rna-tools
User Documentation
Install
Quickstart
rna-pdb-tools
rna-tools
rna-tools & PyMOL [PyMOL4RNA]
rna-tools & Mac/Linux
rna-tools & Jupyter Notebooks / Colab
rna-tools & Emacs
rna-tools & geekbook
RNA Puzzle Submission
Selection
Tips
Examples of workflows
Developer Documentation
Install & Configure
Git Quickref
Configuration
Documentation
Add a new tool to the package
rna-tools
Index
Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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H
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I
|
J
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L
|
M
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N
|
O
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P
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R
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S
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T
|
U
|
W
|
X
Symbols
--alignfn
random_assignment_of_nucleotides.py command line option
--all-stars
rna_align_foldability.py command line option
--backbone-only
rna_pdb_tools.py command line option
rna_standardize.py command line option
--bases-only
rna_pdb_tools.py command line option
rna_standardize.py command line option
--bfactor
rna_pdb_edit_occupancy_bfactor.py command line option
--bins
rna_plot_hist.py command line option
--chain
rna_add_chain.py command line option
rna_ec2x.py command line option
--chain-first
rna_pdb_tools.py command line option
--check-geometry
rna_standardize.py command line option
--cif2pdb
rna_pdb_tools.py command line option
--clean
rna_pdb_tools.py command line option
--cleanup
rna_simrna_extract.py command line option
--cluster
rna_simrnaweb_download_job.py command line option
--collapsed-view
rna_pdb_tools.py command line option
--color-seq
rna_pdb_tools.py command line option
--column
rna_plot_density.py command line option
rna_plot_hist.py command line option
--compact
rna_pdb_tools.py command line option
--cpus
rna_rosetta_min.py command line option
rna_rosetta_run.py command line option
--csv
rna_alignment_calc_energy.py command line option
--cv
rna_pdb_tools.py command line option
--dca
rna_dca_mapping.py command line option
--debug
rna_alignment_calc_energy.py command line option
rna_alignment_get_species.py command line option
rna_calc_inf.py command line option
--delete
rna_pdb_tools.py command line option
--delete-anisou
rna_pdb_tools.py command line option
--dev
rna_align_foldability.py command line option
--dist
rna_pairs2SimRNArestrs.py command line option
--dont-fix-missing-atoms
rna_pdb_tools.py command line option
rna_standardize.py command line option
--dont-remove-sel-files
rna_calc_inf.py command line option
--dont-rename-chains
rna_pdb_tools.py command line option
rna_standardize.py command line option
--dont-replace-hetatm
rna_standardize.py command line option
--dont-report-missing-atoms
rna_pdb_tools.py command line option
rna_standardize.py command line option
--download-trajectory
rna_simrnaweb_download_job.py command line option
--ec-pairs
rna_ec2x.py command line option
--edit
rna_pdb_tools.py command line option
--evo-mapping
rna_alignment_get_species.py command line option
--evo-mapping-default
rna_alignment_get_species.py command line option
--extract
rna_pdb_tools.py command line option
rna_simrnaweb_download_job.py command line option
--extract-chain
rna_pdb_tools.py command line option
--fasta
rna_pdb_tools.py command line option
--fetch
rna_pdb_tools.py command line option
--fetch-ba
rna_pdb_tools.py command line option
--fetch-chain
rna_pdb_tools.py command line option
--fetch-cif
rna_pdb_tools.py command line option
--fetch-fasta
rna_pdb_tools.py command line option
--fix
rna_pdb_tools.py command line option
--flanks
rna_alignment_calc_energy.py command line option
--force
rna_calc_inf.py command line option
--get-chain
rna_pdb_tools.py command line option
--get-rnapuzzle-ready
rna_pdb_tools.py command line option
--get-seq
rna_pdb_tools.py command line option
--get-ss
rna_pdb_tools.py command line option
--go
rna_rosetta_min.py command line option
rna_rosetta_run.py command line option
--gseq
rna_dca_mapping.py command line option
--helices
rna_rosetta_run.py command line option
--help
pdbs_measure_atom_dists.py command line option
random_assignment_of_nucleotides.py command line option
renum_to_aln.py command line option
rna_add_chain.py command line option
rna_align_distance_to_seq.py command line option
rna_align_foldability.py command line option
rna_align_get_ss_from_fasta.py command line option
rna_align_get_ss_from_stk.py command line option
rna_alignment_calc_energy.py command line option
rna_alignment_get_species.py command line option
rna_cal_rmsd_trafl_plot command line option
rna_calc_evo_rmsd command line option
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_all_vs_all command line option
rna_calc_rmsd_multi_targets.py command line option
rna_dca_mapping.py command line option
rna_dot2ct.py command line option
rna_ec2x.py command line option
rna_filter.py command line option
rna_mq_rnakb.py command line option
rna_pairs2SimRNArestrs.py command line option
rna_pairs_diff.py command line option
rna_pdb_edit_occupancy_bfactor.py command line option
rna_pdb_tools.py command line option
rna_plot_density.py command line option
rna_plot_hist.py command line option
rna_refinement.py command line option
rna_rosetta_cluster.py command line option
,
[1]
rna_rosetta_extract_lowscore_decoys.py command line option
rna_rosetta_min.py command line option
rna_rosetta_n.py command line option
,
[1]
rna_rosetta_run.py command line option
rna_sali2dotbracket command line option
rna_simrna_extract.py command line option
rna_simrna_lowest.py command line option
rna_simrnaweb_download_job.py command line option
rna_ss_get_bps.py command line option
rna_standardize.py command line option
rna_torsions.py command line option
--here
rna_pdb_tools.py command line option
rna_standardize.py command line option
--hide-warnings
rna_pdb_tools.py command line option
--id-width
rna_alignment_get_species.py command line option
--ignore-files
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_pdb_tools.py command line option
--init
rna_rosetta_run.py command line option
--inplace
rna_pdb_tools.py command line option
rna_standardize.py command line option
--input-dir
rna_calc_rmsd_all_vs_all command line option
--inspect
rna_pdb_tools.py command line option
--interactive
rna_refinement.py command line option
--is-nmr
rna_pdb_tools.py command line option
--is-pdb
rna_pdb_tools.py command line option
--keep-hetatm
rna_pdb_tools.py command line option
rna_standardize.py command line option
--kill
rna_rosetta_cluster.py command line option
--limit-clusters
rna_rosetta_cluster.py command line option
--loop-seq
rna_alignment_calc_energy.py command line option
--matrix-fn
rna_calc_rmsd_all_vs_all command line option
--mdr
rna_pdb_tools.py command line option
rna_standardize.py command line option
--method
rna_alignment_calc_energy.py command line option
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_all_vs_all command line option
--min-only
rna_rosetta_cluster.py command line option
--model-ignore-selection
rna_calc_rmsd command line option
--model-selection
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_multi_targets.py command line option
--models
rna_calc_rmsd_multi_targets.py command line option
--more_clusters
rna_simrnaweb_download_job.py command line option
--motif
rna_rosetta_run.py command line option
--mss
rna_dca_mapping.py command line option
--mutate
rna_pdb_tools.py command line option
--name-rmsd-column
rna_calc_rmsd command line option
--nmr-dir
rna_pdb_tools.py command line option
--no-backbone
rna_pdb_tools.py command line option
rna_standardize.py command line option
--no-hr
rna_pdb_tools.py command line option
rna_standardize.py command line option
--no-progress-bar
rna_pdb_tools.py command line option
rna_standardize.py command line option
--no-stacking
rna_calc_inf.py command line option
--no_select
rna_rosetta_cluster.py command line option
--noshort
rna_dca_mapping.py command line option
--noss
rna_dca_mapping.py command line option
--nstruc
rna_rosetta_n.py command line option
rna_rosetta_run.py command line option
rna_simrna_lowest.py command line option
rna_simrnaweb_download_job.py command line option
--number-of-threads
rna_calc_inf.py command line option
--number_of_structures
rna_simrna_extract.py command line option
--occupancy
rna_pdb_edit_occupancy_bfactor.py command line option
--offset
rna_dca_mapping.py command line option
rna_filter.py command line option
rna_pairs2SimRNArestrs.py command line option
rna_ss_get_bps.py command line option
--one
rna_alignment_calc_energy.py command line option
rna_alignment_get_species.py command line option
--oneline
rna_pdb_tools.py command line option
--orgmode
rna_pdb_tools.py command line option
--osfn
rna_alignment_get_species.py command line option
--out_fn
rna_calc_inf.py command line option
--outfn
random_assignment_of_nucleotides.py command line option
renum_to_aln.py command line option
--output
rna_pdb_edit_occupancy_bfactor.py command line option
rna_plot_density.py command line option
rna_plot_hist.py command line option
--output-csv
rna_calc_rmsd_multi_targets.py command line option
--output_file
rna_refinement.py command line option
--p-only
rna_pdb_tools.py command line option
--pairs-delta
rna_ec2x.py command line option
--pdb2cif
rna_pdb_tools.py command line option
--potential
rna_mq_rnakb.py command line option
--prefix
rna_simrnaweb_download_job.py command line option
--print-progress
rna_calc_rmsd command line option
--print-results
rna_calc_inf.py command line option
rna_calc_rmsd command line option
--radius-inc-step
rna_rosetta_cluster.py command line option
--ref-frame-only
rna_pdb_tools.py command line option
--remove-trajectory
rna_simrnaweb_download_job.py command line option
--remove0
rna_pdb_tools.py command line option
--rename-chain
rna_pdb_tools.py command line option
--renum-atoms
rna_pdb_tools.py command line option
--renum-nmr
rna_pdb_tools.py command line option
rna_standardize.py command line option
--renum-residues-dirty
rna_pdb_tools.py command line option
--renumber-residues
rna_calc_inf.py command line option
rna_pdb_tools.py command line option
rna_standardize.py command line option
--replace-chain
rna_pdb_tools.py command line option
--replace-hetatm
rna_pdb_tools.py command line option
--replace-htm
rna_pdb_tools.py command line option
--report
rna_pdb_tools.py command line option
--residue_index_start
renum_to_aln.py command line option
--restraints_fn
rna_filter.py command line option
--rfam
rna_alignment_get_species.py command line option
--rgyration
rna_pdb_tools.py command line option
--rmsds-fn
rna_calc_rmsd command line option
--rosetta
rna_rosetta_run.py command line option
--rosetta2generic
rna_pdb_tools.py command line option
--rpr
rna_pdb_tools.py command line option
--sandbox
rna_rosetta_run.py command line option
--save-single-res
rna_pdb_tools.py command line option
--select
rna_pdb_edit_occupancy_bfactor.py command line option
rna_rosetta_cluster.py command line option
--select-atoms
rna_pdb_edit_occupancy_bfactor.py command line option
--sep
rna_ec2x.py command line option
rna_plot_density.py command line option
rna_plot_hist.py command line option
--seq
rna_dca_mapping.py command line option
--seqfn
random_assignment_of_nucleotides.py command line option
--set-chain
rna_pdb_tools.py command line option
--set-not-selected-to
rna_pdb_edit_occupancy_bfactor.py command line option
--set-to
rna_pdb_edit_occupancy_bfactor.py command line option
--skip-mcfold
rna_align_foldability.py command line option
--sort-results
rna_calc_inf.py command line option
rna_calc_rmsd command line option
--split-alt-locations
rna_pdb_tools.py command line option
--ss
rna_calc_inf.py command line option
--ss-pairs
rna_ec2x.py command line option
--steps
rna_refinement.py command line option
--suffix
rna_pdb_tools.py command line option
rna_standardize.py command line option
--swap-chains
rna_pdb_tools.py command line option
--target-column-name
rna_calc_rmsd command line option
--target-fn
rna_calc_rmsd command line option
--target-ignore-selection
rna_calc_rmsd command line option
--target-selection
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_multi_targets.py command line option
--target_fn
rna_calc_inf.py command line option
--targets
rna_calc_rmsd_multi_targets.py command line option
--template
rna_alignment_calc_energy.py command line option
rna_simrna_extract.py command line option
--to-mol2
rna_pdb_tools.py command line option
--top100
rna_simrnaweb_download_job.py command line option
--top200
rna_simrnaweb_download_job.py command line option
--trafl
rna_simrna_extract.py command line option
--un-nmr
rna_pdb_tools.py command line option
--undo
rna_pdb_tools.py command line option
--uniq
rna_pdb_tools.py command line option
--verbose
pdbs_measure_atom_dists.py command line option
random_assignment_of_nucleotides.py command line option
renum_to_aln.py command line option
rna_align_foldability.py command line option
rna_alignment_calc_energy.py command line option
rna_alignment_get_species.py command line option
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_multi_targets.py command line option
rna_dca_mapping.py command line option
rna_dot2ct.py command line option
rna_filter.py command line option
rna_mq_rnakb.py command line option
rna_pairs2SimRNArestrs.py command line option
rna_pairs_diff.py command line option
rna_pdb_edit_occupancy_bfactor.py command line option
rna_pdb_tools.py command line option
rna_refinement.py command line option
rna_rosetta_cluster.py command line option
rna_rosetta_extract_lowscore_decoys.py command line option
rna_rosetta_n.py command line option
,
[1]
rna_ss_get_bps.py command line option
rna_standardize.py command line option
rna_torsions.py command line option
--version
rna_pdb_tools.py command line option
rna_standardize.py command line option
--way
rna_calc_rmsd command line option
--web
rna_calc_inf.py command line option
--web-models
rna_simrnaweb_download_job.py command line option
--weight
rna_pairs2SimRNArestrs.py command line option
--well
rna_pairs2SimRNArestrs.py command line option
--zero
rna_rosetta_n.py command line option
-0
rna_rosetta_n.py command line option
-c
rna_add_chain.py command line option
rna_pdb_tools.py command line option
rna_rosetta_min.py command line option
rna_rosetta_run.py command line option
rna_simrna_extract.py command line option
rna_simrnaweb_download_job.py command line option
-d
rna_simrnaweb_download_job.py command line option
-e
rna_rosetta_run.py command line option
rna_simrnaweb_download_job.py command line option
-f
rna_calc_inf.py command line option
rna_simrna_extract.py command line option
-g
rna_rosetta_min.py command line option
rna_rosetta_run.py command line option
-h
pdbs_measure_atom_dists.py command line option
random_assignment_of_nucleotides.py command line option
renum_to_aln.py command line option
rna_add_chain.py command line option
rna_align_distance_to_seq.py command line option
rna_align_foldability.py command line option
rna_align_get_ss_from_fasta.py command line option
rna_align_get_ss_from_stk.py command line option
rna_alignment_calc_energy.py command line option
rna_alignment_get_species.py command line option
rna_cal_rmsd_trafl_plot command line option
rna_calc_evo_rmsd command line option
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_all_vs_all command line option
rna_calc_rmsd_multi_targets.py command line option
rna_dca_mapping.py command line option
rna_dot2ct.py command line option
rna_ec2x.py command line option
rna_filter.py command line option
rna_mq_rnakb.py command line option
rna_pairs2SimRNArestrs.py command line option
rna_pairs_diff.py command line option
rna_pdb_edit_occupancy_bfactor.py command line option
rna_pdb_tools.py command line option
rna_plot_density.py command line option
rna_plot_hist.py command line option
rna_refinement.py command line option
rna_rosetta_cluster.py command line option
,
[1]
rna_rosetta_extract_lowscore_decoys.py command line option
rna_rosetta_min.py command line option
rna_rosetta_n.py command line option
,
[1]
rna_rosetta_run.py command line option
rna_sali2dotbracket command line option
rna_simrna_extract.py command line option
rna_simrna_lowest.py command line option
rna_simrnaweb_download_job.py command line option
rna_ss_get_bps.py command line option
rna_standardize.py command line option
rna_torsions.py command line option
-i
rna_calc_rmsd_all_vs_all command line option
rna_refinement.py command line option
rna_rosetta_run.py command line option
-k
rna_rosetta_cluster.py command line option
-m
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_all_vs_all command line option
rna_rosetta_cluster.py command line option
rna_rosetta_run.py command line option
rna_simrnaweb_download_job.py command line option
-n
rna_rosetta_n.py command line option
rna_rosetta_run.py command line option
rna_simrna_extract.py command line option
rna_simrna_lowest.py command line option
rna_simrnaweb_download_job.py command line option
-o
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_all_vs_all command line option
rna_pdb_edit_occupancy_bfactor.py command line option
rna_plot_density.py command line option
rna_plot_hist.py command line option
rna_refinement.py command line option
-p
rna_mq_rnakb.py command line option
rna_simrnaweb_download_job.py command line option
-pp
rna_calc_rmsd command line option
-pr
rna_calc_inf.py command line option
rna_calc_rmsd command line option
-r
rna_filter.py command line option
rna_pdb_tools.py command line option
rna_rosetta_run.py command line option
rna_simrnaweb_download_job.py command line option
-s
rna_calc_inf.py command line option
rna_filter.py command line option
rna_refinement.py command line option
rna_rosetta_cluster.py command line option
-sr
rna_calc_inf.py command line option
rna_calc_rmsd command line option
-t
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_filter.py command line option
rna_simrna_extract.py command line option
-v
pdbs_measure_atom_dists.py command line option
random_assignment_of_nucleotides.py command line option
renum_to_aln.py command line option
rna_align_foldability.py command line option
rna_alignment_calc_energy.py command line option
rna_alignment_get_species.py command line option
rna_calc_inf.py command line option
rna_calc_rmsd command line option
rna_calc_rmsd_multi_targets.py command line option
rna_dot2ct.py command line option
rna_filter.py command line option
rna_mq_rnakb.py command line option
rna_pairs2SimRNArestrs.py command line option
rna_pairs_diff.py command line option
rna_pdb_tools.py command line option
rna_refinement.py command line option
rna_rosetta_cluster.py command line option
rna_rosetta_extract_lowscore_decoys.py command line option
rna_rosetta_n.py command line option
,
[1]
rna_ss_get_bps.py command line option
rna_standardize.py command line option
rna_torsions.py command line option
A
aa3to1() (in module rna_tools.rna_tools_lib)
add_ids() (rna_tools.tools.clanstix.rna_clanstix.RNAStructClans method)
align_seq() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
alignfn
pdbs_measure_atom_dists.py command line option
renum_to_aln.py command line option
alignment
rna_alignment_calc_energy.py command line option
rna_alignment_get_species.py command line option
AnalyzeGeometry (class in rna_tools.tools.mq.AnalyzeGeometry.AnalyzeGeometry)
Atom (class in rna_tools.tools.simrna_trajectory.simrna_trajectory)
B
best_energy (rna_tools.tools.mq.FARNA.FARNA.FARNA attribute)
BlastPDB (class in rna_tools.BlastPDB)
C
calc_rmsd() (in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd)
(in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd_all_vs_all)
calc_rmsd_pymol() (in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd)
check_geometry() (rna_tools.rna_tools_lib.RNAStructure method)
check_symmetric() (in module rna_tools.tools.clanstix.rna_clanstix)
clarna_compare() (in module rna_tools.tools.clarna_app.rna_clarna_app)
clarna_run() (in module rna_tools.tools.clarna_app.rna_clarna_app)
ClashScore (class in rna_tools.tools.mq.ClashScore.ClashScore)
clean_up() (rna_tools.tools.rna_x3dna.rna_x3dna.x3DNA method)
cleanup() (rna_tools.tools.mq.AnalyzeGeometry.AnalyzeGeometry.AnalyzeGeometry method)
(rna_tools.tools.mq.ClashScore.ClashScore.ClashScore method)
(rna_tools.tools.mq.FARNA.FARNA.FARNA method)
cluster() (in module rna_tools.tools.rna_rosetta.rna_rosetta_cluster)
cluster_loop() (in module rna_tools.tools.rna_rosetta.rna_rosetta_cluster)
CMAlign (class in rna_tools.tools.rna_alignment.rna_alignment)
cmscan() (rna_tools.RfamSearch.RfamSearch method)
collapsed_view() (in module rna_tools.rna_tools_lib)
colour_by_local_score() (rna_tools.tools.mq.RASP.RASP.RASP method)
convert_sali2dotbracket() (in module rna_tools.tools.rna_sali2dotbracket.rna_sali2dotbracket)
copy_ss_cons_to_all() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
copy_ss_cons_to_all_editing_sequence() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
CustomFormatter (class in rna_tools.tools.rna_rosetta.rna_rosetta_run)
D
db_path (rna_tools.tools.mq.FARNA.FARNA.FARNA attribute)
describe() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
Dfire (class in rna_tools.tools.mq.Dfire.Dfire)
dir
rna_rosetta_cluster.py command line option
dist_from_matrix() (rna_tools.tools.clanstix.rna_clanstix.RNAStructClans method)
dist_from_matrix_mp() (rna_tools.tools.clanstix.rna_clanstix.RNAStructClans method)
do_job() (in module rna_tools.tools.rna_calc_inf.rna_calc_inf)
draw_circle() (in module rna_tools.tools.pymol_drawing.pymol_drawing)
draw_circle_selection() (in module rna_tools.tools.pymol_drawing.pymol_drawing)
draw_dist() (in module rna_tools.tools.pymol_drawing.pymol_drawing)
draw_dists() (in module rna_tools.tools.pymol_drawing.pymol_drawing)
draw_ss() (in module rna_tools.SecondaryStructure)
(rna_tools.tools.rna_alignment.rna_alignment.RNASeq method)
draw_vector() (in module rna_tools.tools.pymol_drawing.pymol_drawing)
E
edit_occupancy_of_pdb() (in module rna_tools.tools.rna_pdb_edit_occupancy_bfactor.rna_pdb_edit_occupancy_bfactor)
(rna_tools.rna_tools_lib.RNAStructure method)
edit_pdb() (in module rna_tools.rna_tools_lib)
,
[1]
eSCORE (class in rna_tools.tools.mq.eSCORE.eSCORE)
eval() (rna_tools.Seq.RNASequence method)
ExceptionOpenPairsProblem
exe() (in module rna_tools.tools.mq.eSCORE.eSCORE)
executable (rna_tools.tools.mq.FARNA.FARNA.FARNA attribute)
(rna_tools.tools.mq.RASP.RASP.RASP attribute)
(rna_tools.tools.mq.RNAkb.RNAkb.RNAkb attribute)
extract() (in module rna_tools.tools.rna_rosetta.rna_rosetta_cluster)
F
FARNA (class in rna_tools.tools.mq.FARNA.FARNA)
fetch() (in module rna_tools.rna_tools_lib)
,
[1]
fetch_ba() (in module rna_tools.rna_tools_lib)
,
[1]
fetch_cif() (in module rna_tools.rna_tools_lib)
fetch_cif_ba() (in module rna_tools.rna_tools_lib)
file
rna_add_chain.py command line option
rna_align_distance_to_seq.py command line option
rna_align_foldability.py command line option
rna_align_get_ss_from_fasta.py command line option
rna_align_get_ss_from_stk.py command line option
rna_cal_rmsd_trafl_plot command line option
rna_dot2ct.py command line option
rna_mq_rnakb.py command line option
rna_pdb_edit_occupancy_bfactor.py command line option
rna_pdb_tools.py command line option
rna_plot_density.py command line option
rna_plot_hist.py command line option
rna_rosetta_cluster.py command line option
rna_rosetta_extract_lowscore_decoys.py command line option
rna_rosetta_min.py command line option
rna_rosetta_n.py command line option
,
[1]
rna_rosetta_run.py command line option
rna_ss_get_bps.py command line option
rna_standardize.py command line option
rna_torsions.py command line option
filename
rna_sali2dotbracket command line option
files
rna_calc_inf.py command line option
rna_calc_rmsd command line option
find_core() (in module rna_tools.tools.pdbs_measure_atom_dists.pdbs_measure_atom_dists)
(rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
find_seq() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
find_seq_exact() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
fix_O_in_UC() (rna_tools.rna_tools_lib.RNAStructure method)
fix_op_atoms() (rna_tools.rna_tools_lib.RNAStructure method)
fix_with_qrnas() (rna_tools.rna_tools_lib.RNAStructure method)
fn
rna_refinement.py command line option
fn (rna_tools.rna_tools_lib.RNAStructure attribute)
,
[1]
,
[2]
,
[3]
format_annotation() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
Frame (class in rna_tools.tools.simrna_trajectory.simrna_trajectory)
G
get_align() (in module rna_tools.tools.rna_alignment.random_assignment_of_nucleotides)
get_all_chain_ids() (rna_tools.rna_tools_lib.RNAStructure method)
get_atom_code() (rna_tools.rna_tools_lib.RNAStructure method)
get_atom_coords() (rna_tools.rna_tools_lib.RNAStructure method)
get_atom_num() (rna_tools.rna_tools_lib.RNAStructure method)
get_atoms() (rna_tools.tools.simrna_trajectory.simrna_trajectory.Residue method)
get_center() (rna_tools.tools.simrna_trajectory.simrna_trajectory.Residue method)
get_ClaRNA_output_from_dot_bracket() (in module rna_tools.tools.clarna_app.rna_clarna_app)
get_clean_ss() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_conserved() (rna_tools.tools.rna_alignment.rna_alignment.RNASeq method)
get_coord() (rna_tools.tools.simrna_trajectory.simrna_trajectory.Atom method)
get_distance_to() (rna_tools.tools.rna_alignment.rna_alignment.RNASeq method)
get_distances() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_dot_bracket_from_ClaRNAoutput() (in module rna_tools.tools.clarna_app.rna_clarna_app)
get_foldability() (rna_tools.Seq.RNASequence method)
get_gc_rf() (rna_tools.tools.rna_alignment.rna_alignment.CMAlign method)
(rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_info_chains() (rna_tools.rna_tools_lib.RNAStructure method)
get_ion_water_report() (rna_tools.tools.rna_x3dna.rna_x3dna.x3DNA method)
,
[1]
get_modifications() (rna_tools.tools.rna_x3dna.rna_x3dna.x3DNA method)
,
[1]
get_multiple_lines() (in module rna_tools.tools.rna_convert_pseudoknot_formats.rna_ss_pk_to_simrna)
get_no_structures() (in module rna_tools.tools.rna_rosetta.rna_rosetta_cluster)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_min)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_n)
get_no_structures_in_first_cluster() (in module rna_tools.tools.rna_rosetta.rna_rosetta_cluster)
get_parser() (in module rna_tools.tools.clanstix.rna_clanstix)
(in module rna_tools.tools.clarna_app.rna_clarna_app)
(in module rna_tools.tools.cluster_load.cluster_load)
(in module rna_tools.tools.misc.rna_add_chain)
(in module rna_tools.tools.mq.Dfire.Dfire)
(in module rna_tools.tools.pdbs_measure_atom_dists.pdbs_measure_atom_dists)
(in module rna_tools.tools.renum_pdb_to_aln.renum_pdb_to_aln)
(in module rna_tools.tools.rna_alignment.random_assignment_of_nucleotides)
(in module rna_tools.tools.rna_calc_inf.rna_calc_inf)
(in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd)
(in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd_all_vs_all)
(in module rna_tools.tools.rna_convert_pseudoknot_formats.rna_ss_pk_to_simrna)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_check_progress)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_cluster)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_extract_lowscore_decoys)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_head)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_min)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_n)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_run)
(in module rna_tools.tools.rna_sali2dotbracket.rna_sali2dotbracket)
(in module rna_tools.tools.rna_x3dna.rna_x3dna)
get_remarks_text() (rna_tools.rna_tools_lib.RNAStructure method)
get_report() (rna_tools.rna_tools_lib.RNAStructure method)
get_res_code() (rna_tools.rna_tools_lib.RNAStructure method)
get_res_num() (rna_tools.rna_tools_lib.RNAStructure method)
get_res_text() (rna_tools.rna_tools_lib.RNAStructure method)
get_result() (rna_tools.tools.mq.FARNA.FARNA.FARNA method)
get_rna_models_from_dir() (in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd)
(in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd_all_vs_all)
get_rna_tools_path() (in module rna_tools.rna_tools_lib)
get_rnapuzzle_ready() (rna_tools.rna_tools_lib.RNAStructure method)
,
[1]
,
[2]
,
[3]
get_secstruc() (rna_tools.tools.rna_x3dna.rna_x3dna.x3DNA method)
,
[1]
get_selected() (in module rna_tools.tools.rna_rosetta.rna_rosetta_cluster)
get_seq() (in module rna_tools.tools.pdbs_measure_atom_dists.pdbs_measure_atom_dists)
(in module rna_tools.tools.renum_pdb_to_aln.renum_pdb_to_aln)
(rna_tools.rna_tools_lib.RNAStructure method)
,
[1]
(rna_tools.tools.rna_alignment.rna_alignment.CMAlign method)
(rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
(rna_tools.tools.rna_x3dna.rna_x3dna.x3DNA method)
,
[1]
get_seq_ss() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_seq_with_name() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_sequences() (in module rna_tools.tools.rna_alignment.random_assignment_of_nucleotides)
get_shift_seq_in_align() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_ss_cons() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_ss_cons_pk() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_ss_remove_gaps() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_ss_std() (rna_tools.tools.rna_alignment.rna_alignment.RNASeq method)
get_text() (rna_tools.rna_tools_lib.RNAStructure method)
get_the_closest_seq_to_ref_seq() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
get_torsions() (rna_tools.tools.rna_x3dna.rna_x3dna.x3DNA method)
,
[1]
go() (in module rna_tools.tools.rna_rosetta.rna_rosetta_run)
H
head() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
I
input_file (rna_tools.tools.mq.FARNA.FARNA.FARNA attribute)
input_fn (rna_tools.tools.mq.FARNA.FARNA.FARNA attribute)
interaction_fn
rna_ec2x.py command line option
is_amber_like() (rna_tools.rna_tools_lib.RNAStructure method)
is_mol2() (rna_tools.rna_tools_lib.RNAStructure method)
is_nmr() (rna_tools.rna_tools_lib.RNAStructure method)
is_pdb() (rna_tools.rna_tools_lib.RNAStructure method)
is_pk() (in module rna_tools.tools.rna_convert_pseudoknot_formats.rna_ss_pk_to_simrna)
J
job_id
rna_simrnaweb_download_job.py command line option
L
lines (rna_tools.rna_tools_lib.RNAStructure attribute)
,
[1]
,
[2]
,
[3]
load_fasta_ss_into_RNAseqs() (in module rna_tools.Seq)
load_from_file() (rna_tools.tools.simrna_trajectory.simrna_trajectory.SimRNATrajectory method)
load_from_list() (rna_tools.tools.simrna_trajectory.simrna_trajectory.SimRNATrajectory method)
load_from_string() (rna_tools.tools.simrna_trajectory.simrna_trajectory.SimRNATrajectory method)
load_rnas() (in module rna_tools.rna_tools_lib)
log_stdout_stderr() (rna_tools.tools.mq.RNAkb.RNAkb.RNAkb method)
M
main() (in module rna_tools.tools.mq.AnalyzeGeometry.AnalyzeGeometry)
(in module rna_tools.tools.mq.eSCORE.eSCORE)
(in module rna_tools.tools.mq.RNA3DCNN.RNA3DCNN)
(in module rna_tools.tools.mq.RNAscore.RNAscore)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_run)
map_coords_atom() (in module rna_tools.tools.pdbs_measure_atom_dists.pdbs_measure_atom_dists)
map_seq_on_align() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
map_seq_on_seq() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
max_seq_len (rna_tools.tools.mq.RNA3DCNN.RNA3DCNN.RNA3DCNN attribute)
MethodNotChosen
MethodUnknown
min() (in module rna_tools.tools.rna_rosetta.rna_rosetta_min)
module
rna_tools.BlastPDB
rna_tools.RfamSearch
rna_tools.rna_tools_lib
rna_tools.SecondaryStructure
rna_tools.Seq
rna_tools.tools.clanstix.rna_clanstix
rna_tools.tools.clarna_app.rna_clarna_app
rna_tools.tools.cluster_load.cluster_load
rna_tools.tools.diffpdb.diffpdb
rna_tools.tools.extra_functions.select_fragment
rna_tools.tools.misc.rna_add_chain
rna_tools.tools.mq.AnalyzeGeometry.AnalyzeGeometry
rna_tools.tools.mq.ClashScore.ClashScore
rna_tools.tools.mq.Dfire.Dfire
rna_tools.tools.mq.eSCORE.eSCORE
rna_tools.tools.mq.FARNA.FARNA
rna_tools.tools.mq.RASP.RASP
rna_tools.tools.mq.RNA3DCNN.RNA3DCNN
rna_tools.tools.mq.RNAkb.RNAkb
rna_tools.tools.mq.RNAscore.RNAscore
rna_tools.tools.pdbs_measure_atom_dists.pdbs_measure_atom_dists
rna_tools.tools.pymol_drawing.pymol_drawing
rna_tools.tools.renum_pdb_to_aln.renum_pdb_to_aln
rna_tools.tools.rna_alignment.random_assignment_of_nucleotides
rna_tools.tools.rna_alignment.rna_alignment
rna_tools.tools.rna_calc_inf.rna_calc_inf
rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd
rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd_all_vs_all
rna_tools.tools.rna_convert_pseudoknot_formats.rna_ss_pk_to_simrna
rna_tools.tools.rna_filter.pymol_dists
rna_tools.tools.rna_rosetta.rna_rosetta_check_progress
rna_tools.tools.rna_rosetta.rna_rosetta_cluster
rna_tools.tools.rna_rosetta.rna_rosetta_extract_lowscore_decoys
rna_tools.tools.rna_rosetta.rna_rosetta_head
rna_tools.tools.rna_rosetta.rna_rosetta_min
rna_tools.tools.rna_rosetta.rna_rosetta_n
rna_tools.tools.rna_rosetta.rna_rosetta_run
rna_tools.tools.rna_sali2dotbracket.rna_sali2dotbracket
rna_tools.tools.rna_x3dna.rna_x3dna
,
[1]
rna_tools.tools.simrna_trajectory.simrna_trajectory
mqap() (rna_tools.tools.mq.FARNA.FARNA.FARNA method)
N
n
rna_rosetta_cluster.py command line option
name (rna_tools.rna_tools_lib.RNAStructure attribute)
,
[1]
,
[2]
,
[3]
nstruc
rna_rosetta_extract_lowscore_decoys.py command line option
O
open_pdb() (in module rna_tools.tools.pdbs_measure_atom_dists.pdbs_measure_atom_dists)
(in module rna_tools.tools.renum_pdb_to_aln.renum_pdb_to_aln)
output
rna_align_distance_to_seq.py command line option
rna_align_foldability.py command line option
P
pairs
rna_pairs2SimRNArestrs.py command line option
pairs1
rna_pairs_diff.py command line option
pairs2
rna_pairs_diff.py command line option
parse_vienna_to_pairs() (in module rna_tools.SecondaryStructure)
PDBFetchError
pdbfn
renum_to_aln.py command line option
pdbfn1
pdbs_measure_atom_dists.py command line option
pdbfn2
pdbs_measure_atom_dists.py command line option
pdbs_measure_atom_dists.py command line option
--help
--verbose
-h
-v
alignfn
pdbfn1
pdbfn2
seqid1
seqid2
per_user() (in module rna_tools.tools.cluster_load.cluster_load)
plot() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
plot_cov() (rna_tools.tools.rna_alignment.rna_alignment.RChie method)
plot_energy() (rna_tools.tools.simrna_trajectory.simrna_trajectory.SimRNATrajectory method)
predict_ss() (rna_tools.Seq.RNASequence method)
prepare_folder() (in module rna_tools.tools.rna_rosetta.rna_rosetta_run)
prepare_helices() (in module rna_tools.tools.rna_rosetta.rna_rosetta_run)
prepare_rosetta() (in module rna_tools.tools.rna_rosetta.rna_rosetta_run)
program_name (rna_tools.tools.mq.FARNA.FARNA.FARNA attribute)
(rna_tools.tools.mq.RASP.RASP.RASP attribute)
(rna_tools.tools.mq.RNAscore.RNAscore.RNAscore attribute)
R
random_assignment_of_nucleotides.py command line option
--alignfn
--help
--outfn
--seqfn
--verbose
-h
-v
RASP (class in rna_tools.tools.mq.RASP.RASP)
RChie (class in rna_tools.tools.rna_alignment.rna_alignment)
reload() (rna_tools.rna_tools_lib.RNAStructure method)
reload_alignment() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
remove() (rna_tools.rna_tools_lib.RNAStructure method)
remove_columns() (rna_tools.tools.rna_alignment.rna_alignment.RNASeq method)
remove_empty_columns() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
remove_gaps() (rna_tools.tools.rna_alignment.rna_alignment.RNASeq method)
remove_ion() (rna_tools.rna_tools_lib.RNAStructure method)
remove_water() (rna_tools.rna_tools_lib.RNAStructure method)
rename_chain() (rna_tools.rna_tools_lib.RNAStructure method)
renum_atoms() (rna_tools.rna_tools_lib.RNAStructure method)
renum_to_aln.py command line option
--help
--outfn
--residue_index_start
--verbose
-h
-v
alignfn
pdbfn
seqid
renumber() (in module rna_tools.tools.renum_pdb_to_aln.renum_pdb_to_aln)
repl() (in module rna_tools.tools.rna_sali2dotbracket.rna_sali2dotbracket)
replace_atoms() (in module rna_tools.rna_tools_lib)
replace_chain() (in module rna_tools.rna_tools_lib)
Residue (class in rna_tools.tools.simrna_trajectory.simrna_trajectory)
RfamSearch (class in rna_tools.RfamSearch)
RfamSearchError
rmsd_to() (rna_tools.tools.simrna_trajectory.simrna_trajectory.Frame method)
rmsds_fn
rna_calc_evo_rmsd command line option
RNA3DCNN (class in rna_tools.tools.mq.RNA3DCNN.RNA3DCNN)
rna_add_chain.py command line option
--chain
--help
-c
-h
file
rna_align_distance_to_seq.py command line option
--help
-h
file
output
rna_align_foldability.py command line option
--all-stars
--dev
--help
--skip-mcfold
--verbose
-h
-v
file
output
rna_align_get_ss_from_fasta.py command line option
--help
-h
file
rna_align_get_ss_from_stk.py command line option
--help
-h
file
rna_alignment_calc_energy.py command line option
--csv
--debug
--flanks
--help
--loop-seq
--method
--one
--template
--verbose
-h
-v
alignment
rna_alignment_get_species.py command line option
--debug
--evo-mapping
--evo-mapping-default
--help
--id-width
--one
--osfn
--rfam
--verbose
-h
-v
alignment
rna_cal_rmsd_trafl_plot command line option
--help
-h
file
rna_calc_evo_rmsd command line option
--help
-h
rmsds_fn
struc1
struc2
trafl
rna_calc_inf.py command line option
--debug
--dont-remove-sel-files
--force
--help
--ignore-files
--method
--model-selection
--no-stacking
--number-of-threads
--out_fn
--print-results
--renumber-residues
--sort-results
--ss
--target-selection
--target_fn
--verbose
--web
-f
-h
-m
-o
-pr
-s
-sr
-t
-v
files
rna_calc_rmsd command line option
--help
--ignore-files
--method
--model-ignore-selection
--model-selection
--name-rmsd-column
--print-progress
--print-results
--rmsds-fn
--sort-results
--target-column-name
--target-fn
--target-ignore-selection
--target-selection
--verbose
--way
-h
-m
-o
-pp
-pr
-sr
-t
-v
files
rna_calc_rmsd_all_vs_all command line option
--help
--input-dir
--matrix-fn
--method
-h
-i
-m
-o
rna_calc_rmsd_multi_targets.py command line option
--help
--model-selection
--models
--output-csv
--target-selection
--targets
--verbose
-h
-v
rna_dca_mapping.py command line option
--dca
--gseq
--help
--mss
--noshort
--noss
--offset
--seq
--verbose
-h
rna_dot2ct.py command line option
--help
--verbose
-h
-v
file
rna_ec2x.py command line option
--chain
--ec-pairs
--help
--pairs-delta
--sep
--ss-pairs
-h
interaction_fn
rna_filter.py command line option
--help
--offset
--restraints_fn
--verbose
-h
-r
-s
-t
-v
rna_mq_rnakb.py command line option
--help
--potential
--verbose
-h
-p
-v
file
rna_pairs2SimRNArestrs.py command line option
--dist
--help
--offset
--verbose
--weight
--well
-h
-v
pairs
rna_pairs_diff.py command line option
--help
--verbose
-h
-v
pairs1
pairs2
rna_pdb_edit_occupancy_bfactor.py command line option
--bfactor
--help
--occupancy
--output
--select
--select-atoms
--set-not-selected-to
--set-to
--verbose
-h
-o
file
rna_pdb_tools.py command line option
--backbone-only
--bases-only
--chain-first
--cif2pdb
--clean
--collapsed-view
--color-seq
--compact
--cv
--delete
--delete-anisou
--dont-fix-missing-atoms
--dont-rename-chains
--dont-report-missing-atoms
--edit
--extract
--extract-chain
--fasta
--fetch
--fetch-ba
--fetch-chain
--fetch-cif
--fetch-fasta
--fix
--get-chain
--get-rnapuzzle-ready
--get-seq
--get-ss
--help
--here
--hide-warnings
--ignore-files
--inplace
--inspect
--is-nmr
--is-pdb
--keep-hetatm
--mdr
--mutate
--nmr-dir
--no-backbone
--no-hr
--no-progress-bar
--oneline
--orgmode
--p-only
--pdb2cif
--ref-frame-only
--remove0
--rename-chain
--renum-atoms
--renum-nmr
--renum-residues-dirty
--renumber-residues
--replace-chain
--replace-hetatm
--replace-htm
--report
--rgyration
--rosetta2generic
--rpr
--save-single-res
--set-chain
--split-alt-locations
--suffix
--swap-chains
--to-mol2
--un-nmr
--undo
--uniq
--verbose
--version
-c
-h
-r
-v
file
rna_plot_density.py command line option
--column
--help
--output
--sep
-h
-o
file
rna_plot_hist.py command line option
--bins
--column
--help
--output
--sep
-h
-o
file
rna_refinement.py command line option
--help
--interactive
--output_file
--steps
--verbose
-h
-i
-o
-s
-v
fn
rna_rosetta_cluster.py command line option
--help
,
[1]
--kill
--limit-clusters
--min-only
--no_select
--radius-inc-step
--select
--verbose
-h
,
[1]
-k
-m
-s
-v
dir
file
n
rna_rosetta_extract_lowscore_decoys.py command line option
--help
--verbose
-h
-v
file
nstruc
rna_rosetta_min.py command line option
--cpus
--go
--help
-c
-g
-h
file
rna_rosetta_n.py command line option
--help
,
[1]
--nstruc
--verbose
,
[1]
--zero
-0
-h
,
[1]
-n
-v
,
[1]
file
,
[1]
rna_rosetta_run.py command line option
--cpus
--go
--helices
--help
--init
--motif
--nstruc
--rosetta
--sandbox
-c
-e
-g
-h
-i
-m
-n
-r
file
rna_sali2dotbracket command line option
--help
-h
filename
rna_simrna_extract.py command line option
--cleanup
--help
--number_of_structures
--template
--trafl
-c
-f
-h
-n
-t
rna_simrna_lowest.py command line option
--help
--nstruc
-h
-n
trafl
rna_simrnaweb_download_job.py command line option
--cluster
--download-trajectory
--extract
--help
--more_clusters
--nstruc
--prefix
--remove-trajectory
--top100
--top200
--web-models
-c
-d
-e
-h
-m
-n
-p
-r
job_id
rna_ss_get_bps.py command line option
--help
--offset
--verbose
-h
-v
file
rna_standardize.py command line option
--backbone-only
--bases-only
--check-geometry
--dont-fix-missing-atoms
--dont-rename-chains
--dont-replace-hetatm
--dont-report-missing-atoms
--help
--here
--inplace
--keep-hetatm
--mdr
--no-backbone
--no-hr
--no-progress-bar
--renum-nmr
--renumber-residues
--suffix
--verbose
--version
-h
-v
file
rna_tools.BlastPDB
module
rna_tools.RfamSearch
module
rna_tools.rna_tools_lib
module
rna_tools.SecondaryStructure
module
rna_tools.Seq
module
rna_tools.tools.clanstix.rna_clanstix
module
rna_tools.tools.clarna_app.rna_clarna_app
module
rna_tools.tools.cluster_load.cluster_load
module
rna_tools.tools.diffpdb.diffpdb
module
rna_tools.tools.extra_functions.select_fragment
module
rna_tools.tools.misc.rna_add_chain
module
rna_tools.tools.mq.AnalyzeGeometry.AnalyzeGeometry
module
rna_tools.tools.mq.ClashScore.ClashScore
module
rna_tools.tools.mq.Dfire.Dfire
module
rna_tools.tools.mq.eSCORE.eSCORE
module
rna_tools.tools.mq.FARNA.FARNA
module
rna_tools.tools.mq.RASP.RASP
module
rna_tools.tools.mq.RNA3DCNN.RNA3DCNN
module
rna_tools.tools.mq.RNAkb.RNAkb
module
rna_tools.tools.mq.RNAscore.RNAscore
module
rna_tools.tools.pdbs_measure_atom_dists.pdbs_measure_atom_dists
module
rna_tools.tools.pymol_drawing.pymol_drawing
module
rna_tools.tools.renum_pdb_to_aln.renum_pdb_to_aln
module
rna_tools.tools.rna_alignment.random_assignment_of_nucleotides
module
rna_tools.tools.rna_alignment.rna_alignment
module
rna_tools.tools.rna_calc_inf.rna_calc_inf
module
rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd
module
rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd_all_vs_all
module
rna_tools.tools.rna_convert_pseudoknot_formats.rna_ss_pk_to_simrna
module
rna_tools.tools.rna_filter.pymol_dists
module
rna_tools.tools.rna_rosetta.rna_rosetta_check_progress
module
rna_tools.tools.rna_rosetta.rna_rosetta_cluster
module
rna_tools.tools.rna_rosetta.rna_rosetta_extract_lowscore_decoys
module
rna_tools.tools.rna_rosetta.rna_rosetta_head
module
rna_tools.tools.rna_rosetta.rna_rosetta_min
module
rna_tools.tools.rna_rosetta.rna_rosetta_n
module
rna_tools.tools.rna_rosetta.rna_rosetta_run
module
rna_tools.tools.rna_sali2dotbracket.rna_sali2dotbracket
module
rna_tools.tools.rna_x3dna.rna_x3dna
module
,
[1]
rna_tools.tools.simrna_trajectory.simrna_trajectory
module
rna_torsions.py command line option
--help
--verbose
-h
-v
file
RNAalignment (class in rna_tools.tools.rna_alignment.rna_alignment)
RNAkb (class in rna_tools.tools.mq.RNAkb.RNAkb)
RNAscore (class in rna_tools.tools.mq.RNAscore.RNAscore)
RNASeq (class in rna_tools.tools.rna_alignment.rna_alignment)
RNASequence (class in rna_tools.Seq)
RNAStructClans (class in rna_tools.tools.clanstix.rna_clanstix)
RNAStructure (class in rna_tools.rna_tools_lib)
,
[1]
,
[2]
,
[3]
rosetta_extract_lowscore_decoys() (in module rna_tools.tools.rna_rosetta.rna_rosetta_extract_lowscore_decoys)
run() (in module rna_tools.tools.rna_rosetta.rna_rosetta_cluster)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_head)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_min)
(in module rna_tools.tools.rna_rosetta.rna_rosetta_n)
(rna_tools.tools.mq.AnalyzeGeometry.AnalyzeGeometry.AnalyzeGeometry method)
(rna_tools.tools.mq.ClashScore.ClashScore.ClashScore method)
(rna_tools.tools.mq.Dfire.Dfire.Dfire method)
(rna_tools.tools.mq.eSCORE.eSCORE.eSCORE method)
(rna_tools.tools.mq.FARNA.FARNA.FARNA method)
(rna_tools.tools.mq.RASP.RASP.RASP method)
(rna_tools.tools.mq.RNA3DCNN.RNA3DCNN.RNA3DCNN method)
(rna_tools.tools.mq.RNAkb.RNAkb.RNAkb method)
(rna_tools.tools.mq.RNAscore.RNAscore.RNAscore method)
run_cmalign() (rna_tools.tools.rna_alignment.rna_alignment.CMAlign method)
run_cmd() (in module rna_tools.tools.rna_rosetta.rna_rosetta_check_progress)
run_x3dna() (rna_tools.tools.rna_x3dna.rna_x3dna.x3DNA method)
,
[1]
S
sandbox() (rna_tools.tools.mq.FARNA.FARNA.FARNA method)
save() (rna_tools.tools.simrna_trajectory.simrna_trajectory.SimRNATrajectory method)
search() (rna_tools.BlastPDB.BlastPDB method)
select_pdb_fragment() (in module rna_tools.tools.extra_functions.select_fragment)
select_pdb_fragment_pymol_style() (in module rna_tools.tools.extra_functions.select_fragment)
seq_no_gaps (rna_tools.tools.rna_alignment.rna_alignment.RNASeq attribute)
seqid
renum_to_aln.py command line option
seqid1
pdbs_measure_atom_dists.py command line option
seqid2
pdbs_measure_atom_dists.py command line option
set_atom_code() (rna_tools.rna_tools_lib.RNAStructure method)
set_atom_coords() (rna_tools.rna_tools_lib.RNAStructure method)
set_atom_occupancy() (rna_tools.rna_tools_lib.RNAStructure method)
set_chain_for_struc() (in module rna_tools.rna_tools_lib)
set_occupancy_atoms() (rna_tools.rna_tools_lib.RNAStructure method)
set_res_code() (rna_tools.rna_tools_lib.RNAStructure method)
show() (rna_tools.tools.rna_alignment.rna_alignment.RChie method)
SimRNATrajectory (class in rna_tools.tools.simrna_trajectory.simrna_trajectory)
sort() (rna_tools.tools.simrna_trajectory.simrna_trajectory.SimRNATrajectory method)
sort_nicely() (in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd)
(in module rna_tools.tools.rna_calc_rmsd.rna_calc_rmsd_all_vs_all)
sort_strings() (in module rna_tools.rna_tools_lib)
src_bin (rna_tools.tools.mq.FARNA.FARNA.FARNA attribute)
ss_cons_std (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment property)
ss_cons_with_pk (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment property)
ss_cons_with_pk_std (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment property)
ss_no_gaps (rna_tools.tools.rna_alignment.rna_alignment.RNASeq attribute)
ss_to_bps() (rna_tools.tools.rna_alignment.rna_alignment.RNASeq method)
stats_for_cluster() (in module rna_tools.tools.cluster_load.cluster_load)
stats_for_user() (in module rna_tools.tools.cluster_load.cluster_load)
std_resn() (rna_tools.rna_tools_lib.RNAStructure method)
struc1
rna_calc_evo_rmsd command line option
struc2
rna_calc_evo_rmsd command line option
subset() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
T
tail() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
test() (in module rna_tools.tools.mq.ClashScore.ClashScore)
(in module rna_tools.tools.mq.Dfire.Dfire)
trafl
rna_calc_evo_rmsd command line option
rna_simrna_lowest.py command line option
trimmed_rf_and_ss() (rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
U
un_nmr() (rna_tools.rna_tools_lib.RNAStructure method)
W
write() (rna_tools.rna_tools_lib.RNAStructure method)
(rna_tools.tools.rna_alignment.rna_alignment.RChie method)
(rna_tools.tools.rna_alignment.rna_alignment.RNAalignment method)
write_align() (in module rna_tools.tools.rna_alignment.random_assignment_of_nucleotides)
write_seq() (in module rna_tools.tools.rna_alignment.random_assignment_of_nucleotides)
write_struc() (in module rna_tools.tools.renum_pdb_to_aln.renum_pdb_to_aln)
X
x3DNA (class in rna_tools.tools.rna_x3dna.rna_x3dna)
,
[1]
x3DNAMissingFile
,
[1]