LICENSE
README.md
pyproject.toml
src/RNAmotiFold/__init__.py
src/RNAmotiFold/api.py
src/RNAmotiFold.egg-info/PKG-INFO
src/RNAmotiFold.egg-info/SOURCES.txt
src/RNAmotiFold.egg-info/dependency_links.txt
src/RNAmotiFold.egg-info/entry_points.txt
src/RNAmotiFold.egg-info/requires.txt
src/RNAmotiFold.egg-info/top_level.txt
src/RNAmotiFold/RNALoops/LICENSE
src/RNAmotiFold/RNALoops/RNAmotiAlign.gap
src/RNAmotiFold/RNALoops/RNAmotiFold.gap
src/RNAmotiFold/RNALoops/RNAmotiFold_subopt_pfc.gap
src/RNAmotiFold/RNALoops/makefile
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_ali_mfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_ali_mfe_macrostate.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_ali_mfe_motifs.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_ali_outside_mfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_ali_pknot_mfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_ali_puremfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_cofold_mfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_mfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_mfe_SHAPE.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_mfe_macrostate.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_mfe_macrostate_debug.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_outside_mfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/alg_pknot_mfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/Parts/algpart_ali_mfe_basic.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/Parts/algpart_ali_mfe_basic_motifs.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/Parts/algpart_cofold_mfe.gap
src/RNAmotiFold/RNALoops/Algebras/MFE/Parts/algpart_mfe_basic.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/alg_ali_motBracket.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/alg_ali_motif.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/alg_ali_shapes_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/alg_hishapes_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/alg_hishapes_mot_shaped.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/alg_motBracket.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/alg_motif.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/alg_shapes_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/alg_motBracket_basic.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/alg_motif_basic.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shape1_basic_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shape1_macrostate_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shape2_basic_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shape3_basic_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shape4_basic_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shape5_basic_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shape5_macrostate_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shapeX_basic_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Motif/Parts/algpart_shapeX_macrostate_mot.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_ali_outside_pfunc.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_ali_pfunc.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_ali_pfunc_macrostate.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_ali_pknot_pfunc.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_cofold_pfunc.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_outside_pfunc.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_pfunc.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_pfunc_macrostate.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/alg_pknot_pfunc.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/Parts/algpart_ali_pfunc_basic.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/Parts/algpart_cofold_pfunc.gap
src/RNAmotiFold/RNALoops/Algebras/Pfunc/Parts/algpart_pfunc_basic.gap
src/RNAmotiFold/RNALoops/Extensions/MotifMap.hh
src/RNAmotiFold/RNALoops/Extensions/alifold.hh
src/RNAmotiFold/RNALoops/Extensions/alignment.hh
src/RNAmotiFold/RNALoops/Extensions/bpfilter.hh
src/RNAmotiFold/RNALoops/Extensions/mfesubopt.hh
src/RNAmotiFold/RNALoops/Extensions/mot_header.hh
src/RNAmotiFold/RNALoops/Extensions/motif.hh
src/RNAmotiFold/RNALoops/Extensions/probabilities.hh
src/RNAmotiFold/RNALoops/Extensions/rnaoptions.hh
src/RNAmotiFold/RNALoops/Extensions/rnaoptions_defaults.hh
src/RNAmotiFold/RNALoops/Extensions/rules.hh
src/RNAmotiFold/RNALoops/Extensions/shapes.hh
src/RNAmotiFold/RNALoops/Extensions/singlefold.hh
src/RNAmotiFold/RNALoops/Extensions/twotrack.hh
src/RNAmotiFold/RNALoops/Extensions/typesRNAfolding.hh
src/RNAmotiFold/RNALoops/Grammars/gra_macrostate.gap
src/RNAmotiFold/RNALoops/Grammars/gra_macrostate_npm.gap
src/RNAmotiFold/RNALoops/Grammars/gra_microstate.gap
src/RNAmotiFold/RNALoops/Grammars/gra_microstate_npm.gap
src/RNAmotiFold/RNALoops/Grammars/gra_motified_macrostate.gap
src/RNAmotiFold/RNALoops/Grammars/gra_motified_microstate.gap
src/RNAmotiFold/RNALoops/Misc/Applications/addRNAoptions.pl
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/compile.sh
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/RNAmoSh/makefile
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/RNAmotiAlign/makefile
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/RNAmotiCes/makefile
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/RNAmotiFold/makefile
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/__init__.py
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/get_RNA3D_motifs.py
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/group_by_motif.sh
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/motifs.json
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/nucleotide_conversion.json
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/test_RNA_3D_motifs.py
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/update_hexdump.sh
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/empty.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/combined/3_94/rna3d_bulges.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/combined/3_94/rna3d_hairpins.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/combined/3_94/rna3d_internals.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/combined/3_95/rna3d_bulges.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/combined/3_95/rna3d_hairpins.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/combined/3_95/rna3d_internals.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/combined/3_96/rna3d_bulges.csv
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src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_7_separated/internals/nc_cww_bp.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_7_separated/internals/sarcin_ricin.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_7_separated/internals/uaa_gan.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/bulges/c_loop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/bulges/nc_cww_bp.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/hairpins/gnra.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/hairpins/tRNA_anticodon_loop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/hairpins/tRNA_d_loop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/hairpins/tloop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/hairpins/uncg.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/internals/c_loop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/internals/kink_turn.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/internals/nc_cww_bp.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/internals/sarcin_ricin.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_8_separated/internals/uaa_gan.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/bulges/c_loop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/bulges/nc_cww_bp.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/hairpins/gnra.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/hairpins/tRNA_anticodon_loop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/hairpins/tRNA_d_loop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/hairpins/tloop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/hairpins/uncg.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/internals/c_loop.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/internals/kink_turn.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/internals/nc_cww_bp.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/internals/sarcin_ricin.csv
src/RNAmotiFold/RNALoops/Misc/Applications/RNAmotiFold/motifs/versions/separated/4_9_separated/internals/uaa_gan.csv
src/RNAmotiFold/RNALoops/Misc/Applications/lib/makefile
src/RNAmotiFold/RNALoops/Misc/Applications/lib/foldGrammars/References.pm
src/RNAmotiFold/RNALoops/Misc/Applications/lib/foldGrammars/Settings.pm
src/RNAmotiFold/RNALoops/Misc/Applications/lib/foldGrammars/Structure.pm
src/RNAmotiFold/RNALoops/Misc/Applications/lib/foldGrammars/Utils.pm
src/RNAmotiFold/RNALoops/Signatures/sig_foldrna.gap
src/RNAmotiFold/RNALoops/Signatures/Parts/sigpart_basic.gap
src/RNAmotiFold/bgap_rna/alg_setup.py
src/RNAmotiFold/bgap_rna/call_handler.py
src/RNAmotiFold/bgap_rna/input_handler.py
src/RNAmotiFold/bgap_rna/motif_handler.py
src/RNAmotiFold/bgap_rna/subprocess_handler.py
src/RNAmotiFold/configs/defaults.ini
src/RNAmotiFold/configs/paths.ini
src/RNAmotiFold/input/action_overwrites.py
src/RNAmotiFold/input/arg_parsing.py
src/RNAmotiFold/input/cli.py
src/RNAmotiFold/input/dependency_finder.py
src/RNAmotiFold/input/parameters.py
src/RNAmotiFold/results/outputs.py
src/RNAmotiFold/results/results.py