tWH_CA.pdb │ │ │ │ ├── tWH_CC.pdb │ │ │ │ ├── tWH_CG.pdb │ │ │ │ ├── tWH_GG.pdb │ │ │ │ ├── tWH_GU.pdb │ │ │ │ ├── tWH_UA.pdb │ │ │ │ ├── tWH_UG.pdb │ │ │ │ ├── tWH_UU.pdb │ │ │ │ ├── tWHa_CA.pdb │ │ │ │ ├── tWHa_CG.pdb │ │ │ │ ├── tWHa_UA.pdb │ │ │ │ ├── tWS_AA.pdb │ │ │ │ ├── tWS_AC.pdb │ │ │ │ ├── tWS_AG.pdb │ │ │ │ ├── tWS_AU.pdb │ │ │ │ ├── tWS_CA.pdb │ │ │ │ ├── tWS_CC.pdb │ │ │ │ ├── tWS_CG.pdb │ │ │ │ ├── tWS_CU.pdb │ │ │ │ ├── tWS_GC.pdb │ │ │ │ ├── tWS_GU.pdb │ │ │ │ ├── tWS_UA.pdb │ │ │ │ ├── tWS_UC.pdb │ │ │ │ ├── tWS_UG.pdb │ │ │ │ ├── tWS_UU.pdb │ │ │ │ ├── tWSa_AG.pdb │ │ │ │ ├── tWW_AA.pdb │ │ │ │ ├── tWW_AC.pdb │ │ │ │ ├── tWW_AU.pdb │ │ │ │ ├── tWW_CA.pdb │ │ │ │ ├── tWW_CC.pdb │ │ │ │ ├── tWW_CG.pdb │ │ │ │ ├── tWW_CU.pdb │ │ │ │ ├── tWW_GC.pdb │ │ │ │ ├── tWW_GG.pdb │ │ │ │ ├── tWW_GU.pdb │ │ │ │ ├── tWW_UA.pdb │ │ │ │ ├── tWW_UC.pdb │ │ │ │ ├── tWW_UG.pdb │ │ │ │ └── tWW_UU.pdb │ │ │ ├── helix.pdb │ │ │ ├── modification_fragments │ │ │ │ ├── 1wts_N1C6C5_N6_mm.pdb │ │ │ │ ├── C1pC2pC3p.pdb │ │ │ │ ├── C1pC2pC3p_O2p.pdb │ │ │ │ ├── C1pC2pC3p_O2p_m.pdb │ │ │ │ ├── C1pC2pC3p_O2p_r_P.pdb │ │ │ │ ├── C1pC2pC3p_O2p_rp.pdb │ │ │ │ ├── C2N1C6_D.pdb │ │ │ │ ├── C2N1C6_m.pdb │ │ │ │ ├── C2N1C6_m5D.pdb │ │ │ │ ├── C2N3C4_acp.pdb │ │ │ │ ├── C2N3C4_m.pdb │ │ │ │ ├── C4C5C6_C7.pdb │ │ │ │ ├── C4C5C6_Y.pdb │ │ │ │ ├── C4C5C6_f.pdb │ │ │ │ ├── C4C5C6_m.pdb │ │ │ │ ├── C4C5C6_m1Y.pdb │ │ │ │ ├── C4C5C6_m1acp3Y.pdb │ │ │ │ ├── C4C5C6_m3Y.pdb │ │ │ │ ├── C4C5C6_mc.pdb │ │ │ │ ├── C4C5C6_mcm.pdb │ │ │ │ ├── C4C5C6_mcn.pdb │ │ │ │ ├── C4C5C6_mh.pdb │ │ │ │ ├── C4C5C6_mhc.pdb │ │ │ │ ├── C4C5C6_mhcm.pdb │ │ │ │ ├── C4C5C6_mn.pdb │ │ │ │ ├── C4C5C6_mnm.pdb │ │ │ │ ├── C4C5C6_mnmc.pdb │ │ │ │ ├── C4C5C6_mt.pdb │ │ │ │ ├── C4C5C6_oh.pdb │ │ │ │ ├── C4C5C6_om.pdb │ │ │ │ ├── C4C5C6_omc.pdb │ │ │ │ ├── C4C5C6_omcm.pdb │ │ │ │ ├── C4N9C8_QtRNA.pdb │ │ │ │ ├── C4N9C8_galQtRNA.pdb │ │ │ │ ├── C4N9C8_gluQtRNA.pdb │ │ │ │ ├── C4N9C8_manQtRNA.pdb │ │ │ │ ├── C4N9C8_oQtRNA.pdb │ │ │ │ ├── C4N9C8_preQ0tRNA.pdb │ │ │ │ ├── C4N9C8_preQ1tRNA.pdb │ │ │ │ ├── C5C7C8_arch.pdb │ │ │ │ ├── C5N7C8_m.pdb │ │ │ │ ├── C6N7C8_m.pdb │ │ │ │ ├── N1C2N2_i.pdb │ │ │ │ ├── N1C2N2_mi.pdb │ │ │ │ ├── N1C2N2_o2yW.pdb │ │ │ │ ├── N1C2N2_ohyW.pdb │ │ │ │ ├── N1C2N2_ohyW_star.pdb │ │ │ │ ├── N1C2N2_yW.pdb │ │ │ │ ├── N1C2N3_N2_m.pdb │ │ │ │ ├── N1C2N3_N2_mm.pdb │ │ │ │ ├── N1C2N3_k.pdb │ │ │ │ ├── N1C2N3_m.pdb │ │ │ │ ├── N1C2N3_s.pdb │ │ │ │ ├── N1C2N3_se.pdb │ │ │ │ ├── N1C2N3_sm.pdb │ │ │ │ ├── N1C6C5_N6_g.pdb │ │ │ │ ├── N1C6C5_N6_hn.pdb │ │ │ │ ├── N1C6C5_N6_i.pdb │ │ │ │ ├── N1C6C5_N6_io.pdb │ │ │ │ ├── N1C6C5_N6_m.pdb │ │ │ │ ├── N1C6C5_N6_m_t.pdb │ │ │ │ ├── N1C6C5_N6_mm.pdb │ │ │ │ ├── N1C6C5_N6_t.pdb │ │ │ │ ├── N1C6C5_O.pdb │ │ │ │ ├── N1C6C5_ac.pdb │ │ │ │ ├── N3C4C5_N4_ac.pdb │ │ │ │ ├── N3C4C5_N4_m.pdb │ │ │ │ ├── N3C4C5_N4_mm.pdb │ │ │ │ ├── N3C4C5_s.pdb │ │ │ │ └── ribose_C.pdb │ │ │ ├── modification_names_table │ │ │ ├── modification_topologies.txt │ │ │ ├── modifications │ │ │ ├── pair_fragment.pdb │ │ │ ├── phosphate_group.pdb │ │ │ ├── rnaDB05_list.txt │ │ │ ├── rnaDB05_list_without_tRNA.txt │ │ │ ├── single_strand.pdb │ │ │ ├── standard_bases │ │ │ │ ├── A.ent │ │ │ │ ├── C.ent │ │ │ │ ├── G.ent │ │ │ │ ├── P_atom.ent │ │ │ │ └── U.ent │ │ │ └── suite_clusters.txt │ │ │ ├── examples │ │ │ ├── __init__.py │ │ │ └── usage_examples.py │ │ │ ├── fragment_library │ │ │ ├── LIR.py │ │ │ ├── LIRdb.py │ │ │ ├── SearchLIR.py │ │ │ ├── StructureLibrary.py │ │ │ └── __init__.py │ │ │ ├── isosteric │ │ │ ├── IsostericModelling.py │ │ │ ├── Isostericity.py │ │ │ ├── IsostericityMatrices.py │ │ │ └── __init__.py │ │ │ ├── moderna.py │ │ │ ├── modifications │ │ │ ├── BaseExchanger.py │ │ │ ├── ModificationAdder.py │ │ │ ├── ModificationRemover.py │ │ │ ├── ModifyResidue.py │ │ │ ├── ResidueEditor.py │ │ │ └── __init__.py │ │ │ ├── sequence │ │ │ ├── AlignmentMatcher.py │ │ │ ├── ModernaAlphabet.py │ │ │ ├── ModernaSequence.py │ │ │ ├── RNAAlignment.py │ │ │ ├── __init__.py │ │ │ └── commands.py │ │ │ └── util │ │ │ ├── Errors.py │ │ │ ├── LogFile.py │ │ │ ├── __init__.py │ │ │ ├── decorators.py │ │ │ └── validators.py │ ├── misc │ │ ├── __init__.py │ │ ├── reverse.py │ │ ├── rna_add_chain.py │ │ ├── rna_dict2fasta.py │ │ ├── rna_ok │ │ ├── rna_ok_mail.py │ │ ├── rna_remote_run.py │ │ ├── rna_test_cuda.py │ │ ├── rna_tools_demo.py │ │ ├── rna_tools_which.py │ │ ├── rna_topdb.py │ │ ├── test.sh │ │ └── translate.py │ ├── mq │ │ ├── AnalyzeGeometry │ │ │ ├── AnalyzeGeometry.py │ │ │ ├── __init__.py │ │ │ ├── rna_mq_analyzegeometry.py │ │ │ └── test.sh │ │ ├── ClashScore │ │ │ ├── ClashScore.py │ │ │ ├── __init__.py │ │ │ ├── rna_mq_clashscore.py │ │ │ └── test.sh │ │ ├── Dfire │ │ │ ├── Dfire.py │ │ │ ├── __init__.py │ │ │ ├── rna_mq_dfire.py │ │ │ ├── test.output │ │ │ └── test.sh │ │ ├── FARFAR2 │ │ │ ├── FARFAR2.py │ │ │ ├── __init__.py │ │ │ ├── rna_mq_farfar2.py │ │ │ ├── test.sh │ │ │ └── test_output │ │ │ │ ├── .python-version │ │ │ │ ├── ff2.csv │ │ │ │ ├── ff2_hires.csv │ │ │ │ ├── ff2_hires_rna_mq_collect.csv │ │ │ │ └── ff2_rna_mq_collect.csv │ │ ├── FARNA │ │ │ ├── FARNA.py │ │ │ ├── __init__.py │ │ │ ├── rna_mq_farna.py │ │ │ ├── test.sh │ │ │ └── test_output │ │ │ │ ├── 1xjrA_rna_mq_collect_FARNA_hires.csv │ │ │ │ ├── 1y26X_output4_01-000001_AA.pdb_rna_mq_collect_FARNA_lores.csv │ │ │ │ └── 1y26X_output4_01-000001_AA.pdb_rna_mq_farna_lores.csv │ │ ├── QRNAS │ │ │ ├── QRNAS.py │ │ │ ├── __init__.py │ │ │ ├── test.sh │ │ │ └── test │ │ │ │ ├── 1a9n.pdb │ │ │ │ ├── __init__.py │ │ │ │ ├── test.output │ │ │ │ ├── test.py │ │ │ │ └── unmod_Val3_tRNA_model_si.pdb │ │ ├── RASP │ │ │ ├── RASP.py │ │ │ ├── __init__.py │ │ │ ├── rasp_for_pymol.py │ │ │ ├── rna_mq_rasp.py │ │ │ ├── test.py │ │ │ ├── test.sh │ │ │ └── test │ │ │ │ ├── 17_Bujnicki_7_rpr.pdb │ │ │ │ ├── 17_Das_1_rpr.pdb │ │ │ │ ├── 17_Das_4_rpr.pdb │ │ │ │ ├── __init__.py │ │ │ │ ├── mq.csv │ │ │ │ ├── test.csv │ │ │ │ ├── test.py │ │ │ │ └── test_sorted_rasp_all.csv │ │ ├── README.md │ │ ├── RNA3DCNN │ │ │ ├── RNA3DCNN.py │ │ │ ├── __init__.py │ │ │ ├── rna_mq_rna3dcnn.py │ │ │ ├── test.output │ │ │ └── test.sh │ │ ├── RNAkb │ │ │ ├── RNAkb.py │ │ │ ├── __init__.py │ │ │ ├── rna_mq_rnakb.py │ │ │ ├── test.sh │ │ │ └── test_data │ │ │ │ ├── 1dqf.pdb │ │ │ │ ├── 1dqf_noCA+ResnShift.pdb │ │ │ │ ├── 1dqf_noCA.pdb │ │ │ │ ├── 1duq.pdb │ │ │ │ ├── 1msy_nt1.pdb │ │ │ │ ├── 1msy_output4_01-000001_AA.pdb │ │ │ │ ├── 1ykq.pdb │ │ │ │ ├── 1z58.pdb │ │ │ │ ├── 333d.pdb │ │ │ │ ├── 434d.pdb │ │ │ │ ├── C.pdb │ │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clean.pdb │ │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clean_error.pdb │ │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clean_error_fx.pdb │ │ │ │ ├── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clean_noC.pdb │ │ │ │ └── cat_chunk003_2r8s_5kcycles_decoys_nonativefrags.cluster1.0_clx.pdb │ │ ├── RNAscore │ │ │ ├── RNAscore.py │ │ │ └── __init__.py │ │ ├── SimRNA │ │ │ ├── SimRNA.py │ │ │ ├── __init__.py │ │ │ ├── rna_mq_simrna.py │ │ │ ├── test.sh │ │ │ └── test │ │ │ │ ├── 1duq_clx_decoy4_clx.pdb │ │ │ │ ├── output.csv │ │ │ │ └── test.py │ │ ├── __init__.py │ │ ├── eSCORE │ │ │ ├── __init__.py │ │ │ ├── eSCORE.py │ │ │ ├── rna_mq_eSCORE.py │ │ │ ├── test.sh │ │ │ └── test │ │ │ │ └── escore.txt │ │ ├── lib │ │ │ ├── __init__.py │ │ │ ├── shellgraphics │ │ │ │ ├── LICENSE │ │ │ │ ├── README.md │ │ │ │ ├── __init__.py │ │ │ │ ├── output.txt │ │ │ │ └── shellgraphics.py │ │ │ ├── timex │ │ │ │ ├── .gitignore │ │ │ │ ├── LICENSE │ │ │ │ ├── README.md │ │ │ │ ├── __init__.py │ │ │ │ └── timex.py │ │ │ └── wrappers │ │ │ │ ├── README.md │ │ │ │ ├── SubprocessUtils.py │ │ │ │ ├── __init__.py │ │ │ │ ├── base_wrappers.py │ │ │ │ └── test │ │ │ │ ├── __init__.py │ │ │ │ └── test.py │ │ ├── rna_mq_collect.py │ │ ├── rna_mq_collect_tqdm.py │ │ ├── rna_mq_exp.py │ │ ├── rna_mq_plot.py │ │ ├── rna_mq_remote.sh │ │ ├── rna_mq_score.py │ │ ├── rna_mq_wx_collect.py │ │ ├── rsRNASP │ │ │ ├── __init__.py │ │ │ ├── rna_mq_rsRNASP.py │ │ │ ├── rsRNASP.py │ │ │ └── test.sh │ │ ├── test.sh │ │ ├── test │ │ │ ├── 1a9n.pdb │ │ │ ├── 1msy_output4_01-000001_AA_edited.pdb │ │ │ ├── 1xjrA.pdb │ │ │ ├── 1xjrA_M1.pdb │ │ │ ├── 1xjrA_M500.pdb │ │ │ ├── 1xjrA_output4_04-000056_AA.pdb │ │ │ ├── 1y26X_output4_01-000001_AA.pdb │ │ │ ├── 1zhoH.pdb │ │ │ ├── 2pcw_1_2chains.pdb │ │ │ ├── 3e5f_output4_01-000001_AA+ResnShift.pdb │ │ │ ├── 6TNA.pdb │ │ │ ├── all.csv │ │ │ ├── dfire.csv │ │ │ ├── gcu-t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr.pdb │ │ │ ├── gcu-t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr_2.pdb │ │ │ ├── gcu-t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr_6.pdb │ │ │ ├── gcu-t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr_SwapChains.pdb │ │ │ ├── gcu-t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr_SwapChainsAB.pdb │ │ │ ├── gcu-t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr_SwapChainsOneChain.pdb │ │ │ ├── gcu-t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr_x4chains.pdb │ │ │ ├── ggg-t1_yCs_5MPS.pdb2-21g-6-61g+80g-rpr.pdb │ │ │ ├── test.pdb │ │ │ └── test2.pdb │ │ └── tmp │ │ │ └── yC_5LJ3_U2U6_core_1st_triplex_6-61A_2-21U_refx │ │ │ └── configfile.txt │ ├── pdb_formatix │ │ ├── PDBFile.py │ │ ├── README.md │ │ ├── RosettaUtils.py │ │ ├── SingleLineUtils.py │ │ ├── __init__.py │ │ ├── rebuilder.py │ │ ├── test-quick-and-dirty.py │ │ └── test │ │ │ ├── 1kxkA_rasp.native.pdb │ │ │ ├── 1xjrA_M1+ter.pdb │ │ │ ├── 1xjrA_M1.pdb │ │ │ ├── __init__.py │ │ │ ├── protein.pdb │ │ │ ├── sample_for_distance.pdb │ │ │ ├── test.py │ │ │ ├── test0.in │ │ │ ├── test0.out │ │ │ ├── test0_3to1.out │ │ │ ├── test1.in │ │ │ ├── test1.out │ │ │ ├── test_nmr.in │ │ │ ├── test_nmr.out │ │ │ └── test_nmr_atom.out │ ├── pdbs_measure_atom_dists │ │ ├── __init__.py │ │ ├── pdbs_measure_atom_dists.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── ALN_OBJ1_OBJ2.fa │ │ │ ├── obj01.pdb │ │ │ └── obj02.pdb │ ├── plotting │ │ ├── __init__.py │ │ ├── rna_plot_boxplotlike.py │ │ ├── rna_plot_dendogram.py │ │ ├── rna_plot_density.py │ │ ├── rna_plot_heatmap.py │ │ ├── rna_plot_hist.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── rmsds.csv │ │ │ ├── rmsds_dens.png │ │ │ └── rmsds_hist.png │ ├── proteins │ │ ├── 1djf.pdb │ │ ├── calc_distances.py │ │ ├── test.sh │ │ └── u2-u6-cwc15-trim2_proteinOnly.pdb │ ├── pymol_color_by_conserv │ │ ├── conserv_to_csv.py │ │ ├── data │ │ │ └── cwc15 │ │ │ │ ├── cwc15.pml │ │ │ │ ├── cwc15_consensus.csv │ │ │ │ ├── cwc15_conserv.csv │ │ │ │ └── psiblast_8183496.aln │ │ ├── docs │ │ │ ├── consensus-file.png │ │ │ ├── cwc15.png │ │ │ └── jalview.png │ │ ├── pymol_color_by_conserv.py │ │ ├── readme.md │ │ └── test.sh │ ├── pymol_drawing │ │ ├── README.md │ │ ├── __init__.py │ │ ├── docs │ │ │ ├── draw_circle.png │ │ │ ├── draw_dist.png │ │ │ └── draw_vector.png │ │ ├── pymol_drawing.py │ │ └── test_data │ │ │ └── CG.pdb │ ├── pymol_preview_generator │ │ ├── bash │ │ │ └── PyMOL Preview.workflow │ │ │ │ └── Contents │ │ │ │ ├── Info.plist │ │ │ │ ├── QuickLook │ │ │ │ └── Thumbnail.png │ │ │ │ └── document.wflow │ │ ├── docs │ │ │ ├── demo.gif │ │ │ ├── demo.png │ │ │ ├── linux.png │ │ │ ├── popup-ok.png │ │ │ ├── popup-progress.png │ │ │ ├── preview.png │ │ │ └── preview_2021-10-24_at_11.29.15.png │ │ ├── pymol_preview_generator.py │ │ ├── pymol_preview_install.py │ │ ├── readme.md │ │ └── zsh │ │ │ └── PyMOL Preview.workflow │ │ │ └── Contents │ │ │ ├── Info.plist │ │ │ ├── QuickLook │ │ │ └── Thumbnail.png │ │ │ └── document.wflow │ ├── renum_pdb_to_aln │ │ ├── __init__.py │ │ ├── renum_pdb_to_aln.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── ALN_OBJ1_OBJ2.fa │ │ │ ├── obj01.pdb │ │ │ └── obj01_out.pdb │ ├── rna_alignment │ │ ├── __init__.py │ │ ├── pngs │ │ │ ├── rchie.png │ │ │ └── rscape.png │ │ ├── random_assignment_of_nucleotides.py │ │ ├── rna_align_coverage.py │ │ ├── rna_align_distance_to_seq.py │ │ ├── rna_align_fetch_cm.py │ │ ├── rna_align_fetch_seed.py │ │ ├── rna_align_find_core.py │ │ ├── rna_align_find_seq_in_alignment.py │ │ ├── rna_align_foldability.py │ │ ├── rna_align_get_ss_from_fasta.py │ │ ├── rna_align_get_ss_from_stk.py │ │ ├── rna_align_seq_to_alignment.py │ │ ├── rna_alignment.ipynb │ │ ├── rna_alignment.py │ │ ├── rna_alignment_IA1.ipynb │ │ ├── rna_alignment_IE2.ipynb │ │ ├── rna_alignment_r2r.py │ │ ├── test.py │ │ ├── test.sh │ │ ├── test_data │ │ │ ├── 4lvv.seq │ │ │ ├── 4lvv_RF01831_cmalign.txt │ │ │ ├── 4lvv_cmalign.txt │ │ │ ├── IA1.gissd.sto │ │ │ ├── IE2.gissd.sto │ │ │ ├── RF00001.blocked.stk │ │ │ ├── RF00002.stockholm.stk │ │ │ ├── RF00167.stockholm.sto │ │ │ ├── RF00379.cm │ │ │ ├── RF00379.stockholm.stk │ │ │ ├── RF01831.cm │ │ │ ├── RF01831.short.stk │ │ │ ├── RF01831.stockholm.sto │ │ │ ├── RF02221.stockholm.sto │ │ │ ├── ade.fa │ │ │ ├── ade_gapped.fa │ │ │ ├── af27.fa │ │ │ ├── aln1.fasta │ │ │ ├── aln1_out.fasta │ │ │ ├── fasta.fasta │ │ │ ├── fasta_out.fasta │ │ │ ├── foldability │ │ │ │ └── rp17_foldability.png │ │ │ ├── rchie_test_files │ │ │ │ ├── bpseq.txt │ │ │ │ ├── connect.txt │ │ │ │ ├── fasta.txt │ │ │ │ ├── helix.txt │ │ │ │ └── vienna.txt │ │ │ ├── rfam_hit.txt │ │ │ ├── target.seq │ │ │ ├── u6_isl_rfam.sto │ │ │ ├── xrrna_rfam.sto │ │ │ └── xx.fa │ │ ├── test_output │ │ │ ├── RF00167_subset.sto │ │ │ ├── ade_gapped.fa │ │ │ ├── mini.sto │ │ │ ├── out.sto │ │ │ ├── plot.png │ │ │ └── subset.sto │ │ ├── test_rchie.sh │ │ ├── test_rna_alignment.py │ │ └── utils │ │ │ ├── R2R.cpp │ │ │ ├── R2R.cpp.readme.md │ │ │ ├── __init__.py │ │ │ ├── mfa-get-seq-for-species.py │ │ │ ├── rna_align_strip_stk.py │ │ │ ├── rna_alignment_calc_energy.py │ │ │ ├── rna_alignment_get_species.py │ │ │ ├── rna_alignment_merge_by_species.py │ │ │ ├── rna_alignment_process_id.py │ │ │ ├── rna_alignment_r2r.py │ │ │ ├── rna_alignment_sto_remove_uniq_ids.py │ │ │ ├── test.sh │ │ │ └── test_data │ │ │ ├── RF00026_demo.fa │ │ │ ├── mustela.fa │ │ │ ├── mustela_format.fa │ │ │ ├── mutant_list.stk │ │ │ ├── mutant_list.txt │ │ │ ├── pustela.fa │ │ │ └── u5_rfam_u5only.stk │ ├── rna_binding_affinity │ │ ├── rna_dG2kd.py │ │ ├── rna_kd2dG.py │ │ ├── rna_kd2pkd.py │ │ ├── rna_pkd2dG.py │ │ ├── rna_pkd2kd.py │ │ └── test.sh │ ├── rna_bp │ │ ├── __init__.py │ │ └── base_pair.py │ ├── rna_calc_evo_rmsd │ │ ├── RNAalignment.py │ │ ├── RNAmodel.py │ │ ├── __init__.py │ │ ├── evoclust_rmsd.csv │ │ ├── evoclust_rmsd.png │ │ ├── output.txt │ │ ├── readme.md │ │ ├── rna_calc_evo_rmsd.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── 1ehz_std.pdb │ │ │ ├── 4qk8_cl.pdb │ │ │ ├── 4qlm_cl.pdb │ │ │ ├── 6Y2L_2_std.pdb │ │ │ ├── aln.sto │ │ │ ├── aln_nox.sto │ │ │ ├── mapping.txt │ │ │ ├── test.sh │ │ │ ├── trna.sto │ │ │ └── trna_no_selector.sto │ ├── rna_calc_gdt │ │ ├── rna_calc_gdt.py │ │ └── test.sh │ ├── rna_calc_hbonds │ │ ├── docs │ │ │ └── hbonds_pymol.jpg │ │ ├── mdanalysis_hbonds.py │ │ ├── mdtraj_hbonds.py │ │ ├── pymol_list_hbonds.py │ │ ├── pytraj_hbond.py │ │ ├── readme.md │ │ ├── rna_calc_hbonds.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── 7jnh-AUA.csv │ │ │ ├── 7jnh-AUA.pdb │ │ │ ├── 7jnh-AUA_ha.csv │ │ │ ├── 7jnh-AUA_ha.pdb │ │ │ ├── Triple_cWW_cHW_UAU_rpr.pdb │ │ │ ├── Triple_cWW_cHW_UAU_rpr.pse │ │ │ ├── Triple_cWW_cHW_UAU_rpr_addChimera.pdb │ │ │ ├── Triple_cWW_cHW_UAU_rpr_addChimera_onlyBases.csv │ │ │ ├── Triple_cWW_cHW_UAU_rpr_addChimera_onlyBases.pdb │ │ │ ├── Triple_cWW_cHW_UAU_rpr_addh.pdb │ │ │ ├── Triple_cWW_cHW_UAU_rpr_bases_only.pdb │ │ │ └── Triple_cWW_cHW_UAU_rpr_bases_only_addhpymol.pdb │ ├── rna_calc_inf │ │ ├── __init__.py │ │ ├── doc │ │ │ ├── 1y26_dinf.png │ │ │ └── 1y26_dinf2.png │ │ ├── readme.md │ │ ├── rna_calc_dinf.py │ │ ├── rna_calc_inf.py │ │ ├── test.sh │ │ ├── test_data │ │ │ ├── 13_0_solution_4XW7_rpr.pdb │ │ │ ├── 13_Bujnicki_1_rpr.pdb │ │ │ ├── 1Y26.pdb │ │ │ ├── 1Y26_dinf │ │ │ ├── 1Y26_dinf_comparison.txt │ │ │ ├── 1prot.pdb │ │ │ ├── 1y26X_M451.pdb │ │ │ ├── 1y26X_M451_dinf │ │ │ ├── pistol.fa │ │ │ ├── pistol_inf_from_SeqSS.csv │ │ │ ├── pistol_inf_m1.csv │ │ │ ├── pistol_inf_m10.csv │ │ │ ├── pistol_inf_selection.csv │ │ │ ├── pistol_inf_stacking.csv │ │ │ ├── rp13 │ │ │ │ ├── 13_0_solution_4XW7_rpr.pdb │ │ │ │ ├── 13_0_solution_4XW7_rpr_del46-56.pdb │ │ │ │ ├── 13_Adamiak_1_rpr.pdb │ │ │ │ ├── 13_Adamiak_1_rpr_del46-56.pdb │ │ │ │ ├── 13_Bujnicki_1_rpr.pdb │ │ │ │ ├── 13_Bujnicki_1_rpr_del46-56.pdb │ │ │ │ ├── del.inf │ │ │ │ ├── inf.csv │ │ │ │ └── orignal.inf │ │ │ └── test.pdb │ │ └── test_dinf.sh │ ├── rna_calc_rmsd │ │ ├── README.md │ │ ├── __init__.py │ │ ├── lib │ │ │ ├── __init__.py │ │ │ └── rmsd │ │ │ │ ├── .gitignore │ │ │ │ ├── LICENSE │ │ │ │ ├── README.md │ │ │ │ ├── __init__.py │ │ │ │ ├── calculate_rmsd.py │ │ │ │ ├── examples │ │ │ │ ├── 1ypa.pdb │ │ │ │ ├── 3ci2.pdb │ │ │ │ ├── ethane.xyz │ │ │ │ ├── ethane_bond.xyz │ │ │ │ ├── ethane_mini.xyz │ │ │ │ └── ethane_translate.xyz │ │ │ │ └── rmsds.csv │ │ ├── rna_calc_rmsd.py │ │ ├── rna_calc_rmsd_all_vs_all.py │ │ ├── rna_calc_rmsd_biopython.py │ │ ├── rna_calc_rmsd_multi_targets.py │ │ ├── rna_calc_rmsd_pymol.py │ │ ├── test.sh │ │ ├── test_data │ │ │ ├── 21_solution_0_ChainA.csv │ │ │ ├── 21_solution_0_ChainB.csv │ │ │ ├── 21_solution_1_ChainA.csv │ │ │ ├── 21_solution_1_ChainB.csv │ │ │ ├── 21_solution_2.csv │ │ │ ├── multi-targets │ │ │ │ ├── rp21 │ │ │ │ │ ├── 21_3dRNA_1_rpr.pdb │ │ │ │ │ ├── 21_Adamiak_1_rpr.pdb │ │ │ │ │ ├── 21_ChenHighLig_1_rpr.pdb │ │ │ │ │ ├── 21_Das_1_rpr.pdb │ │ │ │ │ └── solutions │ │ │ │ │ │ ├── 21_solution_0_ChainA.pdb │ │ │ │ │ │ ├── 21_solution_0_ChainB.pdb │ │ │ │ │ │ ├── 21_solution_1_ChainA.pdb │ │ │ │ │ │ ├── 21_solution_1_ChainB.pdb │ │ │ │ │ │ └── 21_solution_2.pdb │ │ │ │ └── rp7 │ │ │ │ │ ├── 7.aln │ │ │ │ │ ├── 7_solution_0.pdb │ │ │ │ │ ├── 7_solution_1.pdb │ │ │ │ │ └── models │ │ │ │ │ ├── 7_Ding_1.pdb │ │ │ │ │ └── 7_Major_1.pdb │ │ │ ├── pistol │ │ │ │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb │ │ │ │ └── clusters │ │ │ │ │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb │ │ │ │ │ ├── pistol_thrs0.50A_clust01-000001_AA.pdb │ │ │ │ │ ├── pistol_thrs0.50A_clust02-000001_AA.pdb │ │ │ │ │ └── pistol_thrs0.50A_clust03-000001_AA.pdb │ │ │ ├── plot.ipynb │ │ │ ├── rmsd_calc_dir.tsv │ │ │ ├── rmsd_calc_dir_to_target.tsv │ │ │ ├── rmsd_calc_dir_to_target_align.tsv │ │ │ ├── rmsd_calc_dir_to_target_fit.tsv │ │ │ ├── rna_calc_rmsd_multi_targets_output.csv │ │ │ ├── struc1.pdb │ │ │ ├── struc2.pdb │ │ │ ├── struc3.pdb │ │ │ ├── struc4.pdb │ │ │ └── ways │ │ │ │ ├── backbone+sugar.csv │ │ │ │ ├── rmsd.csv │ │ │ │ ├── rmsd_all.csv │ │ │ │ ├── rmsd_bases.csv │ │ │ │ ├── rmsd_c1p.csv │ │ │ │ ├── yC_5LJ3_U2U6_core_mdrFx_addh_MD_100.pdb_rpr.pdb_fixChains.pdb │ │ │ │ ├── yC_5LJ3_U2U6_core_mdrFx_addh_MD_1_rpr_rchain.pdb_fixChains.pdb │ │ │ │ └── yC_5LJ3_U2U6_core_mdrFx_onlyTriplex_rpr.pdb │ │ └── test_output │ │ │ ├── pistol_rmsd.csv │ │ │ └── pistol_rmsd_name-rmsd-column.csv │ ├── rna_calc_rmsd_trafl │ │ ├── __init__.py │ │ ├── rna_cal_rmsd_trafl_plot.py │ │ └── rna_calc_rmsd_trafl.py │ ├── rna_convert_pseudoknot_formats │ │ ├── __init__.py │ │ ├── doc │ │ │ └── varna_2pk.png │ │ ├── readme.md │ │ ├── rna_pk_simrna_to_one_line.py │ │ ├── rna_ss_pk_to_simrna.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── simrna.ss │ │ │ ├── simrna3.ss │ │ │ ├── simrna_2chains.ss │ │ │ └── ss_with_pk.ss │ ├── rna_filter │ │ ├── .gitignore │ │ ├── README.md │ │ ├── __init__.py │ │ ├── pymol_dists.py │ │ ├── rna_csv2pairs.py │ │ ├── rna_dca_mapping.py │ │ ├── rna_dca_select_interactions.py │ │ ├── rna_ec2x.py │ │ ├── rna_filter.py │ │ ├── rna_get_distances.py │ │ ├── rna_get_dists.py │ │ ├── rna_pairs2SimRNArestrs.py │ │ ├── rna_pairs2rfilter.py │ │ ├── rna_pairs_diff.py │ │ ├── rna_restrs2SimRNArestrs.py │ │ ├── rna_restrs2mqapRNA.py │ │ ├── rna_ss_get_bps.py │ │ ├── simrna_get_restraints.py │ │ ├── test.sh │ │ ├── test_data │ │ │ ├── CG.pdb │ │ │ ├── CG.trafl │ │ │ ├── restraints.txt │ │ │ └── rna_filter.txt │ │ ├── test_dca.sh │ │ └── test_rna_filter.py │ ├── rna_get_restraints │ │ ├── .gitignore │ │ ├── README.md │ │ ├── rna_farna_get_restraints_vs_all.py │ │ ├── rna_simrna_get_restraints_vs_all.py │ │ └── test.sh │ ├── rna_helix_vis │ │ ├── README.md │ │ ├── __init__.py │ │ ├── doc │ │ │ └── rna_helix_vis.png │ │ ├── rna_helix_vis.py │ │ └── test_data │ │ │ ├── rp14.ss │ │ │ └── rp14_farna_eloop.out.1.pdb │ ├── rna_multimodels │ │ ├── check.sh │ │ ├── data │ │ │ ├── rp17_n3_ideal.pdb │ │ │ └── seq.fa │ │ ├── readme.md │ │ ├── rna_pdb_merge_into_one.py │ │ ├── test_in │ │ │ ├── 17_Adamiak_1_rpr.pdb │ │ │ ├── 17_Bujnicki_1_rpr.pdb │ │ │ └── 17_Chen_1_rpr.pdb │ │ ├── test_out │ │ │ └── rp17.pdb │ │ └── test_util.py │ ├── rna_pdb_edit_occupancy_bfactor │ │ ├── README.md │ │ ├── __init__.py │ │ ├── rna_pdb_edit_occupancy_bfactor.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── 3w3s_homologymodel.pdb │ │ │ ├── 3w3s_homologymodel_out.pdb │ │ │ └── 3w3s_homologymodel_select_atoms_out.pdb │ ├── rna_pdb_merge_structure_with_fragments │ │ ├── README.md │ │ ├── __init__.py │ │ ├── rna_pdb_merge_structure_with_fragments.py │ │ └── test_data │ │ │ ├── 1xjr_root.pdb │ │ │ ├── 1xjr_simrna_nstep_1.pdb │ │ │ └── rna_sq_renumber.pdb │ ├── rna_prediction_significance │ │ ├── .gitignore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── __init__.py │ │ ├── opt │ │ │ └── RNA_PredictionSignificance.cpp │ │ └── rna_prediction_significance.py │ ├── rna_refinement │ │ ├── .gitignore │ │ ├── __init__.py │ │ ├── rna_refinement.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── 179c48aa-c0d3-4bd6-8e06-12081da22998_ALL_thrs6.20A_clust01-000001_AA.pdb │ │ │ ├── 19_Bujnicki_Human_4_rpr_n0-000001.pdb_thrs0.50A_clust99-000001_AA.pdb │ │ │ ├── 19_Bujnicki_Human_4_rpr_n0-000001_refx.pdb_thrs0.50A_clust99-000001_AA_refx.pdb │ │ │ ├── input.pdb │ │ │ ├── input_refx.pdb │ │ │ ├── output.pdb │ │ │ ├── rp17_179c48aa-c0d3-4bd6-8e06-12081da22998_ALL_thrs6.20A_clust01-000001_AA._refx.pdb │ │ │ └── rp17_179c48aa-c0d3-4bd6-8e06-12081da22998_ALL_thrs6.20A_clust01-000001_AA._refx_refx.pdb │ ├── rna_rfam │ │ ├── list.txt │ │ ├── rna_download_rfam.py │ │ └── test.sh │ ├── rna_rosetta │ │ ├── .gitignore │ │ ├── __init__.py │ │ ├── rna_rosetta_check_progress.py │ │ ├── rna_rosetta_cluster.py │ │ ├── rna_rosetta_easy_cat.py │ │ ├── rna_rosetta_extract.py │ │ ├── rna_rosetta_extract_lowscore_decoys.py │ │ ├── rna_rosetta_get_score.py │ │ ├── rna_rosetta_head.py │ │ ├── rna_rosetta_min.py │ │ ├── rna_rosetta_n.py │ │ ├── rna_rosetta_run.py │ │ ├── rna_rosetta_silent_file_sort_and_select.py │ │ ├── rna_rosetta_silent_random.py │ │ ├── rna_rosetta_silent_split.py │ │ ├── test.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── S_000005_032.out │ │ │ ├── S_000020_024.out │ │ │ ├── S_000027_058.out │ │ │ ├── S_000035_003.out │ │ │ ├── a04.fa │ │ │ ├── a99.fa │ │ │ ├── ade.fa │ │ │ ├── selected.out │ │ │ ├── selected.out.rand2.out │ │ │ ├── selected.out.rand5.out │ │ │ ├── silent_sort.out │ │ │ ├── tetraloop.fa │ │ │ └── tl │ │ │ ├── CMDLINES │ │ │ ├── helix0.fasta │ │ │ ├── helix0.out │ │ │ ├── helix0.params │ │ │ ├── input.fa │ │ │ ├── qsubMINI │ │ │ ├── seq.fa │ │ │ ├── ss.fa │ │ │ ├── tl.fasta │ │ │ └── tl.params │ ├── rna_sali2dotbracket │ │ ├── README.MD │ │ ├── __init__.py │ │ ├── rna_sali2dotbracket.py │ │ └── test_data │ │ │ ├── IA1.sali │ │ │ └── IA1_dotbracket.txt │ ├── rna_seq_identity │ │ ├── RF03167.cm │ │ ├── output.sto │ │ ├── pairwase.py │ │ ├── readme.md │ │ ├── seq1.fa │ │ ├── seq12.fa │ │ ├── seq2.fa │ │ └── test.sh │ ├── rna_seq_search_BLASTn_outfmt-6 │ │ ├── select_seq_fromBLAStn_6outfm.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── db_nt.fasta │ │ │ ├── db_nt_out.fasta │ │ │ └── output_55 │ ├── rna_x3dna │ │ ├── __init__.py │ │ ├── readme.rst │ │ ├── rna_x3dna.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── 1xjr.pdb │ │ │ ├── 1xjr_output.pdb │ │ │ ├── 6TNA.pdb │ │ │ ├── CG.pdb │ │ │ └── rp2_bujnicki_1_rpr.pdb │ ├── rnapuzzle_sender │ │ ├── .gitignore │ │ ├── files │ │ │ ├── DASLAB_Problem13_Rank1.pdb │ │ │ ├── DASLAB_Problem13_Rank10.pdb │ │ │ ├── DASLAB_Problem13_Rank2.pdb │ │ │ ├── DASLAB_Problem13_Rank3.pdb │ │ │ ├── DASLAB_Problem13_Rank4.pdb │ │ │ ├── DASLAB_Problem13_Rank5.pdb │ │ │ ├── DASLAB_Problem13_Rank6.pdb │ │ │ ├── DASLAB_Problem13_Rank7.pdb │ │ │ ├── DASLAB_Problem13_Rank8.pdb │ │ │ └── DASLAB_Problem13_Rank9.pdb │ │ ├── rnapuzzle_sender.py │ │ ├── test.sh │ │ └── test_of_email_content │ │ │ ├── model1.pdb │ │ │ ├── test.pdb │ │ │ ├── test.txt │ │ │ ├── test02.pdb │ │ │ └── test3.pdb │ ├── rnashape2ascii │ │ ├── LICENSE │ │ ├── README.md │ │ ├── rnashape2ascii.py │ │ ├── test.sh │ │ └── test_data │ │ │ ├── RNAPZ12_1M7_0000.rdat │ │ │ └── r1_raw.txt │ ├── sandbox │ │ └── rna_compare │ │ │ ├── rmsds.csv │ │ │ ├── rna_compare.py │ │ │ └── test_data │ │ │ ├── 1y26_clean.pdb │ │ │ └── ade_pk_82a6_100low-000006_AA.pdb │ ├── simrna_trajectory │ │ ├── .gitignore │ │ ├── __init__.py │ │ ├── rna_simrna_cluster.py │ │ ├── rna_simrna_energy_plot.py │ │ ├── rna_simrna_extract.py │ │ ├── rna_simrna_lowest.py │ │ ├── rna_simrna_subset.py │ │ ├── simrna_trajectory.py │ │ ├── subset.trafl │ │ ├── test_data │ │ │ └── mini.trafl │ │ ├── test_rmsd.py │ │ └── test_rna_simrna.py │ ├── triplexibility │ │ ├── .gitignore │ │ ├── data │ │ │ ├── XcWWX.csv │ │ │ ├── cWW_cHS_GCU.csv │ │ │ ├── db.csv │ │ │ ├── db_trx2.csv │ │ │ ├── t1-1-Triple_cWW_cHS_GCU_exemplar_rpr_fx.csv │ │ │ └── t1-1-Triple_cWW_cHS_GCU_exemplar_rpr_fx.pdb │ │ ├── db │ │ │ └── gendb.py │ │ ├── download-all-pdbs.py │ │ ├── download-all-triples.py │ │ ├── download-all.py │ │ ├── lib.py │ │ ├── process_triple.py │ │ ├── readme.md │ │ ├── splix.py │ │ ├── test.sh │ │ ├── test_all.sh │ │ ├── triple-db.csv │ │ ├── triplexibility.py │ │ ├── triplexibility2.py │ │ ├── trx-mutget-t1-1.py │ │ ├── trx-mutget-t1-2.py │ │ ├── trx.ipynb │ │ ├── trx.py │ │ ├── trx_analysis.py │ │ ├── trx_analysis.txt │ │ ├── trx_mutagen.py │ │ ├── trx_mutagen_allvsall.py │ │ ├── trx_score.py │ │ ├── trx_score_allvsall.py │ │ ├── trx_score_growth.py │ │ ├── trx_score_onCol.py │ │ └── trx_score_onCol_allvsall.py │ ├── webserver-engine │ │ ├── .gitignore │ │ ├── README.md │ │ ├── __init__.py │ │ ├── ac │ │ ├── admin │ │ │ ├── css │ │ │ │ ├── base.css │ │ │ │ ├── changelists.css │ │ │ │ ├── dashboard.css │ │ │ │ ├── forms.css │ │ │ │ ├── ie.css │ │ │ │ ├── rtl.css │ │ │ │ └── widgets.css │ │ │ ├── img │ │ │ │ ├── changelist-bg.gif │ │ │ │ ├── changelist-bg_rtl.gif │ │ │ │ ├── chooser-bg.gif │ │ │ │ ├── chooser_stacked-bg.gif │ │ │ │ ├── default-bg-reverse.gif │ │ │ │ ├── default-bg.gif │ │ │ │ ├── deleted-overlay.gif │ │ │ │ ├── gis │ │ │ │ │ └── move_vertex_on.png │ │ │ │ ├── icon-no.gif │ │ │ │ ├── icon-unknown.gif │ │ │ │ ├── icon-yes.gif │ │ │ │ ├── icon_addlink.gif │ │ │ │ ├── icon_alert.gif │ │ │ │ ├── icon_calendar.gif │ │ │ │ ├── icon_changelink.gif │ │ │ │ ├── icon_clock.gif │ │ │ │ ├── icon_deletelink.gif │ │ │ │ ├── icon_error.gif │ │ │ │ ├── icon_searchbox.png │ │ │ │ ├── icon_success.gif │ │ │ │ ├── inline-delete-8bit.png │ │ │ │ ├── inline-delete.png │ │ │ │ ├── inline-restore-8bit.png │ │ │ │ ├── inline-restore.png │ │ │ │ ├── inline-splitter-bg.gif │ │ │ │ ├── nav-bg-grabber.gif │ │ │ │ ├── nav-bg-reverse.gif │ │ │ │ ├── nav-bg-selected.gif │ │ │ │ ├── nav-bg.gif │ │ │ │ ├── selector-icons.gif │ │ │ │ ├── selector-search.gif │ │ │ │ ├── sorting-icons.gif │ │ │ │ ├── tool-left.gif │ │ │ │ ├── tool-left_over.gif │ │ │ │ ├── tool-right.gif │ │ │ │ ├── tool-right_over.gif │ │ │ │ ├── tooltag-add.gif │ │ │ │ ├── tooltag-add_over.gif │ │ │ │ ├── tooltag-arrowright.gif │ │ │ │ └── tooltag-arrowright_over.gif │ │ │ └── js │ │ │ │ ├── LICENSE-JQUERY.txt │ │ │ │ ├── SelectBox.js │ │ │ │ ├── SelectFilter2.js │ │ │ │ ├── actions.js │ │ │ │ ├── actions.min.js │ │ │ │ ├── admin │ │ │ │ ├── DateTimeShortcuts.js │ │ │ │ ├── RelatedObjectLookups.js │ │ │ │ └── ordering.js │ │ │ │ ├── calendar.js │ │ │ │ ├── collapse.js │ │ │ │ ├── collapse.min.js │ │ │ │ ├── compress.py │ │ │ │ ├── core.js │ │ │ │ ├── getElementsBySelector.js │ │ │ │ ├── inlines.js │ │ │ │ ├── inlines.min.js │ │ │ │ ├── jquery.init.js │ │ │ │ ├── jquery.js │ │ │ │ ├── jquery.min.js │ │ │ │ ├── prepopulate.js │ │ │ │ ├── prepopulate.min.js │ │ │ │ ├── timeparse.js │ │ │ │ └── urlify.js │ │ ├── app │ │ │ ├── __init__.py │ │ │ ├── admin.py │ │ │ ├── models.py │ │ │ ├── static │ │ │ │ └── app │ │ │ │ │ ├── addyosmani-jquery-ui-bootstrap-71f2e47 │ │ │ │ │ ├── README.md │ │ │ │ │ ├── assets │ │ │ │ │ │ ├── css │ │ │ │ │ │ │ ├── bootstrap.min.css │ │ │ │ │ │ │ ├── docs.css │ │ │ │ │ │ │ ├── font-awesome-ie7.min.css │ │ │ │ │ │ │ ├── font-awesome.min.css │ │ │ │ │ │ │ └── font │ │ │ │ │ │ │ │ ├── FontAwesome.otf │ │ │ │ │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ │ │ │ │ └── fontawesome-webfont.woff │ │ │ │ │ │ ├── ico │ │ │ │ │ │ │ ├── apple-touch-icon-114-precomposed.png │ │ │ │ │ │ │ ├── apple-touch-icon-144-precomposed.png │ │ │ │ │ │ │ ├── apple-touch-icon-57-precomposed.png │ │ │ │ │ │ │ ├── apple-touch-icon-72-precomposed.png │ │ │ │ │ │ │ ├── favicon.ico │ │ │ │ │ │ │ └── favicon.png │ │ │ │ │ │ ├── img │ │ │ │ │ │ │ └── bs-docs-masthead-pattern.png │ │ │ │ │ │ └── js │ │ │ │ │ │ │ ├── bootstrap.min.js │ │ │ │ │ │ │ ├── demo.js │ │ │ │ │ │ │ ├── docs.js │ │ │ │ │ │ │ ├── google-code-prettify │ │ │ │ │ │ │ ├── prettify.css │ │ │ │ │ │ │ └── prettify.js │ │ │ │ │ │ │ ├── jquery-1.8.3.min.js │ │ │ │ │ │ │ ├── jquery-1.9.0.min.js │ │ │ │ │ │ │ └── jquery-ui-1.10.0.custom.min.js │ │ │ │ │ ├── css │ │ │ │ │ │ ├── custom-theme │ │ │ │ │ │ │ ├── images │ │ │ │ │ │ │ │ ├── ui-bg_flat_0_aaaaaa_40x100.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_55_fbf9ee_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_65_ffffff_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_75_dadada_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_75_e6e6e6_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_glass_75_ffffff_1x400.png │ │ │ │ │ │ │ │ ├── ui-bg_highlight-soft_75_cccccc_1x100.png │ │ │ │ │ │ │ │ ├── ui-bg_inset-soft_95_fef1ec_1x100.png │ │ │ │ │ │ │ │ ├── ui-icons_222222_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_2e83ff_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_454545_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_888888_256x240.png │ │ │ │ │ │ │ │ ├── ui-icons_cd0a0a_256x240.png │ │ │ │ │ │ │ │ └── ui-icons_f6cf3b_256x240.png │ │ │ │ │ │ │ ├── jquery-ui-1.10.0.custom.css │ │ │ │ │ │ │ ├── jquery-ui-1.9.2.custom.css │ │ │ │ │ │ │ ├── jquery.ui.1.10.0.ie.css │ │ │ │ │ │ │ └── jquery.ui.1.9.2.ie.css │ │ │ │ │ │ └── demo.css │ │ │ │ │ ├── extra.html │ │ │ │ │ ├── index.html │ │ │ │ │ ├── js │ │ │ │ │ │ ├── demo.js │ │ │ │ │ │ ├── jquery-1.8.3.min.js │ │ │ │ │ │ └── jquery-ui-1.9.2.custom.min.js │ │ │ │ │ ├── old_index.html │ │ │ │ │ └── third-party │ │ │ │ │ │ ├── jQuery-UI-Date-Range-Picker │ │ │ │ │ │ ├── css │ │ │ │ │ │ │ └── ui.daterangepicker.css │ │ │ │ │ │ ├── index.html │ │ │ │ │ │ └── js │ │ │ │ │ │ │ ├── date.js │ │ │ │ │ │ │ ├── daterangepicker.jQuery.compressed.js │ │ │ │ │ │ │ └── daterangepicker.jQuery.js │ │ │ │ │ │ ├── jQuery-UI-FileInput │ │ │ │ │ │ ├── css │ │ │ │ │ │ │ └── enhanced.css │ │ │ │ │ │ ├── images │ │ │ │ │ │ │ ├── icon-generic.gif │ │ │ │ │ │ │ ├── icon-image.gif │ │ │ │ │ │ │ ├── icon-media.gif │ │ │ │ │ │ │ └── icon-zip.gif │ │ │ │ │ │ └── js │ │ │ │ │ │ │ ├── enhance.min.js │ │ │ │ │ │ │ └── fileinput.jquery.js │ │ │ │ │ │ └── wijmo │ │ │ │ │ │ ├── jquery.bgiframe-2.1.3-pre.js │ │ │ │ │ │ ├── jquery.mousewheel.min.js │ │ │ │ │ │ ├── jquery.wijmo-open.1.5.0.css │ │ │ │ │ │ └── jquery.wijmo-open.1.5.0.min.js │ │ │ │ │ ├── bootstrap-acknowledgeinput.min.js │ │ │ │ │ ├── bootstrap-filestyle │ │ │ │ │ ├── LICENSE-MIT │ │ │ │ │ ├── README.md │ │ │ │ │ ├── src │ │ │ │ │ │ ├── bootstrap-filestyle.js │ │ │ │ │ │ └── bootstrap-filestyle.min.js │ │ │ │ │ └── test │ │ │ │ │ │ ├── css │ │ │ │ │ │ └── bootstrap.min.css │ │ │ │ │ │ ├── img │ │ │ │ │ │ ├── glyphicons-halflings-white.png │ │ │ │ │ │ └── glyphicons-halflings.png │ │ │ │ │ │ ├── index.html │ │ │ │ │ │ ├── js │ │ │ │ │ │ ├── aplication.js │ │ │ │ │ │ └── bootstrap.min.js │ │ │ │ │ │ ├── upload.php │ │ │ │ │ │ └── upload │ │ │ │ │ │ └── .folder │ │ │ │ │ ├── bootstrap-fileupload │ │ │ │ │ ├── bootstrap-fileupload.css │ │ │ │ │ ├── bootstrap-fileupload.js │ │ │ │ │ ├── bootstrap-fileupload.min.css │ │ │ │ │ └── bootstrap-fileupload.min.js │ │ │ │ │ ├── bootstrap │ │ │ │ │ ├── css │ │ │ │ │ │ ├── bootstrap-responsive.css │ │ │ │ │ │ ├── bootstrap-responsive.min.css │ │ │ │ │ │ ├── bootstrap.css │ │ │ │ │ │ └── bootstrap.min.css │ │ │ │ │ ├── img │ │ │ │ │ │ ├── glyphicons-halflings-white.png │ │ │ │ │ │ └── glyphicons-halflings.png │ │ │ │ │ └── js │ │ │ │ │ │ ├── bootstrap.js │ │ │ │ │ │ ├── bootstrap.min.js │ │ │ │ │ │ └── jquery.js │ │ │ │ │ ├── demo │ │ │ │ │ ├── 1EHZ.cif │ │ │ │ │ ├── 1EHZ.pdb │ │ │ │ │ ├── 1l2x_restraints.txt │ │ │ │ │ ├── 1l2x_rna_clust0.pdb │ │ │ │ │ ├── 1xjr.cif │ │ │ │ │ ├── 1xjr.pdb │ │ │ │ │ ├── 21_3dRNA_1_rpr.pdb │ │ │ │ │ ├── 21_Adamiak_1_rpr.pdb │ │ │ │ │ ├── 21_ChenHighLig_1_rpr.pdb │ │ │ │ │ ├── 21_Das_1_rpr.pdb │ │ │ │ │ ├── 21_solution_2_rpr.pdb │ │ │ │ │ ├── 2gdi.pdb │ │ │ │ │ ├── 2gdi.txt │ │ │ │ │ ├── 2gdi_pred.txt │ │ │ │ │ ├── 2gdi_rnafold.txt │ │ │ │ │ ├── 2gdi_s.txt │ │ │ │ │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr.pdb │ │ │ │ │ ├── 5k7c_clean_onechain_renumber_as_puzzle_srr_min.pdb │ │ │ │ │ ├── MissingAtomsAdded_rpr.pdb │ │ │ │ │ ├── gtp.pdb │ │ │ │ │ ├── missing_op1op2_r43OK.pdb │ │ │ │ │ ├── pistol_thrs0.50A_clust272-000001_AA_min.pdb │ │ │ │ │ ├── rp21.zip │ │ │ │ │ ├── tRNA.txt │ │ │ │ │ ├── tRNA_saxs.dat │ │ │ │ │ ├── tetraloop.pdb │ │ │ │ │ ├── tetraloop_helix.pdb │ │ │ │ │ ├── tetraloop_mdr.pdb │ │ │ │ │ ├── to-replace.pdb │ │ │ │ │ ├── triple-ACA.pdb │ │ │ │ │ ├── unmodified_tRNAPhe_restraints.txt │ │ │ │ │ ├── yC_5lj3_CWC2_C.pdb │ │ │ │ │ ├── yC_5lj3_Cwc2_Exon_Intron.pdb │ │ │ │ │ ├── yC_5lj3_Exon_C.pdb │ │ │ │ │ ├── yC_5lj3_Exon_Intron.pdb │ │ │ │ │ ├── yC_5lj3_Exon_Intron_rpr.pdb │ │ │ │ │ └── yC_5lj3_Intron_C.pdb │ │ │ │ │ ├── dropzone │ │ │ │ │ ├── dropzone.min.css │ │ │ │ │ └── dropzone.min.js │ │ │ │ │ ├── help │ │ │ │ │ ├── 1evv-ss-w11rst2_A.rest │ │ │ │ │ └── submit_seq_w_ss_restraints.png │ │ │ │ │ ├── img │ │ │ │ │ ├── 01.jpg │ │ │ │ │ ├── 01.png │ │ │ │ │ ├── 01b.png │ │ │ │ │ ├── 01c.jpg │ │ │ │ │ ├── 02.png │ │ │ │ │ ├── 02x.png │ │ │ │ │ ├── 03.png │ │ │ │ │ ├── diffpdb.jpg │ │ │ │ │ ├── folder.gif │ │ │ │ │ └── qrnas.png │ │ │ │ │ ├── jsmol.zip │ │ │ │ │ ├── rto.css │ │ │ │ │ └── rto.js │ │ │ ├── templates │ │ │ │ ├── about.html │ │ │ │ ├── analysis.html │ │ │ │ ├── archive │ │ │ │ │ ├── progress.html │ │ │ │ │ ├── result.html │ │ │ │ │ ├── secondary-structure.html │ │ │ │ │ ├── sequence-search.html │ │ │ │ │ └── submit.html │ │ │ │ ├── assess.html │ │ │ │ ├── base.html │ │ │ │ ├── calc-inf.html │ │ │ │ ├── calc-rmsd.html │ │ │ │ ├── cat.html │ │ │ │ ├── clarna.html │ │ │ │ ├── contact.html │ │ │ │ ├── delete.html │ │ │ │ ├── diffpdb.html │ │ │ │ ├── dont_exits.html │ │ │ │ ├── edit.html │ │ │ │ ├── errors.html │ │ │ │ ├── extract.html │ │ │ │ ├── h2a.html │ │ │ │ ├── help.html │ │ │ │ ├── home.html │ │ │ │ ├── mdr.html │ │ │ │ ├── min.html │ │ │ │ ├── mutate.html │ │ │ │ ├── notebase.html │ │ │ │ ├── notes.html │ │ │ │ ├── qrnas.html │ │ │ │ ├── rpl.html │ │ │ │ ├── rpr.html │ │ │ │ ├── seq.html │ │ │ │ ├── ss.html │ │ │ │ ├── swap.html │ │ │ │ ├── tocif.html │ │ │ │ ├── tools.html │ │ │ │ └── topdb.html │ │ │ └── views.py │ │ ├── checker.py │ │ ├── checker.sh │ │ ├── cleanup.py │ │ ├── daemon.py │ │ ├── daemon.sh │ │ ├── ddev.sh │ │ ├── django_extensions │ │ │ ├── __init__.py │ │ │ ├── css │ │ │ │ └── jquery.autocomplete.css │ │ │ ├── img │ │ │ │ └── indicator.gif │ │ │ └── js │ │ │ │ ├── jquery.ajaxQueue.js │ │ │ │ ├── jquery.autocomplete.js │ │ │ │ ├── jquery.bgiframe.min.js │ │ │ │ └── jquery.js │ │ ├── docs │ │ │ ├── admin.png │ │ │ └── demo.png │ │ ├── install.txt │ │ ├── manage.py │ │ ├── notes.md │ │ ├── runme_dev.sh │ │ ├── sendmail.py │ │ ├── web │ │ │ ├── __init__.py │ │ │ ├── settings.py │ │ │ ├── urls.py │ │ │ └── wsgi.py │ │ └── wsgi.py │ └── workflow │ │ ├── README.md │ │ ├── after_peyote_clean.sh │ │ ├── automatix.py │ │ ├── chunker.py │ │ ├── clean.sh │ │ ├── evox.py │ │ ├── inf_all.py │ │ ├── mass_inf.py │ │ ├── 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