Index

Symbols

( command line option () command line option (possible command line option , command line option, [1] --absolute-concentrations command line option --accessibility-dir command line option --alignment-mode command line option, [1] --alignmentLength command line option --all_pf command line option, [1] --allowFlipping command line option --aln command line option, [1], [2] --aln-EPS command line option --aln-EPS-cols command line option, [1], [2] --aln-EPS-ss command line option --aln-stk command line option, [1] --alphabet command line option --auto-id command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --backbone-length command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --backtrack command line option, [1] --backtrack-global command line option --batch command line option, [1], [2], [3] --betaScale command line option, [1], [2], [3], [4], [5], [6] --binaries command line option --binary command line option --bppmThreshold command line option, [1], [2], [3] --canonicalBPonly command line option, [1], [2] --centroid command line option --cfactor command line option, [1], [2] --circ command line option, [1], [2], [3], [4], [5] --color command line option --color-min-sat command line option, [1] --color-threshold command line option, [1] --commands command line option, [1], [2], [3], [4], [5] --compare command line option, [1] --concentrations command line option, [1] --concfile command line option, [1] --constraint command line option, [1], [2], [3], [4], [5], [6] --continuous-ids command line option --contributions command line option --convert-to-bin command line option --covar command line option --covar-min-sat command line option --covar-threshold command line option --csv command line option --csv-delim command line option --csv-noheader command line option --cutoff command line option, [1] --dangles command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] --deltaEnergy command line option, [1], [2] --deltaEnergyPost command line option --detailed-help command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --direct-redraw command line option --distance command line option --dos command line option --dump command line option --duplex-distance command line option, [1] --en-only command line option --endgaps command line option, [1] --energy-threshold command line option, [1] --energyCutoff command line option --energyModel command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] --enforceConstraint command line option, [1], [2], [3] --extend3 command line option --extend5 command line option --extension-cost command line option, [1] --fast-folding command line option, [1] --filename-delim command line option, [1], [2], [3], [4], [5], [6], [7], [8] --filename-full command line option, [1], [2], [3], [4], [5], [6] --final command line option --from-RNAplfold command line option --from-RNAup command line option --full-help command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --function command line option --gape command line option --gapo command line option --gquad command line option, [1], [2], [3], [4], [5], [6], [7], [8] --hashtable-bits command line option --helical-rise command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --help command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --id-delim command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-digits command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-prefix command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-start command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --ignoreAncestorIntersections command line option --ignoreExteriorIntersections command line option --ignoreSiblingIntersections command line option --ImFeelingLucky command line option --include_both command line option --infile command line option, [1], [2], [3], [4], [5] --initialStepSize command line option --initialVector command line option --input command line option --input-format command line option, [1] --interaction-length command line option --interaction_first command line option --interaction_pairwise command line option --intermediatePath command line option --ipoints command line option --jobs command line option, [1], [2], [3], [4], [5], [6] --k-concentration command line option --layout-type command line option, [1], [2] --log-call command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --log-file command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --log-level command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --log-time command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --logML command line option, [1] --max-energy command line option --maxBPspan command line option, [1], [2], [3], [4], [5], [6], [7] --maxDist1 command line option --maxDist2 command line option --maximal-duplex-box-length command line option --maximal-snoRNA-duplex-length command line option --maximal-snoRNA-stem-loop-length command line option --maximal-stem-asymmetry command line option --MEA command line option, [1], [2] --mg-concentration command line option --minimal-duplex command line option --minimal-duplex-box-length command line option --minimal-duplex-stem-energy command line option --minimal-loop-energy command line option --minimal-lower-stem-energy command line option --minimal-right-duplex command line option --minimal-snoRNA-duplex-length command line option --minimal-snoRNA-stem-loop-length command line option --minimal-total-energy command line option --minimizer command line option --minimizerTolerance command line option --minImprovement command line option --minStepSize command line option --mis command line option, [1], [2], [3] --mod-file command line option, [1], [2], [3], [4] --mode command line option --modifications command line option, [1], [2], [3], [4] --motif command line option --msa command line option, [1] --na-concentration command line option --neighborhood command line option --nfactor command line option, [1], [2] --no_header command line option --no_output_file command line option --noBT command line option --noClosingGU command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]

--noconv command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --noDP command line option, [1] --noGU command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --noLP command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --nonRedundant command line option, [1], [2] --noOptimization command line option --noPS command line option, [1], [2] --noTetra command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] --nsp command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --numThreads command line option, [1], [2] --objectiveFunction command line option --old command line option, [1] --opening_energies command line option --outfile command line option, [1], [2] --output command line option --output-format command line option, [1] --output_directory command line option --paramFile command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --partfunc command line option, [1], [2], [3], [4] --pfScale command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9] --plex_output command line option --post command line option --pre command line option --print_onthefly command line option --printAlignment command line option --probe-concentration command line option --probe-mode command line option --produce-ps command line option, [1] --query command line option, [1] --quiet command line option, [1] --random-seed command line option, [1] --repeat command line option --ribosum_file command line option, [1], [2] --ribosum_scoring command line option, [1], [2] --salt command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --saltInit command line option, [1], [2], [3], [4] --sampleSize command line option --scale-accessibility command line option --sci command line option --sequence command line option --seqw command line option --shape command line option, [1], [2], [3], [4], [5], [6], [7] --shapeConversion command line option, [1], [2], [3], [4], [5], [6] --shapeMethod command line option, [1], [2], [3], [4], [5], [6], [7] --shapiro command line option --silent command line option --sorted command line option, [1], [2] --span command line option, [1] --split-contributions command line option --SS_cons command line option --stepsize command line option --stochBT command line option, [1], [2] --stochBT_en command line option, [1] --subopts command line option --suffix command line option --target command line option, [1] --tauSigmaRatio command line option --temp command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] --threshold command line option --Tmax command line option --Tmin command line option --tris-concentration command line option --ulength command line option, [1] --unordered command line option, [1], [2], [3], [4], [5] --vanilla command line option --verbose command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --version command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --window command line option --WindowLength command line option --winsize command line option --without-BulgeE command line option --without-Dangle3 command line option --without-Dangle5 command line option --without-HairpinE command line option --without-IntE command line option --without-Misc command line option --without-MismatchE command line option --without-MismatchH command line option --without-MismatchI command line option --without-MismatchM command line option --without-MultiE command line option --without-StackE command line option --zscore command line option --zscore-pre-filter command line option --zscore-report-subsumed command line option --zuker command line option -3 command line option -4 command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] -5 command line option -A command line option, [1] -a command line option, [1], [2], [3], [4], [5], [6] -B command line option, [1], [2] -b command line option, [1], [2], [3], [4], [5] -C command line option, [1], [2], [3], [4], [5], [6] -c command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] -D command line option, [1] -d command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] -E command line option -e command line option, [1], [2], [3], [4], [5], [6] -F command line option -f command line option, [1], [2], [3], [4], [5], [6], [7] -g command line option, [1], [2], [3], [4], [5], [6], [7], [8] -h command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] -I command line option, [1] -i command line option, [1], [2], [3], [4], [5], [6] -j command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] -K command line option, [1] -k command line option, [1] -L command line option, [1], [2], [3], [4], [5] -l command line option, [1] -M command line option -m command line option, [1], [2], [3], [4], [5], [6] -N command line option, [1], [2], [3], [4] -n command line option, [1] -O command line option, [1] -o command line option, [1], [2], [3], [4], [5], [6] -P command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] -p command line option, [1], [2], [3], [4], [5], [6] -Q command line option -q command line option, [1], [2], [3] -R command line option, [1], [2], [3] -r command line option, [1], [2] -S command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] -s command line option, [1], [2], [3], [4], [5], [6] -T command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] -t command line option, [1], [2], [3], [4] -U command line option, [1] -u command line option, [1] -V command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] -v command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] -W command line option -w command line option, [1] -X command line option, [1], [2] -x command line option -y command line option -z command line option, [1], [2] . command line option, [1] ``m`` command line option { command line option {} command line option | command line option, [1]

_

__E_IntLoop_Co (C function)

A

a2s (RNA.fold_compound attribute) abstract_shapes() (in module RNA) add_auxdata() (RNA.fold_compound method) add_callback() (RNA.fold_compound method) add_root (C function) add_root() (in module RNA) advance() (RNA.SwigPyIterator method) alias (RNA.md attribute) (RNA.md property) aliduplex_subopt() (in module RNA) aliduplexfold() (in module RNA) alifold (C function) alifold() (in module RNA) alignment (RNA.fold_compound attribute) aliLfold (C function) aliLfold() (in module RNA) aliLfold_cb (C function) aliLfold_cb() (in module RNA) alimake_pair_table (C function) alipbacktrack (C function) alipf_circ_fold (C function) alipf_fold (C function) alipf_fold_par (C function) aliPS_color_aln (C function) alloc_sequence_arrays (C function) allowFlipping (RNA.plot_options_puzzler attribute), [1] (RNA.plot_options_puzzler property) aln_consensus_mis() (in module RNA) aln_consensus_sequence() (in module RNA) aln_conservation_col() (in module RNA) aln_conservation_struct() (in module RNA) aln_mpi() (in module RNA) aln_pscore() (in module RNA) alpha (RNA.exp_param attribute), [1] (RNA.exp_param property) append() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method)

assign() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) assign_plist_from_db (C function) assign_plist_from_pr (C function) aux_grammar (RNA.fold_compound attribute) auxdata (RNA.fold_compound attribute) available (RNA.sc_mod_param attribute), [1]

B

b2C (C function) b2C() (in module RNA) b2HIT (C function) b2HIT() (in module RNA) b2Shapiro (C function) b2Shapiro() (in module RNA) back() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) backbone_length (C var) (RNA.md property) backtrack (RNA.md attribute) (RNA.md property) backtrack() (RNA.fold_compound method) backtrack_fold_from_pair (C function) backtrack_GQuad_IntLoop_L (C function) backtrack_GQuad_IntLoop_L() (in module RNA) backtrack_GQuad_IntLoop_L_comparative (C function) backtrack_GQuad_IntLoop_L_comparative() (in module RNA) backtrack_type (C var) (RNA.md attribute) (RNA.md property)

basepair (class in RNA) begin() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) beginning command line option, [1] benchmark() (RNA.fold_compound method) betaScale (RNA.md attribute) (RNA.md property) bondT (C type) boustrophedon() (in module RNA) bp_distance (C function) bp_distance() (in module RNA) bpdist (RNA.fold_compound attribute) bpp() (RNA.fold_compound method) bppm_symbol (C function) bppm_to_structure (C function) bulge (RNA.param attribute), [1] (RNA.param property)

C

c (RNA.mx_mfe property) capacity() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) cast() (RNA.doubleArray method) (RNA.floatArray method) (RNA.intArray method) cdata() (in module RNA) centroid() (in module RNA) (RNA.fold_compound method) checkAncestorIntersections (RNA.plot_options_puzzler attribute), [1] (RNA.plot_options_puzzler property) checkExteriorIntersections (RNA.plot_options_puzzler attribute), [1] (RNA.plot_options_puzzler property) checkSiblingIntersections (RNA.plot_options_puzzler attribute), [1] (RNA.plot_options_puzzler property) circ (C var) (RNA.md attribute) (RNA.md property) circ_alpha0 (RNA.md property) circ_penalty (RNA.md attribute) (RNA.md property) circalifold (C function) circalifold() (in module RNA) circfold (C function) circfold() (in module RNA) clear() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) cmd (class in RNA) co_pf_fold (C function) co_pf_fold() (in module RNA) co_pf_fold_par (C function) cofold (C function) cofold() (in module RNA) cofold_par (C function) cofoldF (C type) command line option ( () (possible ,, [1] --absolute-concentrations --accessibility-dir --alignment-mode, [1] --alignmentLength --all_pf, [1] --allowFlipping --aln, [1], [2] --aln-EPS --aln-EPS-cols, [1], [2] --aln-EPS-ss --aln-stk, [1] --alphabet --auto-id, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --backbone-length, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --backtrack, [1] --backtrack-global --batch, [1], [2], [3] --betaScale, [1], [2], [3], [4], [5], [6] --binaries --binary --bppmThreshold, [1], [2], [3] --canonicalBPonly, [1], [2] --centroid --cfactor, [1], [2] --circ, [1], [2], [3], [4], [5] --color --color-min-sat, [1] --color-threshold, [1] --commands, [1], [2], [3], [4], [5] --compare, [1] --concentrations, [1] --concfile, [1] --constraint, [1], [2], [3], [4], [5], [6] --continuous-ids --contributions --convert-to-bin --covar --covar-min-sat --covar-threshold --csv --csv-delim --csv-noheader --cutoff, [1] --dangles, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] --deltaEnergy, [1], [2] --deltaEnergyPost --detailed-help, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --direct-redraw --distance --dos --dump --duplex-distance, [1] --en-only --endgaps, [1] --energy-threshold, [1] --energyCutoff --energyModel, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] --enforceConstraint, [1], [2], [3] --extend3 --extend5 --extension-cost, [1] --fast-folding, [1] --filename-delim, [1], [2], [3], [4], [5], [6], [7], [8] --filename-full, [1], [2], [3], [4], [5], [6] --final --from-RNAplfold --from-RNAup --full-help, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --function --gape --gapo --gquad, [1], [2], [3], [4], [5], [6], [7], [8] --hashtable-bits --helical-rise, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --help, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --id-delim, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-digits, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-prefix, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-start, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --ignoreAncestorIntersections --ignoreExteriorIntersections --ignoreSiblingIntersections --ImFeelingLucky --include_both --infile, [1], [2], [3], [4], [5] --initialStepSize --initialVector --input --input-format, [1] --interaction-length --interaction_first --interaction_pairwise --intermediatePath --ipoints --jobs, [1], [2], [3], [4], [5], [6] --k-concentration --layout-type, [1], [2] --log-call, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --log-file, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --log-level, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --log-time, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --logML, [1] --max-energy --maxBPspan, [1], [2], [3], [4], [5], [6], [7] --maxDist1 --maxDist2 --maximal-duplex-box-length --maximal-snoRNA-duplex-length --maximal-snoRNA-stem-loop-length --maximal-stem-asymmetry --MEA, [1], [2] --mg-concentration --minimal-duplex --minimal-duplex-box-length --minimal-duplex-stem-energy --minimal-loop-energy --minimal-lower-stem-energy --minimal-right-duplex --minimal-snoRNA-duplex-length --minimal-snoRNA-stem-loop-length --minimal-total-energy --minimizer --minimizerTolerance --minImprovement --minStepSize --mis, [1], [2], [3] --mod-file, [1], [2], [3], [4] --mode --modifications, [1], [2], [3], [4] --motif --msa, [1] --na-concentration --neighborhood --nfactor, [1], [2] --no_header --no_output_file --noBT --noClosingGU, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --noconv, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --noDP, [1] --noGU, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --noLP, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --nonRedundant, [1], [2] --noOptimization --noPS, [1], [2] --noTetra, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] --nsp, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --numThreads, [1], [2] --objectiveFunction --old, [1] --opening_energies --outfile, [1], [2] --output --output-format, [1] --output_directory --paramFile, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --partfunc, [1], [2], [3], [4] --pfScale, [1], [2], [3], [4], [5], [6], [7], [8], [9] --plex_output --post --pre --print_onthefly --printAlignment --probe-concentration --probe-mode --produce-ps, [1] --query, [1] --quiet, [1] --random-seed, [1] --repeat --ribosum_file, [1], [2] --ribosum_scoring, [1], [2] --salt, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --saltInit, [1], [2], [3], [4] --sampleSize --scale-accessibility --sci --sequence --seqw --shape, [1], [2], [3], [4], [5], [6], [7] --shapeConversion, [1], [2], [3], [4], [5], [6] --shapeMethod, [1], [2], [3], [4], [5], [6], [7] --shapiro --silent --sorted, [1], [2] --span, [1] --split-contributions --SS_cons --stepsize --stochBT, [1], [2] --stochBT_en, [1] --subopts --suffix --target, [1] --tauSigmaRatio --temp, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] --threshold --Tmax --Tmin --tris-concentration --ulength, [1] --unordered, [1], [2], [3], [4], [5] --vanilla --verbose, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --version, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] --window --WindowLength --winsize --without-BulgeE --without-Dangle3 --without-Dangle5 --without-HairpinE --without-IntE --without-Misc --without-MismatchE --without-MismatchH --without-MismatchI --without-MismatchM --without-MultiE --without-StackE --zscore --zscore-pre-filter --zscore-report-subsumed --zuker -3 -4, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] -5 -a, [1], [2], [3], [4], [5], [6] -A, [1] -b, [1], [2], [3], [4], [5] -B, [1], [2] -c, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] -C, [1], [2], [3], [4], [5], [6] -d, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] -D, [1] -e, [1], [2], [3], [4], [5], [6] -E -f, [1], [2], [3], [4], [5], [6], [7] -F -g, [1], [2], [3], [4], [5], [6], [7], [8] -h, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] -i, [1], [2], [3], [4], [5], [6] -I, [1] -j, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] -K, [1] -k, [1] -L, [1], [2], [3], [4], [5] -l, [1] -m, [1], [2], [3], [4], [5], [6] -M -n, [1] -N, [1], [2], [3], [4] -o, [1], [2], [3], [4], [5], [6] -O, [1] -p, [1], [2], [3], [4], [5], [6] -P, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] -q, [1], [2], [3] -Q -R, [1], [2], [3] -r, [1], [2] -S, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] -s, [1], [2], [3], [4], [5], [6] -T, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] -t, [1], [2], [3], [4] -U, [1] -u, [1] -V, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] -v, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] -W -w, [1] -X, [1], [2] -x -y -z, [1], [2] ., [1] ``m`` { {} |, [1] beginning, [1] profiles

commands_apply() (RNA.fold_compound method) compare() (RNA.move method) compare_structure() (in module RNA) compute_BPdifferences (C function) compute_bpp (RNA.md attribute) (RNA.md property) compute_probabilities (C function) ConcEnt (C type) config (RNA.plot_options_puzzler attribute), [1] cons_seq (RNA.fold_compound attribute) consens_mis (C function) consens_mis() (in module RNA) consensus (C function) ConstCharVector (class in RNA) constrain (C struct) (C type) constrain.indx (C var) constrain.ptype (C var) constraints_add() (RNA.fold_compound method) convert_parameter_file (C function) COORDINATE (C struct) (class in RNA) COORDINATE.X (C var) COORDINATE.Y (C var) CoordinateVector (class in RNA) copy() (RNA.SwigPyIterator method) copy_pair_table (C function) copy_parameters (C function) copy_pf_param (C function) cpair (C type) cut_point (C var) cutpoint (RNA.fold_compound attribute) cv_fact (C var) (RNA.md attribute) (RNA.md property)

D

dangle3 (RNA.param attribute), [1] (RNA.param property) dangle3_dG (RNA.sc_mod_param attribute), [1] dangle3_dH (RNA.sc_mod_param attribute), [1] dangle5 (RNA.param attribute), [1] (RNA.param property) dangle5_dG (RNA.sc_mod_param attribute), [1] dangle5_dH (RNA.sc_mod_param attribute), [1] dangles (C var) (RNA.md attribute) (RNA.md property) data (RNA.hc attribute), [1] db_flatten() (in module RNA) db_from_plist() (in module RNA) db_from_probs() (RNA.fold_compound method) db_from_ptable() (in module RNA) db_from_WUSS() (in module RNA) db_pack() (in module RNA) db_pk_remove() (in module RNA) db_to_element_string() (in module RNA) db_to_tree_string() (in module RNA) db_unpack() (in module RNA) ddG (RNA.duplexT attribute) (RNA.duplexT property) decr() (RNA.SwigPyIterator method) delete_doubleP() (in module RNA) delete_floatP() (in module RNA) delete_intP() (in module RNA) delete_shortP() (in module RNA) delete_ushortP() (in module RNA) density_of_states (C var) depot (RNA.hc attribute), [1] deref_any() (in module RNA) destroy_TwoDfold_variables (C function) dG1 (RNA.duplexT attribute) (RNA.duplexT property) dG2 (RNA.duplexT attribute) (RNA.duplexT property) dist_mountain() (in module RNA) distance() (RNA.SwigPyIterator method) do_backtrack (C var) domains_struc (RNA.fold_compound attribute) domains_up (RNA.fold_compound attribute) doubleArray (class in RNA) doubleArray_frompointer() (in module RNA) DoubleDoubleVector (class in RNA)

doubleP_getitem() (in module RNA) doubleP_setitem() (in module RNA) DoublePair (class in RNA) DoubleVector (class in RNA) drawArcs (RNA.plot_options_puzzler attribute), [1] duplex_list_t (class in RNA) duplex_subopt() (in module RNA) duplexfold() (in module RNA) DuplexInit (RNA.param attribute), [1] (RNA.param property) duplexT (C struct) (class in RNA) duplexT.ddG (C var) duplexT.dG1 (C var) duplexT.dG2 (C var) duplexT.end (C var) duplexT.energy (C var) duplexT.energy_backtrack (C var) duplexT.i (C var) duplexT.j (C var) duplexT.offset (C var) duplexT.opening_backtrack_x (C var) duplexT.opening_backtrack_y (C var) duplexT.qb (C var) duplexT.qe (C var) duplexT.structure (C var) duplexT.tb (C var) duplexT.te (C var) DuplexVector (class in RNA) dupVar (C struct) (C type) dupVar.ddG (C var) dupVar.dG1 (C var) dupVar.dG2 (C var) dupVar.end (C var) dupVar.energy (C var) dupVar.i (C var) dupVar.inactive (C var) dupVar.j (C var) dupVar.offset (C var) dupVar.pk_helix (C var) dupVar.processed (C var) dupVar.qb (C var) dupVar.qe (C var) dupVar.structure (C var) dupVar.tb (C var) dupVar.te (C var)

E

E_ext_hp_loop() (RNA.fold_compound method) E_ext_int_loop() (RNA.fold_compound method) E_ExtLoop (C function) E_ExtLoop() (in module RNA) E_gquad (C function) E_gquad() (in module RNA) E_gquad_ali_en (C function) E_gquad_ali_en() (in module RNA) E_GQuad_IntLoop_L() (in module RNA) E_GQuad_IntLoop_L_comparative() (in module RNA) E_Hairpin (C function) E_Hairpin() (in module RNA) E_hp_loop() (RNA.fold_compound method) E_int_loop() (RNA.fold_compound method) E_IntLoop (C function) E_IntLoop() (in module RNA) E_IntLoop_Co (C function) E_IntLoop_Co() (in module RNA) E_ml_rightmost_stem() (in module RNA) E_MLstem (C function) E_MLstem() (in module RNA) E_stack() (RNA.fold_compound method) E_Stem (C function) E_Stem() (in module RNA) ElemProbVector (class in RNA) empty() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) en (RNA.path property) encode_ali_sequence (C function) encode_seq() (in module RNA) encoding3 (RNA.fold_compound attribute) encoding5 (RNA.fold_compound attribute) end (RNA.duplexT attribute) (RNA.duplexT property) (RNA.hx property) end() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) energy (RNA.duplex_list_t property) (RNA.duplexT attribute) (RNA.duplexT property) (RNA.SOLUTION property) (RNA.struct_en attribute), [1] (RNA.struct_en property) (RNA.subopt_solution property) energy_backtrack (RNA.duplexT attribute) (RNA.duplexT property) energy_of_circ_struct (C function) energy_of_circ_struct() (in module RNA) energy_of_circ_struct_par (C function) energy_of_circ_structure (C function) energy_of_circ_structure() (in module RNA) energy_of_gquad_struct_par (C function) energy_of_gquad_structure (C function) energy_of_gquad_structure() (in module RNA) energy_of_move (C function) energy_of_move() (in module RNA) energy_of_move_pt (C function) energy_of_move_pt() (in module RNA) energy_of_struct (C function) energy_of_struct() (in module RNA) energy_of_struct_par (C function) energy_of_struct_pt (C function) energy_of_struct_pt() (in module RNA) energy_of_struct_pt_par (C function) energy_of_structure (C function) energy_of_structure() (in module RNA) energy_of_structure_pt (C function) energy_of_structure_pt() (in module RNA) energy_set (C var) (RNA.md attribute) (RNA.md property) ensemble_defect() (RNA.fold_compound method) enumerate_necklaces() (in module RNA) eos_debug (C var) ep (class in RNA) equal() (RNA.SwigPyIterator method) erase() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method)

eval_circ_gquad_structure() (in module RNA) eval_circ_structure() (in module RNA) eval_covar_structure() (RNA.fold_compound method) eval_ext_hp_loop() (RNA.fold_compound method) eval_ext_stem() (RNA.fold_compound method) eval_gquad_structure() (in module RNA) eval_hp_loop() (RNA.fold_compound method) eval_int_loop() (RNA.fold_compound method) eval_loop_pt() (RNA.fold_compound method) eval_move() (RNA.fold_compound method) eval_move_pt() (RNA.fold_compound method) eval_structure() (RNA.fold_compound method) eval_structure_pt() (RNA.fold_compound method) eval_structure_pt_simple() (in module RNA) eval_structure_pt_verbose() (RNA.fold_compound method) eval_structure_simple() (in module RNA) eval_structure_verbose() (RNA.fold_compound method) exp_E_ext_stem() (RNA.fold_compound method) exp_E_ExtLoop (C function) exp_E_ExtLoop() (in module RNA) exp_E_gquad (C function) exp_E_gquad() (in module RNA) exp_E_gquad_ali (C function) exp_E_gquad_ali() (in module RNA) exp_E_Hairpin (C function) exp_E_Hairpin() (in module RNA) exp_E_hp_loop() (RNA.fold_compound method) exp_E_int_loop() (RNA.fold_compound method) exp_E_interior_loop() (RNA.fold_compound method) exp_E_IntLoop (C function) exp_E_IntLoop() (in module RNA) exp_E_MLstem (C function) exp_E_MLstem() (in module RNA) exp_E_Stem (C function) exp_E_Stem() (in module RNA) exp_matrices (RNA.fold_compound attribute) (RNA.fold_compound property) exp_param (class in RNA) exp_params (RNA.fold_compound attribute) (RNA.fold_compound property) exp_params_rescale() (RNA.fold_compound method) exp_params_reset() (RNA.fold_compound method) exp_params_subst() (RNA.fold_compound method) expand_Full (C function) expand_Full() (in module RNA) expand_Shapiro (C function) expand_Shapiro() (in module RNA) expbulge (RNA.exp_param attribute), [1] (RNA.exp_param property) expdangle3 (RNA.exp_param attribute), [1] (RNA.exp_param property) expdangle5 (RNA.exp_param attribute), [1] (RNA.exp_param property) expDuplexInit (RNA.exp_param attribute), [1] (RNA.exp_param property) expgquad (RNA.exp_param attribute), [1] (RNA.exp_param property) expgquadLayerMismatch (RNA.exp_param attribute), [1] (RNA.exp_param property) exphairpin (RNA.exp_param attribute), [1] (RNA.exp_param property) exphex (RNA.exp_param attribute), [1] (RNA.exp_param property) expint11 (RNA.exp_param attribute), [1] (RNA.exp_param property) expint21 (RNA.exp_param attribute), [1] (RNA.exp_param property) expint22 (RNA.exp_param attribute), [1] (RNA.exp_param property) expinternal (RNA.exp_param attribute), [1] (RNA.exp_param property) expmismatch1nI (RNA.exp_param attribute), [1] (RNA.exp_param property) expmismatch23I (RNA.exp_param attribute), [1] (RNA.exp_param property) expmismatchExt (RNA.exp_param attribute), [1] (RNA.exp_param property) expmismatchH (RNA.exp_param attribute), [1] (RNA.exp_param property) expmismatchI (RNA.exp_param attribute), [1] (RNA.exp_param property) expmismatchM (RNA.exp_param attribute), [1] (RNA.exp_param property) expMLbase (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.mx_pf property) expMLclosing (RNA.exp_param attribute), [1] (RNA.exp_param property) expMLintern (RNA.exp_param attribute), [1] (RNA.exp_param property) expMultipleCA (RNA.exp_param attribute), [1] (RNA.exp_param property) expMultipleCB (RNA.exp_param attribute), [1] (RNA.exp_param property) expninio (RNA.exp_param attribute), [1] (RNA.exp_param property) export_ali_bppm (C function) export_bppm (C function) export_circfold_arrays (C function) export_circfold_arrays_par (C function) export_co_bppm (C function) export_cofold_arrays (C function) export_cofold_arrays_gq (C function) export_fold_arrays (C function) export_fold_arrays_par (C function) expSaltLoop (RNA.exp_param attribute), [1] (RNA.exp_param property) expSaltStack (RNA.exp_param attribute), [1] (RNA.exp_param property) expstack (RNA.exp_param attribute), [1] (RNA.exp_param property) expTermAU (RNA.exp_param attribute), [1] (RNA.exp_param property) exptetra (RNA.exp_param attribute), [1] (RNA.exp_param property) exptri (RNA.exp_param attribute), [1] (RNA.exp_param property) expTriloop (RNA.exp_param attribute), [1] (RNA.exp_param property) expTripleC (RNA.exp_param attribute), [1] (RNA.exp_param property) extract_record_rest_structure (C function) extract_record_rest_structure() (in module RNA)

F

f (RNA.hc attribute), [1] F1 (RNA.score property) f3 (RNA.mx_mfe property) f5 (RNA.mx_mfe property) F_monomer (C var) fallback (RNA.sc_mod_param attribute), [1] fallback_encoding (RNA.sc_mod_param attribute), [1] Fc (RNA.mx_mfe property) fc_add_pycallback() (in module RNA) fc_add_pydata() (in module RNA) FcH (RNA.mx_mfe property) FcI (RNA.mx_mfe property) FcM (RNA.mx_mfe property) FDR (RNA.score property) file_commands_apply() (RNA.fold_compound method) file_commands_read() (in module RNA) file_connect_read_record() (in module RNA) file_fasta_read() (in module RNA) file_msa_detect_format() (in module RNA) file_msa_read() (in module RNA) file_msa_read_record() (in module RNA) file_msa_write() (in module RNA) file_PS_aln() (in module RNA) file_PS_rnaplot() (in module RNA) file_PS_rnaplot_a() (in module RNA) file_RNAstrand_db_read_record() (in module RNA) file_SHAPE_read() (in module RNA) filename (RNA.plot_options_puzzler attribute), [1] FILENAME_ID_LENGTH (C macro) FILENAME_MAX_LENGTH (C macro) filename_sanitize() (in module RNA) final_cost (C var) find_saddle (C function) find_saddle() (in module RNA) first (RNA.DoublePair property) floatArray (class in RNA) floatArray_frompointer() (in module RNA) floatP_getitem() (in module RNA) floatP_setitem() (in module RNA) FLT_OR_DBL (C type) fM1 (RNA.mx_mfe property) fM2 (RNA.mx_mfe property) fML (RNA.mx_mfe property) FN (RNA.score property) FNR (RNA.score property) fold (C function) fold() (in module RNA)

fold_compound (class in RNA) fold_par (C function) folden (C type) FOR (RNA.score property) FP (RNA.score property) FPR (RNA.score property) free_alifold_arrays (C function) free_alifold_arrays() (in module RNA) free_alipf_arrays (C function) free_arrays (C function) free_arrays() (in module RNA) free_auxdata (RNA.fold_compound attribute) free_co_arrays (C function) free_co_arrays() (in module RNA) free_co_pf_arrays (C function) free_co_pf_arrays() (in module RNA) free_data (RNA.hc attribute), [1] free_interact (C function) free_path (C function) free_path() (in module RNA) free_pf_arrays (C function) free_pf_arrays() (in module RNA) free_profile() (in module RNA) free_pu_contrib (C function) free_pu_contrib_struct (C function) free_sequence_arrays (C function) free_tree() (in module RNA) frompointer() (RNA.doubleArray static method) (RNA.floatArray static method) (RNA.intArray static method) front() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method)

G

get() (RNA.COORDINATE method) (RNA.SOLUTION method) (RNA.varArrayChar method) (RNA.varArrayFLTorDBL method) (RNA.varArrayInt method) (RNA.varArrayMove method) (RNA.varArrayShort method) (RNA.varArrayUChar method) (RNA.varArrayUInt method) get_aligned_line() (in module RNA) get_alipf_arrays (C function) get_allocator() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) get_boltzmann_factor_copy (C function) get_boltzmann_factors (C function) get_boltzmann_factors_ali (C function) get_centroid_struct_pl() (in module RNA) get_centroid_struct_pr() (in module RNA) get_concentrations() (in module RNA) get_gquad_ali_matrix() (in module RNA) get_gquad_count (C function) get_gquad_L_matrix() (in module RNA) get_gquad_matrix() (in module RNA) get_gquad_pattern_exhaustive (C function) get_gquad_pattern_pf (C function) get_gquad_pattern_pf() (in module RNA)

get_gquad_pf_matrix() (in module RNA) get_gquad_pf_matrix_comparative() (in module RNA) get_input_line (C function) get_mpi (C function) get_multi_input_line (C function) get_multi_input_line() (in module RNA) get_parameter_copy (C function) get_path (C function) get_path() (in module RNA) get_pf_arrays (C function) get_plist_gquad_from_db (C function) get_plist_gquad_from_db() (in module RNA) get_plist_gquad_from_pr() (in module RNA) get_plist_gquad_from_pr_max() (in module RNA) get_pr() (in module RNA) get_pu_contrib_struct (C function) get_ribosum (C function) get_scaled_alipf_parameters (C function) get_scaled_parameters (C function) get_scaled_pf_parameters (C function) get_subseq_F (C function) get_TwoDfold_variables (C function) get_ungapped_sequence (C function) get_xy_coordinates() (in module RNA) gettype (C function) gettype() (in module RNA) give_up (C var) gmlRNA (C function) gmlRNA() (in module RNA) gq_parse() (in module RNA) gquad (C var) (RNA.md attribute) (RNA.md property) (RNA.param attribute), [1] (RNA.param property) gquadLayerMismatch (RNA.param attribute), [1] (RNA.param property) gquadLayerMismatchMax (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property)

H

hairpin (RNA.param attribute), [1] (RNA.param property) HairpinE (C function) hamming() (in module RNA) hamming_bound() (in module RNA) hamming_distance() (in module RNA) hamming_distance_bound() (in module RNA) hc (class in RNA) (RNA.fold_compound attribute) (RNA.fold_compound property) hc_add_bp() (RNA.fold_compound method) hc_add_bp_nonspecific() (RNA.fold_compound method) hc_add_bp_strand() (RNA.fold_compound method) hc_add_from_db() (RNA.fold_compound method) hc_add_up() (RNA.fold_compound method) hc_add_up_strand() (RNA.fold_compound method) hc_init() (RNA.fold_compound method) heat_capacity (RNA.heat_capacity_result property)

heat_capacity() (in module RNA) (RNA.fold_compound method) heat_capacity_cb() (RNA.fold_compound method) heat_capacity_result (class in RNA) HeatCapacityVector (class in RNA) helical_rise (C var) (RNA.md property) helix_size (C var) HelixVector (class in RNA) Hexaloop_E (RNA.param attribute), [1] (RNA.param property) Hexaloops (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) hx (class in RNA) hx_from_ptable() (in module RNA) hx_merge() (in module RNA)

I

i (C var) (RNA.basepair attribute), [1] (RNA.basepair property) (RNA.duplex_list_t property) (RNA.duplexT attribute) (RNA.duplexT property) (RNA.ep attribute), [1] (RNA.ep property) id (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) iindx (RNA.fold_compound attribute) (RNA.fold_compound property) incr() (RNA.SwigPyIterator method) init_co_pf_fold (C function) init_pf_circ_fold() (in module RNA) init_pf_fold (C function) init_pf_fold() (in module RNA) init_rand() (in module RNA) initialize_cofold (C function) initialize_cofold() (in module RNA) initialize_fold (C function) insert() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) int11 (RNA.param attribute), [1] (RNA.param property) int21 (RNA.param attribute), [1] (RNA.param property) int22 (RNA.param attribute), [1] (RNA.param property)

int_urn() (in module RNA) intArray (class in RNA) intArray_frompointer() (in module RNA) interact (C struct) (C type) interact.Gi (C var) interact.Gikjl (C var) interact.Gikjl_wo (C var) interact.i (C var) interact.j (C var) interact.k (C var) interact.l (C var) interact.length (C var) interact.Pi (C var) internal_loop (RNA.param attribute), [1] (RNA.param property) IntIntVector (class in RNA) intP_getitem() (in module RNA) intP_setitem() (in module RNA) IntVector (class in RNA) inv_verbose (C var) inverse_fold (C function) inverse_fold() (in module RNA) inverse_pf_fold (C function) inverse_pf_fold() (in module RNA) is_insertion() (RNA.move method) is_removal() (RNA.move method) is_shift() (RNA.move method) iterator() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method)

J

j (C var) (RNA.basepair attribute), [1] (RNA.basepair property) (RNA.duplex_list_t property) (RNA.duplexT attribute) (RNA.duplexT property) (RNA.ep attribute), [1] (RNA.ep property)

jindx (RNA.fold_compound attribute) (RNA.fold_compound property)

K

kT (RNA.exp_param attribute), [1] (RNA.exp_param property)

L

last_parameter_file (C function) last_parameter_file() (in module RNA) length (RNA.fold_compound attribute) (RNA.fold_compound property) (RNA.hx property) (RNA.mx_mfe property) (RNA.mx_pf property) Lfold (C function) Lfold() (in module RNA) Lfold_cb() (in module RNA) Lfoldz (C function) Lfoldz() (in module RNA) Lfoldz_cb() (in module RNA) log_cb_add() (in module RNA) log_cb_add_pycallback() (in module RNA) log_cb_num() (in module RNA) log_fp() (in module RNA) log_fp_set() (in module RNA)

log_level() (in module RNA) log_level_set() (in module RNA) log_options() (in module RNA) log_options_set() (in module RNA) log_reset() (in module RNA) logML (C var) (RNA.md attribute) (RNA.md property) loop_degree (C var) loop_energy (C function) loop_energy() (in module RNA) loop_size (C var) LoopEnergy (C function) loopidx_from_ptable() (in module RNA) loops (C var) lxc (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property)

M

Make_bp_profile() (in module RNA) Make_bp_profile_bppm() (in module RNA) make_loop_index() (in module RNA) make_pair_table (C function) make_pair_table_snoop (C function) make_referenceBP_array (C function) Make_swString() (in module RNA) make_tree() (in module RNA) matrices (RNA.fold_compound attribute) (RNA.fold_compound property) matrix_local (RNA.hc attribute), [1] MAX2 (C macro) MAX3 (C macro) max_bp_span (C var) (RNA.md attribute) (RNA.md property) MAXALPHA (C macro) maxD1 (RNA.fold_compound attribute) maxD2 (RNA.fold_compound attribute) maximum_matching() (in module RNA) maximumNumberOfConfigChangesAllowed (RNA.plot_options_puzzler attribute), [1] maxmimum_matching() (RNA.fold_compound method) MCC (RNA.score property) md (class in RNA) (RNA.plot_data property) MEA (C function) MEA() (RNA.fold_compound method) MEA_from_plist() (in module RNA) mean_bp_distance (C function) mean_bp_distance() (in module RNA) (RNA.fold_compound method) mean_bp_distance_pr (C function) memmove() (in module RNA) mfe() (RNA.fold_compound method) mfe_dimer() (RNA.fold_compound method) mfe_window() (RNA.fold_compound method) mfe_window_cb() (RNA.fold_compound method) mfe_window_zscore() (RNA.fold_compound method) mfe_window_zscore_cb() (RNA.fold_compound method) MIN2 (C macro) MIN3 (C macro) min_loop_size (RNA.md attribute) (RNA.md property) mirnatog (C var)

mismatch1nI (RNA.param attribute), [1] (RNA.param property) mismatch23I (RNA.param attribute), [1] (RNA.param property) mismatch_dG (RNA.sc_mod_param attribute), [1] mismatch_dH (RNA.sc_mod_param attribute), [1] mismatchExt (RNA.param attribute), [1] (RNA.param property) mismatchH (RNA.param attribute), [1] (RNA.param property) mismatchI (RNA.param attribute), [1] (RNA.param property) mismatchM (RNA.param attribute), [1] (RNA.param property) MLbase (RNA.param attribute), [1] (RNA.param property) MLclosing (RNA.param attribute), [1] (RNA.param property) MLintern (RNA.param attribute), [1] (RNA.param property) mm1 (RNA.fold_compound attribute) mm2 (RNA.fold_compound attribute) model_details (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) model_detailsT (C macro) module RNA move (class in RNA) (RNA.path property) move_neighbor_diff() (RNA.fold_compound method) move_standard() (in module RNA) MoveVector (class in RNA) MultipleCA (RNA.param attribute), [1] (RNA.param property) MultipleCB (RNA.param attribute), [1] (RNA.param property) mx (RNA.hc attribute), [1] (RNA.hc property) mx_mfe (class in RNA) mx_pf (class in RNA) my_aln_consensus_sequence2() (in module RNA) my_PS_rna_plot_snoop_a() (in module RNA)

N

n (RNA.hc attribute), [1] (RNA.hc property) n_multichoose_k() (in module RNA) n_seq (RNA.fold_compound attribute) name (RNA.sc_mod_param attribute), [1] naview_xy_coordinates() (in module RNA) NBASES (C macro) nc_fact (C var) (RNA.md attribute) (RNA.md property) neighbors() (RNA.fold_compound method) new_doubleP() (in module RNA) new_floatP() (in module RNA) new_intP() (in module RNA) new_shortP() (in module RNA) new_ushortP() (in module RNA) next (RNA.move attribute), [1] next() (RNA.SwigPyIterator method) (RNA.var_array_Iterator method) ninio (RNA.param attribute), [1] (RNA.param property)

no_closingGU (C var) node (C struct) node.energy (C var) node.k (C var) node.next (C var) noGU (C var) (RNA.md attribute) (RNA.md property) noGUclosure (RNA.md attribute) (RNA.md property) noLonelyPairs (C var) noLP (RNA.md attribute) (RNA.md property) nonstandards (C var) (RNA.md attribute) (RNA.md property) NPV (RNA.score property) nucleotides (RNA.fold_compound attribute) num_ptypes (RNA.sc_mod_param attribute), [1] numberOfChangesAppliedToConfig (RNA.plot_options_puzzler attribute), [1]

O

offset (RNA.duplexT attribute) (RNA.duplexT property) oldAliEn (C var) (RNA.fold_compound attribute) (RNA.md attribute) (RNA.md property) ON_SAME_STRAND (C macro) one_letter_code (RNA.sc_mod_param attribute), [1]

opening_backtrack_x (RNA.duplexT attribute) (RNA.duplexT property) opening_backtrack_y (RNA.duplexT attribute) (RNA.duplexT property) optimize (RNA.plot_options_puzzler attribute), [1] (RNA.plot_options_puzzler property) option_string (C function) option_string() (RNA.md method) options (RNA.plot_data property)

P

p (RNA.ep attribute), [1] (RNA.ep property) pack_structure (C function) pack_structure() (in module RNA) PAIR (C type) pair (RNA.md attribute) (RNA.md property) pair_dist (RNA.md attribute) pair_info (C type) paired (RNA.plot_options_puzzler attribute), [1] pairing_partners (RNA.sc_mod_param attribute), [1] pairing_partners_encoding (RNA.sc_mod_param attribute), [1] pairs (C var) param (class in RNA) param_file (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) params (RNA.fold_compound attribute) (RNA.fold_compound property) params_load() (in module RNA) params_load_DNA_Mathews1999() (in module RNA) params_load_DNA_Mathews2004() (in module RNA) params_load_from_string() (in module RNA) params_load_RNA_Andronescu2007() (in module RNA) params_load_RNA_Langdon2018() (in module RNA) params_load_RNA_misc_special_hairpins() (in module RNA) params_load_RNA_Turner1999() (in module RNA) params_load_RNA_Turner2004() (in module RNA) params_reset() (RNA.fold_compound method) params_save() (in module RNA) params_subst() (RNA.fold_compound method) paramT (C type) parenthesis_structure (C function) parenthesis_zuker (C function) parse_gquad (C function) parse_gquad() (in module RNA) parse_structure (C function) parse_structure() (in module RNA) parset (C enum) parset.B (C enumerator) parset.B_H (C enumerator) parset.D3 (C enumerator) parset.D3_H (C enumerator) parset.D5 (C enumerator) parset.D5_H (C enumerator) parset.HEX (C enumerator) parset.HP (C enumerator) parset.HP_H (C enumerator) parset.IL (C enumerator) parset.IL_H (C enumerator) parset.INT11 (C enumerator) parset.INT11_H (C enumerator) parset.INT21 (C enumerator) parset.INT21_H (C enumerator) parset.INT22 (C enumerator) parset.INT22_H (C enumerator) parset.MISC (C enumerator) parset.ML (C enumerator) parset.MME (C enumerator) parset.MME_H (C enumerator) parset.MMH (C enumerator) parset.MMH_H (C enumerator) parset.MMI (C enumerator) parset.MMI1N (C enumerator) parset.MMI1N_H (C enumerator) parset.MMI23 (C enumerator) parset.MMI23_H (C enumerator) parset.MMI_H (C enumerator) parset.MMM (C enumerator) parset.MMM_H (C enumerator) parset.NIN (C enumerator) parset.QUIT (C enumerator) parset.S (C enumerator) parset.S_H (C enumerator) parset.TL (C enumerator) parset.TRI (C enumerator) parset.UNKNOWN (C enumerator) path (class in RNA) path() (RNA.fold_compound method) path_direct() (RNA.fold_compound method) path_findpath() (RNA.fold_compound method) path_findpath_saddle() (RNA.fold_compound method) path_gradient() (RNA.fold_compound method) path_options (class in RNA) path_options_findpath() (in module RNA) path_random() (RNA.fold_compound method) path_t (C type) PathVector (class in RNA) pbacktrack (C function) pbacktrack() (in module RNA) (RNA.fold_compound method) pbacktrack5 (C function) pbacktrack5() (in module RNA) (RNA.fold_compound method) pbacktrack_circ (C function) pbacktrack_circ() (in module RNA) pbacktrack_mem (class in RNA) pbacktrack_sub() (RNA.fold_compound method) pf() (RNA.fold_compound method) pf_add() (in module RNA) pf_circ_fold (C function) pf_circ_fold() (in module RNA) pf_dimer() (RNA.fold_compound method) pf_float_precision() (in module RNA) pf_fold (C function) pf_fold() (in module RNA) pf_fold_par (C function) pf_interact (C function) pf_paramT (C type) pf_scale (C var) (RNA.exp_param attribute), [1] (RNA.exp_param property) pf_smooth (RNA.md attribute) (RNA.md property) pf_unstru (C function) pfl_fold (C function) pfl_fold() (in module RNA) pfl_fold_cb() (in module RNA) pfl_fold_par (C function) pfl_fold_up() (in module RNA) pfl_fold_up_cb() (in module RNA) plist (C type) plist() (in module RNA) plist_from_probs() (RNA.fold_compound method) plot_data (class in RNA) plot_dp_EPS() (in module RNA) plot_layout (class in RNA) plot_layout_circular() (in module RNA) plot_layout_naview() (in module RNA) plot_layout_puzzler() (in module RNA) plot_layout_simple() (in module RNA) plot_layout_turtle() (in module RNA) plot_options_puzzler (class in RNA)

plot_options_puzzler() (RNA.plot_options_puzzler method) plot_structure() (in module RNA) plot_structure_eps() (in module RNA) plot_structure_gml() (in module RNA) plot_structure_ssv() (in module RNA) plot_structure_svg() (in module RNA) plot_structure_xrna() (in module RNA) pop() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) pop_back() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) pos_3 (RNA.move attribute), [1] (RNA.move property) pos_5 (RNA.move attribute), [1] (RNA.move property) positional_entropy() (RNA.fold_compound method) post (RNA.plot_data property) PPV (RNA.score property) pr_energy() (RNA.fold_compound method) pr_structure() (RNA.fold_compound method) pre (RNA.plot_data property) previous() (RNA.SwigPyIterator method) print_bppm() (in module RNA) print_energy (C var) print_tree() (in module RNA) PRIVATE (C macro) probing_data (class in RNA) probing_data_Deigan2009() (in module RNA) probing_data_Deigan2009_comparative() (in module RNA) probing_data_Eddy2014_2() (in module RNA) probing_data_Eddy2014_2_comparative() (in module RNA) probing_data_free() (in module RNA) probing_data_Zarringhalam2012() (in module RNA) probing_data_Zarringhalam2012_comparative() (in module RNA) probs (RNA.mx_pf property) probs_window() (RNA.fold_compound method) profile_edit_distance() (in module RNA) profiles command line option progress_callback (C type) PS_color_aln (C function) PS_color_dot_plot (C function) PS_color_dot_plot() (in module RNA) PS_color_dot_plot_turn (C function) PS_color_dot_plot_turn() (in module RNA) PS_dot_plot (C function) PS_dot_plot() (in module RNA) PS_dot_plot_list (C function) PS_dot_plot_list() (in module RNA) PS_dot_plot_turn (C function) PS_dot_plot_turn() (in module RNA) PS_rna_plot (C function) PS_rna_plot() (in module RNA) PS_rna_plot_a (C function) PS_rna_plot_a() (in module RNA) PS_rna_plot_a_gquad (C function) PS_rna_plot_a_gquad() (in module RNA) PS_rna_plot_snoop_a (C function) pscore (RNA.fold_compound attribute) pscore_local (RNA.fold_compound attribute) pscore_pf_compat (RNA.fold_compound attribute) psNumber (RNA.plot_options_puzzler attribute), [1] pt_pk_remove() (in module RNA) ptable() (in module RNA) ptable_pk() (in module RNA) ptype (RNA.fold_compound attribute) ptype_local (RNA.fold_compound attribute) ptype_pf_compat (RNA.fold_compound attribute) ptypes (RNA.sc_mod_param attribute), [1] pu_contrib (C struct) (C type) pu_contrib.E (C var) pu_contrib.H (C var) pu_contrib.I (C var) pu_contrib.length (C var) pu_contrib.M (C var) pu_contrib.w (C var) pu_out (C struct) (C type) pu_out.contribs (C var) pu_out.header (C var) pu_out.len (C var) pu_out.u_vals (C var) pu_out.u_values (C var) PUBLIC (C macro) push_back() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) putoutpU_prob (C function) putoutpU_prob_bin (C function)

Q

q (RNA.mx_pf property) q1k (RNA.mx_pf property) qb (RNA.duplexT attribute) (RNA.duplexT property) (RNA.mx_pf property) qe (RNA.duplexT attribute) (RNA.duplexT property)

qho (RNA.mx_pf property) qio (RNA.mx_pf property) qln (RNA.mx_pf property) qm (RNA.mx_pf property) qm1 (RNA.mx_pf property) qm2 (RNA.mx_pf property) qmo (RNA.mx_pf property) qo (RNA.mx_pf property)

R

random_string() (in module RNA) rbegin() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) read_clustal (C function) read_parameter_file (C function) read_parameter_file() (in module RNA) read_record (C function) read_record() (in module RNA) readribosum (C function) reference_pt1 (RNA.fold_compound attribute) reference_pt2 (RNA.fold_compound attribute) referenceBPs1 (RNA.fold_compound attribute) referenceBPs2 (RNA.fold_compound attribute) rend() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method)

reserve() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) reset() (RNA.md method) resize() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) ribo (C var) (RNA.md attribute) (RNA.md property) RNA module rna_plot_type (C var) rotational_symmetry() (in module RNA) rotational_symmetry_db() (RNA.fold_compound method) rtype (RNA.md attribute) (RNA.md property)

S

S (RNA.fold_compound attribute) s (RNA.path property) S3 (RNA.fold_compound attribute) S5 (RNA.fold_compound attribute) S_cons (RNA.fold_compound attribute) salt (C var) (RNA.md attribute) (RNA.md property) salt_duplex_init() (in module RNA) salt_loop() (in module RNA) salt_loop_int() (in module RNA) salt_ml() (in module RNA) salt_stack() (in module RNA) saltDPXInit (C var) SaltDPXInit (RNA.exp_param attribute), [1] (RNA.exp_param property) saltDPXInit (RNA.md attribute) (RNA.md property) SaltDPXInit (RNA.param attribute), [1] (RNA.param property) saltDPXInitFact (RNA.md attribute) (RNA.md property) SaltLoop (RNA.param attribute), [1] (RNA.param property) SaltLoopDbl (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) SaltMLbase (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) SaltMLclosing (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) SaltMLintern (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) saltMLLower (RNA.md attribute) (RNA.md property) saltMLUpper (RNA.md attribute) (RNA.md property) SaltStack (RNA.param attribute), [1] (RNA.param property) sc (RNA.fold_compound attribute) sc_add_bp() (RNA.fold_compound method) sc_add_bt() (RNA.fold_compound method) sc_add_bt_pycallback() (in module RNA) sc_add_data() (RNA.fold_compound method) sc_add_exp_f() (RNA.fold_compound method) sc_add_exp_f_pycallback() (in module RNA) sc_add_f() (RNA.fold_compound method) sc_add_f_pycallback() (in module RNA) sc_add_hi_motif() (RNA.fold_compound method) sc_add_pydata() (in module RNA) sc_add_SHAPE_deigan() (RNA.fold_compound method) sc_add_SHAPE_deigan_ali() (RNA.fold_compound method) sc_add_SHAPE_eddy_2() (RNA.fold_compound method) sc_add_SHAPE_zarringhalam() (RNA.fold_compound method) sc_add_stack() (RNA.fold_compound method) sc_add_up() (RNA.fold_compound method) sc_init() (RNA.fold_compound method) sc_mod() (RNA.fold_compound method) sc_mod_7DA() (RNA.fold_compound method) sc_mod_dihydrouridine() (RNA.fold_compound method) sc_mod_inosine() (RNA.fold_compound method) sc_mod_json() (RNA.fold_compound method) sc_mod_jsonfile() (RNA.fold_compound method) sc_mod_m6A() (RNA.fold_compound method) sc_mod_param (class in RNA) sc_mod_parameters_free() (in module RNA) sc_mod_pseudouridine() (RNA.fold_compound method) sc_mod_purine() (RNA.fold_compound method) sc_mod_read_from_json() (in module RNA) sc_mod_read_from_jsonfile() (in module RNA) sc_multi_cb_add() (RNA.fold_compound method) sc_multi_cb_add_pycallback() (in module RNA) sc_probing() (RNA.fold_compound method) sc_remove() (RNA.fold_compound method) sc_set_bp() (RNA.fold_compound method) sc_set_stack() (RNA.fold_compound method) sc_set_up() (RNA.fold_compound method) scale (RNA.mx_pf property) scale_parameters (C function) scale_pf_parameters (C function) score (class in RNA) scs (RNA.fold_compound attribute) second (RNA.DoublePair property) sect (C type) seq_encode() (in module RNA) sequence (RNA.fold_compound attribute) (RNA.fold_compound property) sequence_add() (RNA.fold_compound method) sequence_encoding (RNA.fold_compound attribute) (RNA.fold_compound property) sequence_encoding2 (RNA.fold_compound attribute) (RNA.fold_compound property) sequence_prepare() (RNA.fold_compound method) sequence_remove() (RNA.fold_compound method) sequence_remove_all() (RNA.fold_compound method) sequences (RNA.fold_compound attribute) set_from_globals() (RNA.md method) set_model_details (C function) set_parameters (C function) set_pf_param (C function) settype (C function) settype() (in module RNA) sfact (RNA.md attribute) (RNA.md property) shortP_getitem() (in module RNA) shortP_setitem() (in module RNA) simple_circplot_coordinates (C function) simple_circplot_coordinates() (in module RNA) simple_xy_coordinates (C function)

simple_xy_coordinates() (in module RNA) size() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTION method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) (RNA.varArrayChar method) (RNA.varArrayFLTorDBL method) (RNA.varArrayInt method) (RNA.varArrayMove method) (RNA.varArrayShort method) (RNA.varArrayUChar method) (RNA.varArrayUInt method) snoopT (C struct) snoopT.Duplex_El (C var) snoopT.Duplex_Er (C var) snoopT.Duplex_Ol (C var) snoopT.Duplex_Or (C var) snoopT.Duplex_Ot (C var) snoopT.energy (C var) snoopT.fullStemEnergy (C var) snoopT.i (C var) snoopT.j (C var) snoopT.Loop_D (C var) snoopT.Loop_E (C var) snoopT.pscd (C var) snoopT.pscg (C var) snoopT.psct (C var) snoopT.structure (C var) snoopT.u (C var) SOLUTION (class in RNA) SOLUTIONVector (class in RNA) special_hp (RNA.md attribute) (RNA.md property) Ss (RNA.fold_compound attribute) ssv_rna_plot (C function) ssv_rna_plot() (in module RNA) st_back (C var) stack (RNA.param attribute), [1] (RNA.param property) stack_dG (RNA.sc_mod_param attribute), [1] stack_dH (RNA.sc_mod_param attribute), [1] stack_prob() (RNA.fold_compound method) stackProb (C function) start (RNA.hx property) stat_cb (RNA.fold_compound attribute) state (RNA.hc attribute), [1] STR (C macro) strand_end (RNA.fold_compound attribute) (RNA.fold_compound property) strand_number (RNA.fold_compound attribute) (RNA.fold_compound property) strand_order (RNA.fold_compound attribute) (RNA.fold_compound property) strand_order_uniq (RNA.fold_compound attribute) strand_start (RNA.fold_compound attribute) (RNA.fold_compound property) strands (RNA.fold_compound attribute) (RNA.fold_compound property) (RNA.mx_mfe property) string_edit_distance() (in module RNA) StringVector (class in RNA) strtrim() (in module RNA) STRUC (C macro) struct_en (class in RNA) structure (RNA.duplex_list_t property) (RNA.duplexT attribute) (RNA.duplexT property) (RNA.SOLUTION property) (RNA.struct_en attribute), [1] (RNA.struct_en property) (RNA.subopt_solution property) subopt (C function) subopt() (in module RNA) (RNA.fold_compound method) subopt_cb() (RNA.fold_compound method) subopt_circ (C function) subopt_par (C function) subopt_solution (class in RNA) subopt_sorted (C var) subopt_zuker() (RNA.fold_compound method) SuboptVector (class in RNA) svg_rna_plot (C function) svg_rna_plot() (in module RNA) swap() (RNA.ConstCharVector method) (RNA.CoordinateVector method) (RNA.DoubleDoubleVector method) (RNA.DoubleVector method) (RNA.DuplexVector method) (RNA.ElemProbVector method) (RNA.HeatCapacityVector method) (RNA.HelixVector method) (RNA.IntIntVector method) (RNA.IntVector method) (RNA.MoveVector method) (RNA.PathVector method) (RNA.SOLUTIONVector method) (RNA.StringVector method) (RNA.SuboptVector method) (RNA.UIntUIntVector method) (RNA.UIntVector method) SwigPyIterator (class in RNA) symbolset (C var)

T

tb (RNA.duplexT attribute) (RNA.duplexT property) te (RNA.duplexT attribute) (RNA.duplexT property) temperature (C var) (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.heat_capacity_result property) (RNA.md attribute) (RNA.md property) (RNA.param attribute), [1] (RNA.param property) terminal_dG (RNA.sc_mod_param attribute), [1] terminal_dH (RNA.sc_mod_param attribute), [1] TerminalAU (RNA.param attribute), [1] (RNA.param property) tetra_loop (C var) Tetraloop_E (RNA.param attribute), [1] (RNA.param property) Tetraloops (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) thisown (RNA.basepair property) (RNA.cmd property) (RNA.ConstCharVector property) (RNA.COORDINATE property) (RNA.CoordinateVector property) (RNA.doubleArray property) (RNA.DoubleDoubleVector property) (RNA.DoublePair property) (RNA.DoubleVector property) (RNA.duplex_list_t property) (RNA.duplexT property) (RNA.DuplexVector property) (RNA.ElemProbVector property) (RNA.ep property) (RNA.exp_param property) (RNA.floatArray property) (RNA.fold_compound property) (RNA.hc property) (RNA.heat_capacity_result property) (RNA.HeatCapacityVector property) (RNA.HelixVector property) (RNA.hx property) (RNA.intArray property) (RNA.IntIntVector property) (RNA.IntVector property) (RNA.md property) (RNA.move property) (RNA.MoveVector property) (RNA.mx_mfe property) (RNA.mx_pf property) (RNA.param property) (RNA.path property) (RNA.path_options property) (RNA.PathVector property) (RNA.pbacktrack_mem property) (RNA.plot_data property) (RNA.plot_layout property) (RNA.plot_options_puzzler property) (RNA.probing_data property) (RNA.sc_mod_param property) (RNA.score property) (RNA.SOLUTION property) (RNA.SOLUTIONVector property) (RNA.StringVector property) (RNA.struct_en property) (RNA.subopt_solution property) (RNA.SuboptVector property) (RNA.SwigPyIterator property) (RNA.UIntUIntVector property) (RNA.UIntVector property) (RNA.varArrayChar property) (RNA.varArrayFLTorDBL property) (RNA.varArrayInt property) (RNA.varArrayMove property) (RNA.varArrayShort property) (RNA.varArrayUChar property) (RNA.varArrayUInt property) threshold (C var) TN (RNA.score property) TNR (RNA.score property) TP (RNA.score property) TPR (RNA.score property) tree_edit_distance() (in module RNA) tree_string_to_db() (in module RNA) tree_string_unweight() (in module RNA) Triloop_E (RNA.param attribute), [1] (RNA.param property) Triloops (RNA.exp_param attribute), [1] (RNA.exp_param property) (RNA.param attribute), [1] (RNA.param property) TripleC (RNA.param attribute), [1] (RNA.param property) TwoDfold (C function) TwoDfold_backtrack_f5 (C function) TwoDfold_solution (C macro)

TwoDfold_vars (C struct) TwoDfold_vars.bpdist (C var) TwoDfold_vars.circ (C var) TwoDfold_vars.compatibility (C var) TwoDfold_vars.dangles (C var) TwoDfold_vars.do_backtrack (C var) TwoDfold_vars.E_C (C var) TwoDfold_vars.E_C_rem (C var) TwoDfold_vars.E_F3 (C var) TwoDfold_vars.E_F3_rem (C var) TwoDfold_vars.E_F5 (C var) TwoDfold_vars.E_F5_rem (C var) TwoDfold_vars.E_Fc (C var) TwoDfold_vars.E_Fc_rem (C var) TwoDfold_vars.E_FcH (C var) TwoDfold_vars.E_FcH_rem (C var) TwoDfold_vars.E_FcI (C var) TwoDfold_vars.E_FcI_rem (C var) TwoDfold_vars.E_FcM (C var) TwoDfold_vars.E_FcM_rem (C var) TwoDfold_vars.E_M (C var) TwoDfold_vars.E_M1 (C var) TwoDfold_vars.E_M1_rem (C var) TwoDfold_vars.E_M2 (C var) TwoDfold_vars.E_M2_rem (C var) TwoDfold_vars.E_M_rem (C var) TwoDfold_vars.k_max_values (C var) TwoDfold_vars.k_max_values_f (C var) TwoDfold_vars.k_max_values_f3 (C var) TwoDfold_vars.k_max_values_fc (C var) TwoDfold_vars.k_max_values_fcH (C var) TwoDfold_vars.k_max_values_fcI (C var) TwoDfold_vars.k_max_values_fcM (C var) TwoDfold_vars.k_max_values_m (C var) TwoDfold_vars.k_max_values_m1 (C var) TwoDfold_vars.k_max_values_m2 (C var) TwoDfold_vars.k_min_values (C var) TwoDfold_vars.k_min_values_f (C var) TwoDfold_vars.k_min_values_f3 (C var) TwoDfold_vars.k_min_values_fc (C var) TwoDfold_vars.k_min_values_fcH (C var) TwoDfold_vars.k_min_values_fcI (C var) TwoDfold_vars.k_min_values_fcM (C var) TwoDfold_vars.k_min_values_m (C var) TwoDfold_vars.k_min_values_m1 (C var) TwoDfold_vars.k_min_values_m2 (C var) TwoDfold_vars.l_max_values (C var) TwoDfold_vars.l_max_values_f (C var) TwoDfold_vars.l_max_values_f3 (C var) TwoDfold_vars.l_max_values_fc (C var) TwoDfold_vars.l_max_values_fcH (C var) TwoDfold_vars.l_max_values_fcI (C var) TwoDfold_vars.l_max_values_fcM (C var) TwoDfold_vars.l_max_values_m (C var) TwoDfold_vars.l_max_values_m1 (C var) TwoDfold_vars.l_max_values_m2 (C var) TwoDfold_vars.l_min_values (C var) TwoDfold_vars.l_min_values_f (C var) TwoDfold_vars.l_min_values_f3 (C var) TwoDfold_vars.l_min_values_fc (C var) TwoDfold_vars.l_min_values_fcH (C var) TwoDfold_vars.l_min_values_fcI (C var) TwoDfold_vars.l_min_values_fcM (C var) TwoDfold_vars.l_min_values_m (C var) TwoDfold_vars.l_min_values_m1 (C var) TwoDfold_vars.l_min_values_m2 (C var) TwoDfold_vars.maxD1 (C var) TwoDfold_vars.maxD2 (C var) TwoDfold_vars.mm1 (C var) TwoDfold_vars.mm2 (C var) TwoDfold_vars.my_iindx (C var) TwoDfold_vars.P (C var) TwoDfold_vars.ptype (C var) TwoDfold_vars.reference_pt1 (C var) TwoDfold_vars.reference_pt2 (C var) TwoDfold_vars.referenceBPs1 (C var) TwoDfold_vars.referenceBPs2 (C var) TwoDfold_vars.S (C var) TwoDfold_vars.S1 (C var) TwoDfold_vars.seq_length (C var) TwoDfold_vars.sequence (C var) TwoDfold_vars.temperature (C var) TwoDfoldList (C function) type (RNA.ep attribute), [1] (RNA.ep property) (RNA.fold_compound attribute) (RNA.fold_compound property) (RNA.hc attribute), [1] (RNA.hc property) (RNA.mx_mfe property) (RNA.mx_pf property) (RNA.path property) type() (RNA.varArrayChar method) (RNA.varArrayFLTorDBL method) (RNA.varArrayInt method) (RNA.varArrayMove method) (RNA.varArrayShort method) (RNA.varArrayUChar method) (RNA.varArrayUInt method)

U

ubf_eval_ext_int_loop (C function) ubf_eval_ext_int_loop() (in module RNA) ubf_eval_int_loop (C function) ubf_eval_int_loop() (in module RNA) ubf_eval_int_loop2 (C function) ubf_eval_int_loop2() (in module RNA) ud_add_motif() (RNA.fold_compound method) ud_remove() (RNA.fold_compound method) ud_set_data() (RNA.fold_compound method) ud_set_exp_prod_cb() (in module RNA) ud_set_exp_prod_rule_cb() (RNA.fold_compound method) ud_set_prob_cb() (in module RNA) (RNA.fold_compound method) ud_set_prod_cb() (in module RNA) ud_set_prod_rule_cb() (RNA.fold_compound method) ud_set_pydata() (in module RNA) UIntUIntVector (class in RNA) UIntVector (class in RNA) unexpand_aligned_F (C function) unexpand_aligned_F() (in module RNA) unexpand_Full (C function) unexpand_Full() (in module RNA) uniq_ML (C var) (RNA.md attribute) (RNA.md property) unmodified (RNA.sc_mod_param attribute), [1] unmodified_encoding (RNA.sc_mod_param attribute), [1] unpack_structure (C function) unpack_structure() (in module RNA) unpaired (C var) (RNA.plot_options_puzzler attribute), [1]

unweight (C function) unweight() (in module RNA) up3 (RNA.hx property) up5 (RNA.hx property) up_ext (RNA.hc attribute), [1] (RNA.hc property) up_hp (RNA.hc attribute), [1] (RNA.hc property) up_int (RNA.hc attribute), [1] (RNA.hc property) up_ml (RNA.hc attribute), [1] (RNA.hc property) Up_plot (C function) update_co_pf_params (C function) update_co_pf_params() (in module RNA) update_co_pf_params_par (C function) update_cofold_params (C function) update_cofold_params() (in module RNA) update_cofold_params_par (C function) update_fold_params (C function) update_fold_params() (in module RNA) update_fold_params_par (C function) update_pf_params (C function) update_pf_params() (in module RNA) update_pf_params_par (C function) update_pf_paramsLP (C function) update_pf_paramsLP_par (C function) urn() (in module RNA) ushortP_getitem() (in module RNA) ushortP_setitem() (in module RNA)

V

value() (RNA.SwigPyIterator method) var_array_Iterator (class in RNA) varArrayChar (class in RNA) varArrayFLTorDBL (class in RNA) varArrayInt (class in RNA) varArrayMove (class in RNA) varArrayShort (class in RNA) varArrayUChar (class in RNA) varArrayUInt (class in RNA) vrna__array_set_capacity (C function) vrna_abstract_shapes (C function) vrna_abstract_shapes_pt (C function) vrna_alifold (C function) vrna_alignment_s (C struct) vrna_alignment_s.a2s (C var) vrna_alignment_s.gapfree_seq (C var) vrna_alignment_s.gapfree_size (C var) vrna_alignment_s.genome_size (C var) vrna_alignment_s.n_seq (C var) vrna_alignment_s.orientation (C var) vrna_alignment_s.sequences (C var) vrna_alignment_s.start (C var) vrna_aliLfold (C function) vrna_aliLfold_cb (C function) vrna_alloc (C function) vrna_aln_consensus_mis (C function) vrna_aln_consensus_sequence (C function) vrna_aln_conservation_col (C function) vrna_aln_conservation_struct (C function) vrna_aln_copy (C function) VRNA_ALN_DEFAULT (C macro) VRNA_ALN_DNA (C macro) vrna_aln_encode (C function) vrna_aln_free (C function) VRNA_ALN_LOWERCASE (C macro) vrna_aln_mpi (C function) vrna_aln_opt_t (C struct) vrna_aln_opt_t.color_min_sat (C var) vrna_aln_opt_t.color_threshold (C var) vrna_aln_opt_t.columns (C var) vrna_aln_opt_t.end (C var) vrna_aln_opt_t.offset (C var) vrna_aln_opt_t.start (C var) vrna_aln_pinfo (C function) vrna_aln_pscore (C function) VRNA_ALN_RNA (C macro) vrna_aln_slice (C function) vrna_aln_toRNA (C function) vrna_aln_uppercase (C function) VRNA_ALN_UPPERCASE (C macro) vrna_annotate_covar_db (C function) vrna_annotate_covar_db_extended (C function) vrna_annotate_covar_pairs (C function) vrna_annotate_covar_pt (C function) VRNA_ANY_LOOP (C macro) vrna_array (C macro) vrna_array_append (C macro) vrna_array_capacity (C macro) vrna_array_free (C macro) vrna_array_grow (C macro) VRNA_ARRAY_GROW_FORMULA (C macro) VRNA_ARRAY_HEADER (C macro) vrna_array_header_s (C struct) vrna_array_header_s.num (C var) vrna_array_header_s.size (C var) vrna_array_header_t (C type) vrna_array_init (C macro) vrna_array_init_size (C macro) vrna_array_make (C macro) vrna_array_set_capacity (C macro) vrna_array_size (C macro) vrna_auxdata_free_f (C type) vrna_auxdata_prepare_f (C type) vrna_backtrack5 (C function) vrna_backtrack5_TwoD (C function) vrna_backtrack_from_intervals (C function) vrna_backtrack_window (C function) vrna_basename (C function) vrna_basepair_s (C struct) vrna_basepair_s.i (C var) vrna_basepair_s.j (C var) vrna_basepair_s.L (C var) vrna_basepair_s.l (C var) vrna_basepair_t (C struct) vrna_basepair_t.i (C var) vrna_basepair_t.j (C var) vrna_boustrophedon (C function) vrna_boustrophedon_pos (C function) vrna_bp_distance (C function) vrna_bp_distance_pt (C function) vrna_bp_stack_t (C struct) vrna_bp_stack_t.i (C var) vrna_bp_stack_t.j (C var) vrna_bp_t (C type) vrna_bpp_symbol (C function) vrna_bps_at (C function) vrna_bps_free (C function) vrna_bps_init (C function) vrna_bps_pop (C function) vrna_bps_push (C function) vrna_bps_size (C function) vrna_bps_t (C type) vrna_bps_top (C function) VRNA_BRACKETS_ALPHA (C macro) VRNA_BRACKETS_ANG (C macro) VRNA_BRACKETS_ANY (C macro) VRNA_BRACKETS_CLY (C macro) VRNA_BRACKETS_DEFAULT (C macro) VRNA_BRACKETS_RND (C macro) VRNA_BRACKETS_SQR (C macro) vrna_bs_result_f (C type) vrna_bt_exterior_f3 (C function) vrna_bt_exterior_f3_pp (C function) vrna_bt_exterior_f5 (C function) vrna_bt_f (C function) vrna_bt_gquad (C function) vrna_BT_gquad_int (C function) vrna_bt_gquad_internal (C function) vrna_BT_gquad_mfe (C function) vrna_bt_gquad_mfe (C function) vrna_bt_hairpin (C function) vrna_bt_internal_loop (C function) vrna_bt_m (C function) vrna_bt_multibranch_loop (C function) vrna_bt_multibranch_split (C function) vrna_bt_stacked_pairs (C function) vrna_bts_free (C function) vrna_bts_init (C function) vrna_bts_pop (C function) vrna_bts_push (C function) vrna_bts_size (C function) vrna_bts_t (C type) vrna_bts_top (C function) vrna_centroid (C function) vrna_centroid_from_plist (C function) vrna_centroid_from_probs (C function) vrna_circalifold (C function) vrna_circfold (C function) VRNA_CMD_PARSE_DEFAULTS (C macro) VRNA_CMD_PARSE_HC (C macro) VRNA_CMD_PARSE_SC (C macro) VRNA_CMD_PARSE_SD (C macro) VRNA_CMD_PARSE_SILENT (C macro) VRNA_CMD_PARSE_UD (C macro) vrna_cmd_t (C type) vrna_cofold (C function) vrna_color_t (C type) vrna_commands_apply (C function) vrna_commands_free (C function) vrna_compare_structure (C function) vrna_compare_structure_pt (C function) VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS (C macro) VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (C macro) VRNA_CONSTRAINT_CONTEXT_HP_LOOP (C macro) VRNA_CONSTRAINT_CONTEXT_INT_LOOP (C macro) VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (C macro) VRNA_CONSTRAINT_CONTEXT_MB_LOOP (C macro) VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (C macro) VRNA_CONSTRAINT_DB (C macro) VRNA_CONSTRAINT_DB_DEFAULT (C macro) VRNA_CONSTRAINT_DB_DOT (C macro) VRNA_CONSTRAINT_DB_ENFORCE_BP (C macro) VRNA_CONSTRAINT_DB_GQUAD (C macro) VRNA_CONSTRAINT_DB_INTERMOL (C macro) VRNA_CONSTRAINT_DB_INTRAMOL (C macro) VRNA_CONSTRAINT_DB_PIPE (C macro) VRNA_CONSTRAINT_DB_RND_BRACK (C macro) VRNA_CONSTRAINT_DB_WUSS (C macro) VRNA_CONSTRAINT_DB_X (C macro) VRNA_CONSTRAINT_FILE (C macro) VRNA_CONSTRAINT_MULTILINE (C macro) VRNA_CONSTRAINT_SOFT_MFE (C macro) VRNA_CONSTRAINT_SOFT_PF (C macro) vrna_constraints_add (C function) vrna_constraints_add_SHAPE (C function) vrna_constraints_add_SHAPE_ali (C function) vrna_convert_dcal_to_kcal (C function) vrna_convert_energy (C function) vrna_convert_kcal_to_dcal (C function) VRNA_CONVERT_OUTPUT_ALL (C macro) VRNA_CONVERT_OUTPUT_BULGE (C macro) VRNA_CONVERT_OUTPUT_DANGLE3 (C macro) VRNA_CONVERT_OUTPUT_DANGLE5 (C macro) VRNA_CONVERT_OUTPUT_DUMP (C macro) VRNA_CONVERT_OUTPUT_HP (C macro) VRNA_CONVERT_OUTPUT_INT (C macro) VRNA_CONVERT_OUTPUT_INT_11 (C macro) VRNA_CONVERT_OUTPUT_INT_21 (C macro) VRNA_CONVERT_OUTPUT_INT_22 (C macro) VRNA_CONVERT_OUTPUT_MISC (C macro) VRNA_CONVERT_OUTPUT_ML (C macro) VRNA_CONVERT_OUTPUT_MM_EXT (C macro) VRNA_CONVERT_OUTPUT_MM_HP (C macro) VRNA_CONVERT_OUTPUT_MM_INT (C macro) VRNA_CONVERT_OUTPUT_MM_INT_1N (C macro) VRNA_CONVERT_OUTPUT_MM_INT_23 (C macro) VRNA_CONVERT_OUTPUT_MM_MULTI (C macro) VRNA_CONVERT_OUTPUT_NINIO (C macro) VRNA_CONVERT_OUTPUT_SPECIAL_HP (C macro) VRNA_CONVERT_OUTPUT_STACK (C macro) VRNA_CONVERT_OUTPUT_VANILLA (C macro) vrna_convert_temperature (C function) vrna_cpair_t (C type) vrna_cstr (C function) vrna_cstr_close (C function) vrna_cstr_discard (C function) vrna_cstr_fflush (C function) vrna_cstr_free (C function) vrna_cstr_message_info (C function) vrna_cstr_message_vinfo (C function) vrna_cstr_message_vwarning (C function) vrna_cstr_message_warning (C function) vrna_cstr_print_eval_ext_loop (C function) vrna_cstr_print_eval_ext_loop_revert (C function) vrna_cstr_print_eval_gquad (C function) vrna_cstr_print_eval_hp_loop (C function) vrna_cstr_print_eval_hp_loop_revert (C function) vrna_cstr_print_eval_int_loop (C function) vrna_cstr_print_eval_int_loop_revert (C function) vrna_cstr_print_eval_mb_loop (C function) vrna_cstr_print_eval_mb_loop_revert (C function) vrna_cstr_print_eval_sd_corr (C function) vrna_cstr_print_fasta_header (C function) vrna_cstr_printf (C function) vrna_cstr_printf_comment (C function) vrna_cstr_printf_structure (C function) vrna_cstr_printf_tbody (C function) vrna_cstr_printf_thead (C function) vrna_cstr_string (C function) vrna_cstr_t (C type) vrna_cstr_vprintf (C function) vrna_cstr_vprintf_comment (C function) vrna_cstr_vprintf_structure (C function) vrna_cstr_vprintf_tbody (C function) vrna_cstr_vprintf_thead (C function) vrna_cut_point_insert (C function) vrna_cut_point_remove (C function) vrna_data_lin_t (C type) vrna_db_flatten (C function) vrna_db_flatten_to (C function) vrna_db_from_bp_stack (C function) vrna_db_from_bps (C function) vrna_db_from_plist (C function) vrna_db_from_probs (C function) vrna_db_from_ptable (C function) vrna_db_from_WUSS (C function) vrna_db_insert_gq (C function) vrna_db_pack (C function) vrna_db_pk_remove (C function) vrna_db_to_element_string (C function) vrna_db_to_tree_string (C function) vrna_db_unpack (C function) VRNA_DECOMP_EXT_EXT (C macro) VRNA_DECOMP_EXT_EXT_EXT (C macro) VRNA_DECOMP_EXT_EXT_STEM (C macro) VRNA_DECOMP_EXT_EXT_STEM1 (C macro) VRNA_DECOMP_EXT_STEM (C macro) VRNA_DECOMP_EXT_STEM_EXT (C macro) VRNA_DECOMP_EXT_STEM_OUTSIDE (C macro) VRNA_DECOMP_EXT_UP (C macro) VRNA_DECOMP_ML_COAXIAL (C macro) VRNA_DECOMP_ML_COAXIAL_ENC (C macro) VRNA_DECOMP_ML_ML (C macro) VRNA_DECOMP_ML_ML_ML (C macro) VRNA_DECOMP_ML_ML_STEM (C macro) VRNA_DECOMP_ML_STEM (C macro) VRNA_DECOMP_ML_UP (C macro) VRNA_DECOMP_PAIR_HP (C macro) VRNA_DECOMP_PAIR_IL (C macro) VRNA_DECOMP_PAIR_ML (C macro) vrna_dimer_conc_t (C type) vrna_dimer_pf_s (C struct) vrna_dimer_pf_s.F0AB (C var) vrna_dimer_pf_s.FA (C var) vrna_dimer_pf_s.FAB (C var) vrna_dimer_pf_s.FB (C var) vrna_dimer_pf_s.FcAB (C var) vrna_dimer_pf_t (C type) vrna_dirname (C function) vrna_dist_mountain (C function) vrna_DNA_complement (C function) vrna_dotplot_auxdata_t (C struct) vrna_dotplot_auxdata_t.bottom (C var) vrna_dotplot_auxdata_t.bottom_title (C var) vrna_dotplot_auxdata_t.comment (C var) vrna_dotplot_auxdata_t.left (C var) vrna_dotplot_auxdata_t.left_title (C var) vrna_dotplot_auxdata_t.right (C var) vrna_dotplot_auxdata_t.right_title (C var) vrna_dotplot_auxdata_t.title (C var) vrna_dotplot_auxdata_t.top (C var) vrna_dotplot_auxdata_t.top_title (C var) vrna_E_consensus_gquad (C function) vrna_E_ext_hp_loop (C function) vrna_E_ext_int_loop (C function) vrna_E_ext_loop_3 (C function) vrna_E_ext_loop_5 (C function) vrna_E_ext_stem (C function) vrna_E_exterior_loop (C function) vrna_E_exterior_stem (C function) vrna_E_gquad (C function) vrna_E_hairpin (C function) vrna_E_hp_loop (C function) vrna_E_int_loop (C function) vrna_E_internal (C function) vrna_E_multibranch_stem (C function) vrna_E_stack (C function) vrna_elem_prob_s (C struct) vrna_elem_prob_s.i (C var) vrna_elem_prob_s.j (C var) vrna_elem_prob_s.p (C var) vrna_elem_prob_s.type (C var) vrna_ensemble_defect (C function) vrna_ensemble_defect_pt (C function) vrna_enumerate_necklaces (C function) vrna_ep_t (C type) vrna_equilibrium_constants (C function) vrna_eval_circ_consensus_structure (C function) vrna_eval_circ_consensus_structure_v (C function) vrna_eval_circ_gquad_consensus_structure (C function) vrna_eval_circ_gquad_consensus_structure_v (C function) vrna_eval_circ_gquad_structure (C function) vrna_eval_circ_gquad_structure_v (C function) vrna_eval_circ_structure (C function) vrna_eval_circ_structure_v (C function) vrna_eval_consensus_structure_pt_simple (C function) vrna_eval_consensus_structure_pt_simple_v (C function) vrna_eval_consensus_structure_pt_simple_verbose (C function) vrna_eval_consensus_structure_simple (C function) vrna_eval_consensus_structure_simple_v (C function) vrna_eval_consensus_structure_simple_verbose (C function) vrna_eval_covar_structure (C function) vrna_eval_ext_hp_loop (C function) vrna_eval_ext_stem (C function) vrna_eval_exterior_stem (C function) vrna_eval_gquad_consensus_structure (C function) vrna_eval_gquad_consensus_structure_v (C function) vrna_eval_gquad_structure (C function) vrna_eval_gquad_structure_v (C function) vrna_eval_hairpin (C function) vrna_eval_hp_loop (C function) vrna_eval_int_loop (C function) vrna_eval_internal (C function) VRNA_EVAL_LOOP_DEFAULT (C macro) VRNA_EVAL_LOOP_NO_CONSTRAINTS (C macro) VRNA_EVAL_LOOP_NO_HC (C macro) VRNA_EVAL_LOOP_NO_SC (C macro) vrna_eval_loop_pt (C function) vrna_eval_loop_pt_v (C function) vrna_eval_move (C function) vrna_eval_move_pt (C function) vrna_eval_move_pt_simple (C function) vrna_eval_move_shift_pt (C function) vrna_eval_stack (C function) vrna_eval_structure (C function) vrna_eval_structure_cstr (C function) vrna_eval_structure_pt (C function) vrna_eval_structure_pt_simple (C function) vrna_eval_structure_pt_simple_v (C function) vrna_eval_structure_pt_simple_verbose (C function) vrna_eval_structure_pt_v (C function) vrna_eval_structure_pt_verbose (C function) vrna_eval_structure_simple (C function) vrna_eval_structure_simple_v (C function) vrna_eval_structure_simple_verbose (C function) vrna_eval_structure_v (C function) vrna_eval_structure_verbose (C function) vrna_exp_E_consensus_gquad (C function) vrna_exp_E_ext_fast (C function) vrna_exp_E_ext_fast_free (C function) vrna_exp_E_ext_fast_init (C function) vrna_exp_E_ext_fast_rotate (C function) vrna_exp_E_ext_fast_update (C function) vrna_exp_E_ext_stem (C function) vrna_exp_E_exterior_loop (C function) vrna_exp_E_exterior_stem (C function) vrna_exp_E_gquad (C function) vrna_exp_E_hairpin (C function) vrna_exp_E_hp_loop (C function) vrna_exp_E_int_loop (C function) vrna_exp_E_interior_loop (C function) vrna_exp_E_internal (C function) vrna_exp_E_m2_fast (C function) vrna_exp_E_mb_loop_fast (C function) vrna_exp_E_ml_fast (C function) vrna_exp_E_ml_fast_free (C function) vrna_exp_E_ml_fast_init (C function) vrna_exp_E_ml_fast_qqm (C function) vrna_exp_E_ml_fast_qqm1 (C function) vrna_exp_E_ml_fast_rotate (C function) vrna_exp_E_multibranch_stem (C function) vrna_exp_eval_hairpin (C function) vrna_exp_eval_internal (C function) vrna_exp_param_s (C struct) vrna_exp_param_s.alpha (C var) vrna_exp_param_s.expbulge (C var) vrna_exp_param_s.expdangle3 (C var) vrna_exp_param_s.expdangle5 (C var) vrna_exp_param_s.expDuplexInit (C var) vrna_exp_param_s.expgquad (C var) vrna_exp_param_s.expgquadLayerMismatch (C var) vrna_exp_param_s.exphairpin (C var) vrna_exp_param_s.exphex (C var) vrna_exp_param_s.expint11 (C var) vrna_exp_param_s.expint21 (C var) vrna_exp_param_s.expint22 (C var) vrna_exp_param_s.expinternal (C var) vrna_exp_param_s.expmismatch1nI (C var) vrna_exp_param_s.expmismatch23I (C var) vrna_exp_param_s.expmismatchExt (C var) vrna_exp_param_s.expmismatchH (C var) vrna_exp_param_s.expmismatchI (C var) vrna_exp_param_s.expmismatchM (C var) vrna_exp_param_s.expMLbase (C var) vrna_exp_param_s.expMLclosing (C var) vrna_exp_param_s.expMLintern (C var) vrna_exp_param_s.expMultipleCA (C var) vrna_exp_param_s.expMultipleCB (C var) vrna_exp_param_s.expninio (C var) vrna_exp_param_s.expSaltLoop (C var) vrna_exp_param_s.expSaltStack (C var) vrna_exp_param_s.expstack (C var) vrna_exp_param_s.expTermAU (C var) vrna_exp_param_s.exptetra (C var) vrna_exp_param_s.exptri (C var) vrna_exp_param_s.expTriloop (C var) vrna_exp_param_s.expTripleC (C var) vrna_exp_param_s.gquadLayerMismatchMax (C var) vrna_exp_param_s.Hexaloops (C var) vrna_exp_param_s.id (C var) vrna_exp_param_s.kT (C var) vrna_exp_param_s.lxc (C var) vrna_exp_param_s.model_details (C var) vrna_exp_param_s.param_file (C var) vrna_exp_param_s.pf_scale (C var) vrna_exp_param_s.SaltDPXInit (C var) vrna_exp_param_s.SaltLoopDbl (C var) vrna_exp_param_s.SaltMLbase (C var) vrna_exp_param_s.SaltMLclosing (C var) vrna_exp_param_s.SaltMLintern (C var) vrna_exp_param_s.temperature (C var) vrna_exp_param_s.Tetraloops (C var) vrna_exp_param_s.Triloops (C var) vrna_exp_param_t (C type) vrna_exp_params (C function) vrna_exp_params_comparative (C function) vrna_exp_params_copy (C function) vrna_exp_params_rescale (C function) vrna_exp_params_reset (C function) vrna_exp_params_subst (C function) VRNA_EXT_LOOP (C macro) vrna_extract_record_rest_constraint (C function) vrna_extract_record_rest_structure (C function) vrna_fc_s (C struct) vrna_fc_s.[anonymous] (C var) vrna_fc_s.a2s (C var) vrna_fc_s.alignment (C var) vrna_fc_s.aux_grammar (C var) vrna_fc_s.auxdata (C var) vrna_fc_s.bpdist (C var) vrna_fc_s.cons_seq (C var) vrna_fc_s.cutpoint (C var) vrna_fc_s.domains_struc (C var) vrna_fc_s.domains_up (C var) vrna_fc_s.encoding3 (C var) vrna_fc_s.encoding5 (C var) vrna_fc_s.exp_matrices (C var) vrna_fc_s.exp_params (C var) vrna_fc_s.free_auxdata (C var) vrna_fc_s.hc (C var) vrna_fc_s.iindx (C var) vrna_fc_s.jindx (C var) vrna_fc_s.length (C var) vrna_fc_s.matrices (C var) vrna_fc_s.maxD1 (C var) vrna_fc_s.maxD2 (C var) vrna_fc_s.mm1 (C var) vrna_fc_s.mm2 (C var) vrna_fc_s.n_seq (C var) vrna_fc_s.nucleotides (C var) vrna_fc_s.oldAliEn (C var) vrna_fc_s.params (C var) vrna_fc_s.pscore (C var) vrna_fc_s.pscore_local (C var) vrna_fc_s.pscore_pf_compat (C var) vrna_fc_s.ptype (C var) vrna_fc_s.ptype_local (C var) vrna_fc_s.ptype_pf_compat (C var) vrna_fc_s.reference_pt1 (C var) vrna_fc_s.reference_pt2 (C var) vrna_fc_s.referenceBPs1 (C var) vrna_fc_s.referenceBPs2 (C var) vrna_fc_s.S (C var) vrna_fc_s.S3 (C var) vrna_fc_s.S5 (C var) vrna_fc_s.S_cons (C var) vrna_fc_s.sc (C var) vrna_fc_s.scs (C var) vrna_fc_s.sequence (C var) vrna_fc_s.sequence_encoding (C var) vrna_fc_s.sequence_encoding2 (C var) vrna_fc_s.sequences (C var) vrna_fc_s.Ss (C var) vrna_fc_s.stat_cb (C var) vrna_fc_s.strand_end (C var) vrna_fc_s.strand_number (C var) vrna_fc_s.strand_order (C var) vrna_fc_s.strand_order_uniq (C var) vrna_fc_s.strand_start (C var) vrna_fc_s.strands (C var) vrna_fc_s.type (C var) vrna_fc_s.window_size (C var) vrna_fc_s.zscore_data (C var) vrna_fc_type_e (C enum) vrna_fc_type_e.VRNA_FC_TYPE_COMPARATIVE (C enumerator) vrna_fc_type_e.VRNA_FC_TYPE_SINGLE (C enumerator) vrna_file_bpseq (C function) vrna_file_commands_apply (C function) vrna_file_commands_read (C function) vrna_file_connect (C function) vrna_file_connect_read_record (C function) vrna_file_copy (C function) vrna_file_exists (C function) vrna_file_fasta_read_record (C function) VRNA_FILE_FORMAT_EPS (C macro) VRNA_FILE_FORMAT_GML (C macro) VRNA_FILE_FORMAT_MSA_APPEND (C macro) VRNA_FILE_FORMAT_MSA_CLUSTAL (C macro) VRNA_FILE_FORMAT_MSA_DEFAULT (C macro) VRNA_FILE_FORMAT_MSA_FASTA (C macro) VRNA_FILE_FORMAT_MSA_MAF (C macro) VRNA_FILE_FORMAT_MSA_MIS (C macro) VRNA_FILE_FORMAT_MSA_NOCHECK (C macro) VRNA_FILE_FORMAT_MSA_QUIET (C macro) VRNA_FILE_FORMAT_MSA_SILENT (C macro) VRNA_FILE_FORMAT_MSA_STOCKHOLM (C macro) VRNA_FILE_FORMAT_MSA_UNKNOWN (C macro) VRNA_FILE_FORMAT_PLOT_DEFAULT (C macro) VRNA_FILE_FORMAT_SSV (C macro) VRNA_FILE_FORMAT_SVG (C macro) VRNA_FILE_FORMAT_XRNA (C macro) vrna_file_helixlist (C function) vrna_file_json (C function) vrna_file_msa_detect_format (C function) vrna_file_msa_read (C function) vrna_file_msa_read_record (C function) vrna_file_msa_write (C function) vrna_file_PS_aln (C function) vrna_file_PS_aln_opt (C function) vrna_file_PS_aln_slice (C function) vrna_file_PS_rnaplot (C function) vrna_file_PS_rnaplot_a (C function) vrna_file_PS_rnaplot_layout (C function) vrna_file_RNAstrand_db_read_record (C function) vrna_file_SHAPE_read (C function) vrna_filename_sanitize (C function) vrna_fold (C function) vrna_fold_compound (C function) vrna_fold_compound_add_auxdata (C function) vrna_fold_compound_add_callback (C function) vrna_fold_compound_comparative (C function) vrna_fold_compound_comparative2 (C function) vrna_fold_compound_free (C function) vrna_fold_compound_prepare (C function) vrna_fold_compound_t (C type) vrna_fold_compound_TwoD (C function) vrna_get_gquad_pattern_pf (C function) vrna_get_ptype (C function) vrna_get_ptype_md (C function) vrna_get_ptype_window (C function) vrna_gq_int_loop_pf (C function) vrna_gq_parse (C function) vrna_gq_pos_pf (C function) VRNA_GQUAD_DB_SYMBOL (C macro) VRNA_GQUAD_DB_SYMBOL_END (C macro) VRNA_GQUAD_MAX_BOX_SIZE (C macro) VRNA_GQUAD_MAX_LINKER_LENGTH (C macro) VRNA_GQUAD_MAX_STACK_SIZE (C macro) VRNA_GQUAD_MIN_BOX_SIZE (C macro) VRNA_GQUAD_MIN_LINKER_LENGTH (C macro) VRNA_GQUAD_MIN_STACK_SIZE (C macro) vrna_gr_add_aux (C function) vrna_gr_add_aux_c (C function) vrna_gr_add_aux_exp (C function) vrna_gr_add_aux_exp_c (C function) vrna_gr_add_aux_exp_f (C function) vrna_gr_add_aux_exp_m (C function) vrna_gr_add_aux_exp_m1 (C function) vrna_gr_add_aux_exp_m2 (C function) vrna_gr_add_aux_f (C function) vrna_gr_add_aux_m (C function) vrna_gr_add_aux_m1 (C function) vrna_gr_add_aux_m2 (C function) vrna_gr_add_status (C function) vrna_gr_aux_t (C type) vrna_gr_inside_exp_f (C type) vrna_gr_inside_f (C type) vrna_gr_outside_exp_f (C type) vrna_gr_outside_f (C type) vrna_gr_prepare (C function) vrna_gr_reset (C function) vrna_gr_serialize_bp_f (C type) vrna_gr_set_serialize_bp (C function) vrna_hamming_distance (C function) vrna_hamming_distance_bound (C function) vrna_hash_table_t (C type) vrna_hc_add_bp (C function) vrna_hc_add_bp_nonspecific (C function) vrna_hc_add_bp_strand (C function) vrna_hc_add_from_db (C function) vrna_hc_add_up (C function) vrna_hc_add_up_batch (C function) vrna_hc_add_up_strand (C function) vrna_hc_eval_f (C type) vrna_hc_free (C function) vrna_hc_init (C function) vrna_hc_s (C struct) vrna_hc_s.data (C var) vrna_hc_s.depot (C var) vrna_hc_s.f (C var) vrna_hc_s.free_data (C var) vrna_hc_s.matrix_local (C var) vrna_hc_s.mx (C var) vrna_hc_s.n (C var) vrna_hc_s.state (C var) vrna_hc_s.type (C var) vrna_hc_s.up_ext (C var) vrna_hc_s.up_hp (C var) vrna_hc_s.up_int (C var) vrna_hc_s.up_ml (C var) vrna_hc_t (C type) vrna_hc_up_s (C struct) vrna_hc_up_s.options (C var) vrna_hc_up_s.position (C var) vrna_hc_up_s.strand (C var) vrna_hc_up_t (C type) vrna_heap_cmp_f (C type) vrna_heap_free (C function) vrna_heap_get_pos_f (C type) vrna_heap_init (C function) vrna_heap_insert (C function) vrna_heap_pop (C function) vrna_heap_remove (C function) vrna_heap_set_pos_f (C type) vrna_heap_size (C function) vrna_heap_t (C type) vrna_heap_top (C function) vrna_heap_update (C function) vrna_heat_capacity (C function) vrna_heat_capacity_cb (C function) vrna_heat_capacity_f (C type) vrna_heat_capacity_s (C struct) vrna_heat_capacity_s.heat_capacity (C var) vrna_heat_capacity_s.temperature (C var) vrna_heat_capacity_simple (C function) vrna_heat_capacity_t (C type) VRNA_HP_LOOP (C macro) vrna_ht_clear (C function) vrna_ht_cmp_f (C type) vrna_ht_collisions (C function) vrna_ht_db_comp (C function) vrna_ht_db_free_entry (C function) vrna_ht_db_hash_func (C function) vrna_ht_entry_db_t (C struct) vrna_ht_entry_db_t.energy (C var) vrna_ht_entry_db_t.structure (C var) vrna_ht_free (C function) vrna_ht_free_f (C type) vrna_ht_get (C function) vrna_ht_hashfunc_f (C type) vrna_ht_init (C function) vrna_ht_insert (C function) vrna_ht_remove (C function) vrna_ht_size (C function) vrna_hx_from_ptable (C function) vrna_hx_merge (C function) vrna_hx_s (C struct) vrna_hx_s.end (C var) vrna_hx_s.length (C var) vrna_hx_s.start (C var) vrna_hx_s.up3 (C var) vrna_hx_s.up5 (C var) vrna_hx_t (C type) vrna_idx_col_wise (C function) vrna_idx_row_wise (C function) vrna_init_rand (C function) vrna_init_rand_seed (C function) VRNA_INPUT_BLANK_LINE (C macro) VRNA_INPUT_COMMENT (C macro) VRNA_INPUT_CONSTRAINT (C macro) VRNA_INPUT_ERROR (C macro) VRNA_INPUT_FASTA_HEADER (C macro) VRNA_INPUT_MISC (C macro) VRNA_INPUT_NO_REST (C macro) VRNA_INPUT_NO_SPAN (C macro) VRNA_INPUT_NO_TRUNCATION (C macro) VRNA_INPUT_NOSKIP_BLANK_LINES (C macro) VRNA_INPUT_NOSKIP_COMMENTS (C macro) VRNA_INPUT_QUIT (C macro) VRNA_INPUT_SEQUENCE (C macro) VRNA_INPUT_VERBOSE (C macro) VRNA_INT_LOOP (C macro) vrna_int_urn (C function) vrna_letter_structure (C function) vrna_Lfold (C function) vrna_Lfold_cb (C function) vrna_Lfoldz (C function) vrna_Lfoldz_cb (C function) vrna_log (C function) vrna_log_cb_add (C function) vrna_log_cb_f (C type) vrna_log_cb_num (C function) vrna_log_cb_remove (C function) vrna_log_critical (C macro) vrna_log_debug (C macro) vrna_log_error (C macro) vrna_log_event_s (C struct) vrna_log_event_s.file_name (C var) vrna_log_event_s.format_string (C var) vrna_log_event_s.level (C var) vrna_log_event_s.line_number (C var) vrna_log_event_s.params (C var) vrna_log_event_t (C type) vrna_log_fp (C function) vrna_log_fp_set (C function) vrna_log_info (C macro) vrna_log_level (C function) VRNA_LOG_LEVEL_DEFAULT (C macro) vrna_log_level_set (C function) vrna_log_levels_e (C enum) vrna_log_levels_e.VRNA_LOG_LEVEL_CRITICAL (C enumerator) vrna_log_levels_e.VRNA_LOG_LEVEL_DEBUG (C enumerator) vrna_log_levels_e.VRNA_LOG_LEVEL_ERROR (C enumerator) vrna_log_levels_e.VRNA_LOG_LEVEL_INFO (C enumerator) vrna_log_levels_e.VRNA_LOG_LEVEL_SILENT (C enumerator) vrna_log_levels_e.VRNA_LOG_LEVEL_UNKNOWN (C enumerator) vrna_log_levels_e.VRNA_LOG_LEVEL_WARNING (C enumerator) vrna_log_lock_f (C type) vrna_log_lock_set (C function) VRNA_LOG_OPTION_DEFAULT (C macro) VRNA_LOG_OPTION_QUIET (C macro) VRNA_LOG_OPTION_TRACE_CALL (C macro) VRNA_LOG_OPTION_TRACE_TIME (C macro) vrna_log_options (C function) vrna_log_options_set (C function) vrna_log_reset (C function) vrna_log_warning (C macro) vrna_logdata_free_f (C type) vrna_loopidx_from_ptable (C function) vrna_loopidx_update (C function) VRNA_MB_LOOP (C macro) vrna_md_copy (C function) vrna_md_defaults_backbone_length (C function) vrna_md_defaults_backbone_length_get (C function) vrna_md_defaults_backtrack (C function) vrna_md_defaults_backtrack_get (C function) vrna_md_defaults_backtrack_type (C function) vrna_md_defaults_backtrack_type_get (C function) vrna_md_defaults_betaScale (C function) vrna_md_defaults_betaScale_get (C function) vrna_md_defaults_circ (C function) vrna_md_defaults_circ_alpha0 (C function) vrna_md_defaults_circ_alpha0_get (C function) vrna_md_defaults_circ_get (C function) vrna_md_defaults_circ_penalty (C function) vrna_md_defaults_circ_penalty_get (C function) vrna_md_defaults_compute_bpp (C function) vrna_md_defaults_compute_bpp_get (C function) vrna_md_defaults_cv_fact (C function) vrna_md_defaults_cv_fact_get (C function) vrna_md_defaults_dangles (C function) vrna_md_defaults_dangles_get (C function) vrna_md_defaults_energy_set (C function) vrna_md_defaults_energy_set_get (C function) vrna_md_defaults_gquad (C function) vrna_md_defaults_gquad_get (C function) vrna_md_defaults_helical_rise (C function) vrna_md_defaults_helical_rise_get (C function) vrna_md_defaults_logML (C function) vrna_md_defaults_logML_get (C function) vrna_md_defaults_max_bp_span (C function) vrna_md_defaults_max_bp_span_get (C function) vrna_md_defaults_min_loop_size (C function) vrna_md_defaults_min_loop_size_get (C function) vrna_md_defaults_nc_fact (C function) vrna_md_defaults_nc_fact_get (C function) vrna_md_defaults_noGU (C function) vrna_md_defaults_noGU_get (C function) vrna_md_defaults_noGUclosure (C function) vrna_md_defaults_noGUclosure_get (C function) vrna_md_defaults_noLP (C function) vrna_md_defaults_noLP_get (C function) vrna_md_defaults_oldAliEn (C function) vrna_md_defaults_oldAliEn_get (C function) vrna_md_defaults_pf_smooth (C function) vrna_md_defaults_pf_smooth_get (C function) vrna_md_defaults_reset (C function) vrna_md_defaults_ribo (C function) vrna_md_defaults_ribo_get (C function) vrna_md_defaults_salt (C function) vrna_md_defaults_salt_get (C function) vrna_md_defaults_saltDPXInit (C function) vrna_md_defaults_saltDPXInit_get (C function) vrna_md_defaults_saltDPXInitFact (C function) vrna_md_defaults_saltDPXInitFact_get (C function) vrna_md_defaults_saltMLLower (C function) vrna_md_defaults_saltMLLower_get (C function) vrna_md_defaults_saltMLUpper (C function) vrna_md_defaults_saltMLUpper_get (C function) vrna_md_defaults_sfact (C function) vrna_md_defaults_sfact_get (C function) vrna_md_defaults_special_hp (C function) vrna_md_defaults_special_hp_get (C function) vrna_md_defaults_temperature (C function) vrna_md_defaults_temperature_get (C function) vrna_md_defaults_uniq_ML (C function) vrna_md_defaults_uniq_ML_get (C function) vrna_md_defaults_window_size (C function) vrna_md_defaults_window_size_get (C function) vrna_md_option_string (C function) vrna_md_s (C struct) vrna_md_s.alias (C var) vrna_md_s.backbone_length (C var) vrna_md_s.backtrack (C var) vrna_md_s.backtrack_type (C var) vrna_md_s.betaScale (C var) vrna_md_s.circ (C var) vrna_md_s.circ_alpha0 (C var) vrna_md_s.circ_penalty (C var) vrna_md_s.compute_bpp (C var) vrna_md_s.cv_fact (C var) vrna_md_s.dangles (C var) vrna_md_s.energy_set (C var) vrna_md_s.gquad (C var) vrna_md_s.helical_rise (C var) vrna_md_s.logML (C var) vrna_md_s.max_bp_span (C var) vrna_md_s.min_loop_size (C var) vrna_md_s.nc_fact (C var) vrna_md_s.noGU (C var) vrna_md_s.noGUclosure (C var) vrna_md_s.noLP (C var) vrna_md_s.nonstandards (C var) vrna_md_s.oldAliEn (C var) vrna_md_s.pair (C var) vrna_md_s.pair_dist (C var) vrna_md_s.pf_smooth (C var) vrna_md_s.ribo (C var) vrna_md_s.rtype (C var) vrna_md_s.salt (C var) vrna_md_s.saltDPXInit (C var) vrna_md_s.saltDPXInitFact (C var) vrna_md_s.saltMLLower (C var) vrna_md_s.saltMLUpper (C var) vrna_md_s.sfact (C var) vrna_md_s.special_hp (C var) vrna_md_s.temperature (C var) vrna_md_s.uniq_ML (C var) vrna_md_s.window_size (C var) vrna_md_set_default (C function) vrna_md_set_nonstandards (C function) vrna_md_t (C type) vrna_md_update (C function) vrna_MEA (C function) vrna_MEA_from_plist (C function) vrna_mean_bp_distance (C function) vrna_mean_bp_distance_pr (C function) VRNA_MEASURE_SHANNON_ENTROPY (C macro) vrna_message_constraint_options (C function) vrna_message_constraint_options_all (C function) vrna_message_error (C function) vrna_message_info (C function) vrna_message_input_msa (C function) vrna_message_input_seq (C function) vrna_message_input_seq_simple (C function) vrna_message_verror (C function) vrna_message_vinfo (C function) vrna_message_vwarning (C function) vrna_message_warning (C function) vrna_mfe (C function) vrna_mfe_dimer (C function) vrna_mfe_exterior_f3 (C function) vrna_mfe_exterior_f5 (C function) vrna_mfe_gquad_internal_loop (C function) vrna_mfe_internal (C function) vrna_mfe_internal_ext (C function) vrna_mfe_multibranch_fast_free (C function) vrna_mfe_multibranch_fast_init (C function)

vrna_mfe_multibranch_fast_rotate (C function) vrna_mfe_multibranch_loop_fast (C function) vrna_mfe_multibranch_loop_stack (C function) vrna_mfe_multibranch_m1 (C function) vrna_mfe_multibranch_m2_fast (C function) vrna_mfe_multibranch_stems_fast (C function) vrna_mfe_TwoD (C function) vrna_mfe_window (C function) vrna_mfe_window_cb (C function) vrna_mfe_window_f (C type) vrna_mfe_window_zscore (C function) vrna_mfe_window_zscore_cb (C function) vrna_mfe_window_zscore_f (C type) VRNA_MINIMIZER_CONJUGATE_FR (C macro) VRNA_MINIMIZER_CONJUGATE_PR (C macro) VRNA_MINIMIZER_DEFAULT (C macro) VRNA_MINIMIZER_STEEPEST_DESCENT (C macro) VRNA_MINIMIZER_VECTOR_BFGS (C macro) VRNA_MINIMIZER_VECTOR_BFGS2 (C macro) vrna_mkdir_p (C function) VRNA_MODEL_BACKBONE_LENGTH_DNA (C macro) VRNA_MODEL_BACKBONE_LENGTH_RNA (C macro) VRNA_MODEL_DEFAULT_ALI_CV_FACT (C macro) VRNA_MODEL_DEFAULT_ALI_NC_FACT (C macro) VRNA_MODEL_DEFAULT_ALI_OLD_EN (C macro) VRNA_MODEL_DEFAULT_ALI_RIBO (C macro) VRNA_MODEL_DEFAULT_BACKBONE_LENGTH (C macro) VRNA_MODEL_DEFAULT_BACKTRACK (C macro) VRNA_MODEL_DEFAULT_BACKTRACK_TYPE (C macro) VRNA_MODEL_DEFAULT_BETA_SCALE (C macro) VRNA_MODEL_DEFAULT_CIRC (C macro) VRNA_MODEL_DEFAULT_CIRC_ALPHA0 (C macro) VRNA_MODEL_DEFAULT_CIRC_PENALTY (C macro) VRNA_MODEL_DEFAULT_COMPUTE_BPP (C macro) VRNA_MODEL_DEFAULT_DANGLES (C macro) VRNA_MODEL_DEFAULT_ENERGY_SET (C macro) VRNA_MODEL_DEFAULT_GQUAD (C macro) VRNA_MODEL_DEFAULT_HELICAL_RISE (C macro) VRNA_MODEL_DEFAULT_LOG_ML (C macro) VRNA_MODEL_DEFAULT_MAX_BP_SPAN (C macro) VRNA_MODEL_DEFAULT_NO_GU (C macro) VRNA_MODEL_DEFAULT_NO_GU_CLOSURE (C macro) VRNA_MODEL_DEFAULT_NO_LP (C macro) VRNA_MODEL_DEFAULT_PF_SCALE (C macro) VRNA_MODEL_DEFAULT_PF_SMOOTH (C macro) VRNA_MODEL_DEFAULT_SALT (C macro) VRNA_MODEL_DEFAULT_SALT_DPXINIT (C macro) VRNA_MODEL_DEFAULT_SALT_DPXINIT_FACT (C macro) VRNA_MODEL_DEFAULT_SALT_MLLOWER (C macro) VRNA_MODEL_DEFAULT_SALT_MLUPPER (C macro) VRNA_MODEL_DEFAULT_SPECIAL_HP (C macro) VRNA_MODEL_DEFAULT_TEMPERATURE (C macro) VRNA_MODEL_DEFAULT_UNIQ_ML (C macro) VRNA_MODEL_DEFAULT_WINDOW_SIZE (C macro) VRNA_MODEL_HELICAL_RISE_DNA (C macro) VRNA_MODEL_HELICAL_RISE_RNA (C macro) VRNA_MODEL_SALT_DPXINIT_FACT_DNA (C macro) VRNA_MODEL_SALT_DPXINIT_FACT_RNA (C macro) vrna_move_apply (C function) vrna_move_apply_db (C function) vrna_move_compare (C function) vrna_move_init (C function) vrna_move_is_insertion (C function) vrna_move_is_removal (C function) vrna_move_is_shift (C function) vrna_move_list_free (C function) vrna_move_neighbor_diff (C function) vrna_move_neighbor_diff_cb (C function) VRNA_MOVE_NO_APPLY (C macro) vrna_move_s (C struct) vrna_move_s.next (C var) vrna_move_s.pos_3 (C var) vrna_move_s.pos_5 (C var) vrna_move_t (C type) vrna_move_update_f (C type) VRNA_MOVESET_DEFAULT (C macro) VRNA_MOVESET_DELETION (C macro) VRNA_MOVESET_INSERTION (C macro) VRNA_MOVESET_NO_LP (C macro) VRNA_MOVESET_SHIFT (C macro) vrna_msa_add (C function) vrna_msa_t (C type) vrna_multimer_pf_s (C struct) vrna_multimer_pf_s.F_connected (C var) vrna_multimer_pf_s.F_monomers (C var) vrna_multimer_pf_s.num_monomers (C var) vrna_mx_add (C function) VRNA_MX_FLAG_C (C macro) VRNA_MX_FLAG_F3 (C macro) VRNA_MX_FLAG_F5 (C macro) VRNA_MX_FLAG_G (C macro) VRNA_MX_FLAG_M (C macro) VRNA_MX_FLAG_M1 (C macro) VRNA_MX_FLAG_M2 (C macro) VRNA_MX_FLAG_MAX (C macro) VRNA_MX_FLAG_MS3 (C macro) VRNA_MX_FLAG_MS5 (C macro) vrna_mx_mfe_add (C function) vrna_mx_mfe_aux_ml_t (C type) vrna_mx_mfe_free (C function) vrna_mx_mfe_s (C struct) vrna_mx_mfe_s.[anonymous] (C var) vrna_mx_mfe_s.c (C var) vrna_mx_mfe_s.c_local (C var) vrna_mx_mfe_s.E_C (C var) vrna_mx_mfe_s.E_C_rem (C var) vrna_mx_mfe_s.E_F3 (C var) vrna_mx_mfe_s.E_F3_rem (C var) vrna_mx_mfe_s.E_F5 (C var) vrna_mx_mfe_s.E_F5_rem (C var) vrna_mx_mfe_s.E_Fc (C var) vrna_mx_mfe_s.E_Fc_rem (C var) vrna_mx_mfe_s.E_FcH (C var) vrna_mx_mfe_s.E_FcH_rem (C var) vrna_mx_mfe_s.E_FcI (C var) vrna_mx_mfe_s.E_FcI_rem (C var) vrna_mx_mfe_s.E_FcM (C var) vrna_mx_mfe_s.E_FcM_rem (C var) vrna_mx_mfe_s.E_M (C var) vrna_mx_mfe_s.E_M1 (C var) vrna_mx_mfe_s.E_M1_rem (C var) vrna_mx_mfe_s.E_M2 (C var) vrna_mx_mfe_s.E_M2_rem (C var) vrna_mx_mfe_s.E_M_rem (C var) vrna_mx_mfe_s.f3 (C var) vrna_mx_mfe_s.f3_local (C var) vrna_mx_mfe_s.f5 (C var) vrna_mx_mfe_s.Fc (C var) vrna_mx_mfe_s.FcH (C var) vrna_mx_mfe_s.FcI (C var) vrna_mx_mfe_s.FcM (C var) vrna_mx_mfe_s.fM1 (C var) vrna_mx_mfe_s.fM1_new (C var) vrna_mx_mfe_s.fM2 (C var) vrna_mx_mfe_s.fM2_real (C var) vrna_mx_mfe_s.fML (C var) vrna_mx_mfe_s.fML_local (C var) vrna_mx_mfe_s.fms3 (C var) vrna_mx_mfe_s.fms5 (C var) vrna_mx_mfe_s.ggg_local (C var) vrna_mx_mfe_s.ggg_local_shift (C var) vrna_mx_mfe_s.k_max_C (C var) vrna_mx_mfe_s.k_max_F3 (C var) vrna_mx_mfe_s.k_max_F5 (C var) vrna_mx_mfe_s.k_max_Fc (C var) vrna_mx_mfe_s.k_max_FcH (C var) vrna_mx_mfe_s.k_max_FcI (C var) vrna_mx_mfe_s.k_max_FcM (C var) vrna_mx_mfe_s.k_max_M (C var) vrna_mx_mfe_s.k_max_M1 (C var) vrna_mx_mfe_s.k_max_M2 (C var) vrna_mx_mfe_s.k_min_C (C var) vrna_mx_mfe_s.k_min_F3 (C var) vrna_mx_mfe_s.k_min_F5 (C var) vrna_mx_mfe_s.k_min_Fc (C var) vrna_mx_mfe_s.k_min_FcH (C var) vrna_mx_mfe_s.k_min_FcI (C var) vrna_mx_mfe_s.k_min_FcM (C var) vrna_mx_mfe_s.k_min_M (C var) vrna_mx_mfe_s.k_min_M1 (C var) vrna_mx_mfe_s.k_min_M2 (C var) vrna_mx_mfe_s.l_max_C (C var) vrna_mx_mfe_s.l_max_F3 (C var) vrna_mx_mfe_s.l_max_F5 (C var) vrna_mx_mfe_s.l_max_Fc (C var) vrna_mx_mfe_s.l_max_FcH (C var) vrna_mx_mfe_s.l_max_FcI (C var) vrna_mx_mfe_s.l_max_FcM (C var) vrna_mx_mfe_s.l_max_M (C var) vrna_mx_mfe_s.l_max_M1 (C var) vrna_mx_mfe_s.l_max_M2 (C var) vrna_mx_mfe_s.l_min_C (C var) vrna_mx_mfe_s.l_min_F3 (C var) vrna_mx_mfe_s.l_min_F5 (C var) vrna_mx_mfe_s.l_min_Fc (C var) vrna_mx_mfe_s.l_min_FcH (C var) vrna_mx_mfe_s.l_min_FcI (C var) vrna_mx_mfe_s.l_min_FcM (C var) vrna_mx_mfe_s.l_min_M (C var) vrna_mx_mfe_s.l_min_M1 (C var) vrna_mx_mfe_s.l_min_M2 (C var) vrna_mx_mfe_s.length (C var) vrna_mx_mfe_s.strands (C var) vrna_mx_mfe_s.type (C var) vrna_mx_mfe_t (C type) vrna_mx_pf_add (C function) vrna_mx_pf_aux_el_t (C type) vrna_mx_pf_aux_ml_t (C type) vrna_mx_pf_free (C function) vrna_mx_pf_s (C struct) vrna_mx_pf_s.[anonymous] (C var) vrna_mx_pf_s.expMLbase (C var) vrna_mx_pf_s.G_local (C var) vrna_mx_pf_s.k_max_Q (C var) vrna_mx_pf_s.k_max_Q_B (C var) vrna_mx_pf_s.k_max_Q_c (C var) vrna_mx_pf_s.k_max_Q_cH (C var) vrna_mx_pf_s.k_max_Q_cI (C var) vrna_mx_pf_s.k_max_Q_cM (C var) vrna_mx_pf_s.k_max_Q_M (C var) vrna_mx_pf_s.k_max_Q_M1 (C var) vrna_mx_pf_s.k_max_Q_M2 (C var) vrna_mx_pf_s.k_min_Q (C var) vrna_mx_pf_s.k_min_Q_B (C var) vrna_mx_pf_s.k_min_Q_c (C var) vrna_mx_pf_s.k_min_Q_cH (C var) vrna_mx_pf_s.k_min_Q_cI (C var) vrna_mx_pf_s.k_min_Q_cM (C var) vrna_mx_pf_s.k_min_Q_M (C var) vrna_mx_pf_s.k_min_Q_M1 (C var) vrna_mx_pf_s.k_min_Q_M2 (C var) vrna_mx_pf_s.l_max_Q (C var) vrna_mx_pf_s.l_max_Q_B (C var) vrna_mx_pf_s.l_max_Q_c (C var) vrna_mx_pf_s.l_max_Q_cH (C var) vrna_mx_pf_s.l_max_Q_cI (C var) vrna_mx_pf_s.l_max_Q_cM (C var) vrna_mx_pf_s.l_max_Q_M (C var) vrna_mx_pf_s.l_max_Q_M1 (C var) vrna_mx_pf_s.l_max_Q_M2 (C var) vrna_mx_pf_s.l_min_Q (C var) vrna_mx_pf_s.l_min_Q_B (C var) vrna_mx_pf_s.l_min_Q_c (C var) vrna_mx_pf_s.l_min_Q_cH (C var) vrna_mx_pf_s.l_min_Q_cI (C var) vrna_mx_pf_s.l_min_Q_cM (C var) vrna_mx_pf_s.l_min_Q_M (C var) vrna_mx_pf_s.l_min_Q_M1 (C var) vrna_mx_pf_s.l_min_Q_M2 (C var) vrna_mx_pf_s.length (C var) vrna_mx_pf_s.pR (C var) vrna_mx_pf_s.probs (C var) vrna_mx_pf_s.Q (C var) vrna_mx_pf_s.q (C var) vrna_mx_pf_s.q1k (C var) vrna_mx_pf_s.q2l (C var) vrna_mx_pf_s.Q_B (C var) vrna_mx_pf_s.Q_B_rem (C var) vrna_mx_pf_s.Q_c (C var) vrna_mx_pf_s.Q_c_rem (C var) vrna_mx_pf_s.Q_cH (C var) vrna_mx_pf_s.Q_cH_rem (C var) vrna_mx_pf_s.Q_cI (C var) vrna_mx_pf_s.Q_cI_rem (C var) vrna_mx_pf_s.Q_cM (C var) vrna_mx_pf_s.Q_cM_rem (C var) vrna_mx_pf_s.q_local (C var) vrna_mx_pf_s.Q_M (C var) vrna_mx_pf_s.Q_M1 (C var) vrna_mx_pf_s.Q_M1_rem (C var) vrna_mx_pf_s.Q_M2 (C var) vrna_mx_pf_s.Q_M2_rem (C var) vrna_mx_pf_s.Q_M_rem (C var) vrna_mx_pf_s.Q_rem (C var) vrna_mx_pf_s.qb (C var) vrna_mx_pf_s.qb_local (C var) vrna_mx_pf_s.qho (C var) vrna_mx_pf_s.QI5 (C var) vrna_mx_pf_s.qio (C var) vrna_mx_pf_s.qln (C var) vrna_mx_pf_s.qm (C var) vrna_mx_pf_s.qm1 (C var) vrna_mx_pf_s.qm1_new (C var) vrna_mx_pf_s.qm2 (C var) vrna_mx_pf_s.qm2_local (C var) vrna_mx_pf_s.qm2_real (C var) vrna_mx_pf_s.qm_local (C var) vrna_mx_pf_s.qmb (C var) vrna_mx_pf_s.qmo (C var) vrna_mx_pf_s.qo (C var) vrna_mx_pf_s.scale (C var) vrna_mx_pf_s.type (C var) vrna_mx_pf_t (C type) vrna_mx_prepare (C function) vrna_mx_type_e (C enum) vrna_mx_type_e.VRNA_MX_2DFOLD (C enumerator) vrna_mx_type_e.VRNA_MX_DEFAULT (C enumerator) vrna_mx_type_e.VRNA_MX_WINDOW (C enumerator) vrna_n_multichoose_k (C function) VRNA_NEIGHBOR_CHANGE (C macro) VRNA_NEIGHBOR_INVALID (C macro) VRNA_NEIGHBOR_NEW (C macro) vrna_neighbors (C function) vrna_neighbors_successive (C function) vrna_nucleotide_decode (C function) vrna_nucleotide_encode (C function) vrna_nucleotide_IUPAC_identity (C function) VRNA_OBJECTIVE_FUNCTION_ABSOLUTE (C macro) VRNA_OBJECTIVE_FUNCTION_QUADRATIC (C macro) VRNA_OPTION_DEFAULT (C macro) VRNA_OPTION_EVAL_ONLY (C macro) VRNA_OPTION_F3 (C macro) VRNA_OPTION_F5 (C macro) VRNA_OPTION_HYBRID (C macro) VRNA_OPTION_MFE (C macro) VRNA_OPTION_MULTILINE (C macro) VRNA_OPTION_PF (C macro) VRNA_OPTION_WINDOW (C macro) VRNA_OPTION_WINDOW_F3 (C macro) VRNA_OPTION_WINDOW_F5 (C macro) vrna_ostream_free (C function) vrna_ostream_init (C function) vrna_ostream_provide (C function) vrna_ostream_request (C function) vrna_ostream_t (C type) vrna_ostream_threadsafe (C function) vrna_pairing_probs (C function) vrna_pairing_tendency (C function) vrna_param_s (C struct) vrna_param_s.bulge (C var) vrna_param_s.dangle3 (C var) vrna_param_s.dangle5 (C var) vrna_param_s.DuplexInit (C var) vrna_param_s.gquad (C var) vrna_param_s.gquadLayerMismatch (C var) vrna_param_s.gquadLayerMismatchMax (C var) vrna_param_s.hairpin (C var) vrna_param_s.Hexaloop_E (C var) vrna_param_s.Hexaloops (C var) vrna_param_s.id (C var) vrna_param_s.int11 (C var) vrna_param_s.int21 (C var) vrna_param_s.int22 (C var) vrna_param_s.internal_loop (C var) vrna_param_s.lxc (C var) vrna_param_s.mismatch1nI (C var) vrna_param_s.mismatch23I (C var) vrna_param_s.mismatchExt (C var) vrna_param_s.mismatchH (C var) vrna_param_s.mismatchI (C var) vrna_param_s.mismatchM (C var) vrna_param_s.MLbase (C var) vrna_param_s.MLclosing (C var) vrna_param_s.MLintern (C var) vrna_param_s.model_details (C var) vrna_param_s.MultipleCA (C var) vrna_param_s.MultipleCB (C var) vrna_param_s.ninio (C var) vrna_param_s.param_file (C var) vrna_param_s.SaltDPXInit (C var) vrna_param_s.SaltLoop (C var) vrna_param_s.SaltLoopDbl (C var) vrna_param_s.SaltMLbase (C var) vrna_param_s.SaltMLclosing (C var) vrna_param_s.SaltMLintern (C var) vrna_param_s.SaltStack (C var) vrna_param_s.stack (C var) vrna_param_s.temperature (C var) vrna_param_s.TerminalAU (C var) vrna_param_s.Tetraloop_E (C var) vrna_param_s.Tetraloops (C var) vrna_param_s.Triloop_E (C var) vrna_param_s.Triloops (C var) vrna_param_s.TripleC (C var) vrna_param_t (C type) VRNA_PARAMETER_FORMAT_DEFAULT (C macro) vrna_params (C function) vrna_params_copy (C function) vrna_params_load (C function) vrna_params_load_defaults (C function) vrna_params_load_DNA_Mathews1999 (C function) vrna_params_load_DNA_Mathews2004 (C function) vrna_params_load_from_string (C function) vrna_params_load_RNA_Andronescu2007 (C function) vrna_params_load_RNA_Langdon2018 (C function) vrna_params_load_RNA_misc_special_hairpins (C function) vrna_params_load_RNA_Turner1999 (C function) vrna_params_load_RNA_Turner2004 (C function) vrna_params_prepare (C function) vrna_params_reset (C function) vrna_params_save (C function) vrna_params_subst (C function) vrna_path (C function) VRNA_PATH_DEFAULT (C macro) vrna_path_direct (C function) vrna_path_direct_ub (C function) vrna_path_findpath (C function) vrna_path_findpath_saddle (C function) vrna_path_findpath_saddle_ub (C function) vrna_path_findpath_ub (C function) vrna_path_free (C function) vrna_path_gradient (C function) VRNA_PATH_NO_TRANSITION_OUTPUT (C macro) vrna_path_options_findpath (C function) vrna_path_options_free (C function) vrna_path_options_t (C type) vrna_path_random (C function) VRNA_PATH_RANDOM (C macro) vrna_path_s (C struct) vrna_path_s.en (C var) vrna_path_s.move (C var) vrna_path_s.s (C var) vrna_path_s.type (C var) VRNA_PATH_STEEPEST_DESCENT (C macro) vrna_path_t (C type) VRNA_PATH_TYPE_DOT_BRACKET (C macro) VRNA_PATH_TYPE_MOVES (C macro) vrna_pbacktrack (C function) vrna_pbacktrack5 (C function) vrna_pbacktrack5_cb (C function) vrna_pbacktrack5_num (C function) vrna_pbacktrack5_resume (C function) vrna_pbacktrack5_resume_cb (C function) vrna_pbacktrack5_TwoD (C function) vrna_pbacktrack_cb (C function) VRNA_PBACKTRACK_DEFAULT (C macro) vrna_pbacktrack_mem_free (C function) vrna_pbacktrack_mem_t (C type) VRNA_PBACKTRACK_NON_REDUNDANT (C macro) vrna_pbacktrack_num (C function) vrna_pbacktrack_resume (C function) vrna_pbacktrack_resume_cb (C function) vrna_pbacktrack_sub (C function) vrna_pbacktrack_sub_cb (C function) vrna_pbacktrack_sub_num (C function) vrna_pbacktrack_sub_resume (C function) vrna_pbacktrack_sub_resume_cb (C function) vrna_pbacktrack_TwoD (C function) vrna_pf (C function) vrna_pf_add (C function) vrna_pf_alifold (C function) vrna_pf_circalifold (C function) vrna_pf_circfold (C function) vrna_pf_co_fold (C function), [1] vrna_pf_dimer (C function) vrna_pf_dimer_concentrations (C function) vrna_pf_dimer_probs (C function) vrna_pf_float_precision (C function) vrna_pf_fold (C function) vrna_pf_substrands (C function) vrna_pf_TwoD (C function) vrna_pfl_fold (C function) vrna_pfl_fold_cb (C function) vrna_pfl_fold_up (C function) vrna_pfl_fold_up_cb (C function) vrna_pinfo_s (C struct) vrna_pinfo_s.bp (C var) vrna_pinfo_s.comp (C var) vrna_pinfo_s.ent (C var) vrna_pinfo_s.i (C var) vrna_pinfo_s.j (C var) vrna_pinfo_s.p (C var) vrna_pinfo_t (C type) vrna_pk_plex (C function) vrna_pk_plex_accessibility (C function) vrna_pk_plex_opt (C function) vrna_pk_plex_opt_defaults (C function) vrna_pk_plex_opt_fun (C function) vrna_pk_plex_opt_t (C type) vrna_pk_plex_result_s (C struct) vrna_pk_plex_result_s.dG1 (C var) vrna_pk_plex_result_s.dG2 (C var) vrna_pk_plex_result_s.dGint (C var) vrna_pk_plex_result_s.dGpk (C var) vrna_pk_plex_result_s.end_3 (C var) vrna_pk_plex_result_s.end_5 (C var) vrna_pk_plex_result_s.energy (C var) vrna_pk_plex_result_s.start_3 (C var) vrna_pk_plex_result_s.start_5 (C var) vrna_pk_plex_result_s.structure (C var) vrna_pk_plex_score_f (C type) vrna_pk_plex_t (C type) vrna_plist (C function) vrna_plist_append (C function) vrna_plist_from_probs (C function) vrna_plist_gquad_from_pr (C function) vrna_plist_gquad_from_pr_max (C function) vrna_plist_t (C type) VRNA_PLIST_TYPE_BASEPAIR (C macro) VRNA_PLIST_TYPE_GQUAD (C macro) VRNA_PLIST_TYPE_H_MOTIF (C macro) VRNA_PLIST_TYPE_I_MOTIF (C macro) VRNA_PLIST_TYPE_STACK (C macro) VRNA_PLIST_TYPE_TRIPLE (C macro) VRNA_PLIST_TYPE_UD_MOTIF (C macro) VRNA_PLIST_TYPE_UNPAIRED (C macro) vrna_plot_coords (C function) vrna_plot_coords_circular (C function) vrna_plot_coords_circular_pt (C function) vrna_plot_coords_pt (C function) vrna_plot_coords_puzzler (C function) vrna_plot_coords_puzzler_pt (C function) vrna_plot_coords_simple (C function) vrna_plot_coords_simple_pt (C function) vrna_plot_coords_turtle (C function) vrna_plot_coords_turtle_pt (C function) vrna_plot_data_s (C struct) vrna_plot_data_s.md (C var) vrna_plot_data_s.options (C var) vrna_plot_data_s.post (C var) vrna_plot_data_s.pre (C var) vrna_plot_data_t (C type) vrna_plot_dp_EPS (C function) vrna_plot_dp_PS_list (C function) vrna_plot_layout (C function) vrna_plot_layout_circular (C function) vrna_plot_layout_free (C function) vrna_plot_layout_puzzler (C function) vrna_plot_layout_s (C struct) vrna_plot_layout_s.arcs (C var) vrna_plot_layout_s.bbox (C var) vrna_plot_layout_s.length (C var) vrna_plot_layout_s.type (C var) vrna_plot_layout_s.x (C var) vrna_plot_layout_s.y (C var) vrna_plot_layout_simple (C function) vrna_plot_layout_t (C type) vrna_plot_layout_turtle (C function) vrna_plot_options_puzzler (C function) vrna_plot_options_puzzler_free (C function) vrna_plot_options_puzzler_t (C struct) vrna_plot_options_puzzler_t.allowFlipping (C var) vrna_plot_options_puzzler_t.checkAncestorIntersections (C var) vrna_plot_options_puzzler_t.checkExteriorIntersections (C var) vrna_plot_options_puzzler_t.checkSiblingIntersections (C var) vrna_plot_options_puzzler_t.config (C var) vrna_plot_options_puzzler_t.drawArcs (C var) vrna_plot_options_puzzler_t.filename (C var) vrna_plot_options_puzzler_t.maximumNumberOfConfigChangesAllowed (C var) vrna_plot_options_puzzler_t.numberOfChangesAppliedToConfig (C var) vrna_plot_options_puzzler_t.optimize (C var) vrna_plot_options_puzzler_t.paired (C var) vrna_plot_options_puzzler_t.psNumber (C var) vrna_plot_options_puzzler_t.unpaired (C var) VRNA_PLOT_PROBABILITIES_ACC (C macro) VRNA_PLOT_PROBABILITIES_BP (C macro) VRNA_PLOT_PROBABILITIES_DEFAULT (C macro) VRNA_PLOT_PROBABILITIES_SC_BP (C macro) VRNA_PLOT_PROBABILITIES_SC_MOTIF (C macro) VRNA_PLOT_PROBABILITIES_SC_UP (C macro) VRNA_PLOT_PROBABILITIES_SD (C macro) VRNA_PLOT_PROBABILITIES_UD (C macro) VRNA_PLOT_PROBABILITIES_UD_LIN (C macro) vrna_plot_structure (C function) vrna_plot_structure_eps (C function) vrna_plot_structure_gml (C function) vrna_plot_structure_ssv (C function) vrna_plot_structure_svg (C function) vrna_plot_structure_xrna (C function) VRNA_PLOT_TYPE_CIRCULAR (C macro) VRNA_PLOT_TYPE_DEFAULT (C macro) VRNA_PLOT_TYPE_NAVIEW (C macro) VRNA_PLOT_TYPE_PUZZLER (C macro) VRNA_PLOT_TYPE_SIMPLE (C macro) VRNA_PLOT_TYPE_TURTLE (C macro) vrna_positional_entropy (C function) vrna_pr_energy (C function) vrna_pr_structure (C function) VRNA_PROBING_DATA_CHECK_SEQUENCE (C macro) vrna_probing_data_Deigan2009 (C function) vrna_probing_data_Deigan2009_comparative (C function) vrna_probing_data_Eddy2014_2 (C function) vrna_probing_data_Eddy2014_2_comparative (C function) vrna_probing_data_free (C function) vrna_probing_data_load_n_distribute (C function) vrna_probing_data_t (C type) vrna_probing_data_Zarringhalam2012 (C function) vrna_probing_data_Zarringhalam2012_comparative (C function) VRNA_PROBING_METHOD_DEIGAN2009 (C macro) VRNA_PROBING_METHOD_DEIGAN2009_DEFAULT_b (C macro) VRNA_PROBING_METHOD_DEIGAN2009_DEFAULT_m (C macro) VRNA_PROBING_METHOD_EDDY2014_2 (C macro) VRNA_PROBING_METHOD_MULTI_PARAMS_0 (C macro) VRNA_PROBING_METHOD_MULTI_PARAMS_1 (C macro) VRNA_PROBING_METHOD_MULTI_PARAMS_2 (C macro) VRNA_PROBING_METHOD_MULTI_PARAMS_3 (C macro) VRNA_PROBING_METHOD_MULTI_PARAMS_DEFAULT (C macro) VRNA_PROBING_METHOD_WASHIETL2012 (C macro) VRNA_PROBING_METHOD_ZARRINGHALAM2012 (C macro) VRNA_PROBING_METHOD_ZARRINGHALAM2012_DEFAULT_beta (C macro) VRNA_PROBING_METHOD_ZARRINGHALAM2012_DEFAULT_conversion (C macro) VRNA_PROBING_METHOD_ZARRINGHALAM2012_DEFAULT_probability (C macro) vrna_probs_window (C function) VRNA_PROBS_WINDOW_BPP (C macro) vrna_probs_window_f (C type) VRNA_PROBS_WINDOW_PF (C macro) VRNA_PROBS_WINDOW_STACKP (C macro) VRNA_PROBS_WINDOW_UP (C macro) VRNA_PROBS_WINDOW_UP_SPLIT (C macro) vrna_pscore (C function) vrna_pscore_freq (C function) vrna_pt_ali_get (C function) vrna_pt_pk_get (C function) vrna_pt_pk_remove (C function) vrna_pt_snoop_get (C function) vrna_ptable (C function) vrna_ptable_copy (C function) vrna_ptable_from_string (C function) vrna_ptypes (C function) vrna_ptypes_prepare (C function) vrna_random_string (C function) vrna_read_line (C function) vrna_realloc (C function) vrna_recursion_status_f (C type) vrna_refBPcnt_matrix (C function) vrna_refBPdist_matrix (C function) vrna_rotational_symmetry (C function) vrna_rotational_symmetry_db (C function) vrna_rotational_symmetry_db_pos (C function) vrna_rotational_symmetry_num (C function) vrna_rotational_symmetry_pos (C function) vrna_rotational_symmetry_pos_num (C function) vrna_salt_duplex_init (C function) vrna_salt_loop (C function) vrna_salt_loop_int (C function) vrna_salt_ml (C function) vrna_salt_stack (C function) vrna_sc_add_auxdata (C function) vrna_sc_add_bp (C function) vrna_sc_add_bp_comparative (C function) vrna_sc_add_bp_comparative_seq (C function) vrna_sc_add_bt (C function) vrna_sc_add_data (C function) vrna_sc_add_exp_f (C function) vrna_sc_add_f (C function) vrna_sc_add_hi_motif (C function) vrna_sc_add_SHAPE_deigan (C function) vrna_sc_add_SHAPE_deigan_ali (C function) vrna_sc_add_SHAPE_eddy_2 (C function) vrna_sc_add_SHAPE_zarringhalam (C function) vrna_sc_add_stack (C function) vrna_sc_add_stack_comparative (C function) vrna_sc_add_stack_comparative_seq (C function) vrna_sc_add_up (C function) vrna_sc_add_up_comparative (C function) vrna_sc_add_up_comparative_seq (C function) vrna_sc_bp_storage_t (C struct) vrna_sc_bp_storage_t.e (C var) vrna_sc_bp_storage_t.interval_end (C var) vrna_sc_bp_storage_t.interval_start (C var) vrna_sc_bt_f (C type) vrna_sc_direct_f (C type) vrna_sc_exp_direct_f (C type) vrna_sc_exp_f (C type) vrna_sc_f (C type) vrna_sc_free (C function) vrna_sc_init (C function) vrna_sc_ligand_detect_motifs (C function) vrna_sc_ligand_get_all_motifs (C function) vrna_sc_minimize_pertubation (C function) vrna_sc_mod (C function) vrna_sc_mod_7DA (C function) VRNA_SC_MOD_CHECK_FALLBACK (C macro) VRNA_SC_MOD_CHECK_UNMOD (C macro) VRNA_SC_MOD_DEFAULT (C macro) vrna_sc_mod_dihydrouridine (C function) vrna_sc_mod_inosine (C function) vrna_sc_mod_json (C function) vrna_sc_mod_jsonfile (C function) vrna_sc_mod_m6A (C function) vrna_sc_mod_param_t (C type) vrna_sc_mod_parameters_free (C function) vrna_sc_mod_pseudouridine (C function) vrna_sc_mod_purine (C function) vrna_sc_mod_read_from_json (C function) vrna_sc_mod_read_from_jsonfile (C function) VRNA_SC_MOD_SILENT (C macro) vrna_sc_motif_s (C struct) vrna_sc_motif_s.i (C var) vrna_sc_motif_s.j (C var) vrna_sc_motif_s.k (C var) vrna_sc_motif_s.l (C var) vrna_sc_motif_s.number (C var) vrna_sc_motif_t (C type) vrna_sc_multi_cb_add (C function) vrna_sc_multi_cb_add_comparative (C function) vrna_sc_prepare (C function) vrna_sc_probing (C function) vrna_sc_remove (C function) vrna_sc_s (C struct) vrna_sc_s.[anonymous] (C var) vrna_sc_s.bp_storage (C var) vrna_sc_s.bt (C var) vrna_sc_s.data (C var) vrna_sc_s.energy_bp (C var) vrna_sc_s.energy_bp_local (C var) vrna_sc_s.energy_stack (C var) vrna_sc_s.energy_up (C var) vrna_sc_s.exp_energy_bp (C var) vrna_sc_s.exp_energy_bp_local (C var) vrna_sc_s.exp_energy_stack (C var) vrna_sc_s.exp_energy_up (C var) vrna_sc_s.exp_f (C var) vrna_sc_s.f (C var) vrna_sc_s.free_data (C var) vrna_sc_s.n (C var) vrna_sc_s.prepare_data (C var) vrna_sc_s.state (C var) vrna_sc_s.type (C var) vrna_sc_s.up_storage (C var) vrna_sc_set_auxdata_comparative (C function) vrna_sc_set_auxdata_comparative_seq (C function) vrna_sc_set_bp (C function) vrna_sc_set_bp_comparative (C function) vrna_sc_set_bp_comparative_seq (C function) vrna_sc_set_data_comparative (C function) vrna_sc_set_data_comparative_seq (C function) vrna_sc_set_exp_f_comparative (C function) vrna_sc_set_f_comparative (C function) vrna_sc_set_stack (C function) vrna_sc_set_stack_comparative (C function) vrna_sc_set_stack_comparative_seq (C function) vrna_sc_set_up (C function) vrna_sc_set_up_comparative (C function) vrna_sc_set_up_comparative_seq (C function) vrna_sc_SHAPE_to_pr (C function) vrna_sc_t (C type) vrna_sc_type_e (C enum) vrna_sc_type_e.VRNA_SC_DEFAULT (C enumerator) vrna_sc_type_e.VRNA_SC_WINDOW (C enumerator) vrna_sc_update (C function) vrna_score_from_confusion_matrix (C function) vrna_score_s (C struct) vrna_score_s.F1 (C var) vrna_score_s.FDR (C var) vrna_score_s.FN (C var) vrna_score_s.FNR (C var) vrna_score_s.FOR (C var) vrna_score_s.FP (C var) vrna_score_s.FPR (C var) vrna_score_s.MCC (C var) vrna_score_s.NPV (C var) vrna_score_s.PPV (C var) vrna_score_s.TN (C var) vrna_score_s.TNR (C var) vrna_score_s.TP (C var) vrna_score_s.TPR (C var) vrna_score_t (C type) vrna_search_BM_BCT (C function) vrna_search_BM_BCT_num (C function) vrna_search_BMH (C function) vrna_search_BMH_num (C function) vrna_sect_s (C struct) vrna_sect_s.i (C var) vrna_sect_s.j (C var) vrna_sect_s.ml (C var) vrna_sect_t (C type) vrna_seq_encode (C function) vrna_seq_encode_simple (C function) vrna_seq_reverse (C function) vrna_seq_t (C type) vrna_seq_toRNA (C function) vrna_seq_toupper (C function) vrna_seq_type_e (C enum) vrna_seq_type_e.VRNA_SEQ_DNA (C enumerator) vrna_seq_type_e.VRNA_SEQ_RNA (C enumerator) vrna_seq_type_e.VRNA_SEQ_UNKNOWN (C enumerator) vrna_seq_ungapped (C function) vrna_sequence (C function) vrna_sequence_add (C function) VRNA_SEQUENCE_DNA (C macro) vrna_sequence_length_max (C function) vrna_sequence_order_update (C function) vrna_sequence_prepare (C function) vrna_sequence_remove (C function) vrna_sequence_remove_all (C function) VRNA_SEQUENCE_RNA (C macro) vrna_sequence_s (C struct) vrna_sequence_s.encoding (C var) vrna_sequence_s.encoding3 (C var) vrna_sequence_s.encoding5 (C var) vrna_sequence_s.length (C var) vrna_sequence_s.name (C var) vrna_sequence_s.string (C var) vrna_sequence_s.type (C var) vrna_sol_TwoD_pf_t (C struct) vrna_sol_TwoD_pf_t.k (C var) vrna_sol_TwoD_pf_t.l (C var) vrna_sol_TwoD_pf_t.q (C var) vrna_sol_TwoD_t (C struct) vrna_sol_TwoD_t.en (C var) vrna_sol_TwoD_t.k (C var) vrna_sol_TwoD_t.l (C var) vrna_sol_TwoD_t.s (C var) vrna_stack_prob (C function) VRNA_STATUS_MFE_POST (C macro) VRNA_STATUS_MFE_PRE (C macro) VRNA_STATUS_PF_POST (C macro) VRNA_STATUS_PF_PRE (C macro) vrna_strcat_printf (C function) vrna_strcat_vprintf (C function) vrna_strchr (C function) vrna_strdup_printf (C function) vrna_strdup_vprintf (C function) vrna_stream_output_f (C type) vrna_string_append (C function) vrna_string_append_cstring (C function) vrna_string_available_space (C function) vrna_string_free (C function) VRNA_STRING_HEADER (C macro) vrna_string_header_s (C struct) vrna_string_header_s.backup (C var) vrna_string_header_s.len (C var) vrna_string_header_s.shift_post (C var) vrna_string_header_s.size (C var) vrna_string_header_t (C type) vrna_string_length (C function) vrna_string_make (C function) vrna_string_make_space_for (C function) vrna_string_size (C function) vrna_string_t (C type) vrna_strjoin (C function) vrna_strsplit (C function) vrna_strtrim (C function) VRNA_STRUCTURE_TREE_EXPANDED (C macro) VRNA_STRUCTURE_TREE_HIT (C macro) VRNA_STRUCTURE_TREE_SHAPIRO (C macro) VRNA_STRUCTURE_TREE_SHAPIRO_EXT (C macro) VRNA_STRUCTURE_TREE_SHAPIRO_SHORT (C macro) VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT (C macro) vrna_subopt (C function) vrna_subopt_cb (C function) vrna_subopt_result_f (C type) vrna_subopt_zuker (C function) vrna_time_stamp (C function) vrna_tree_string_to_db (C function) vrna_tree_string_unweight (C function) VRNA_TRIM_ALL (C macro) VRNA_TRIM_DEFAULT (C macro) VRNA_TRIM_IN_BETWEEN (C macro) VRNA_TRIM_LEADING (C macro) VRNA_TRIM_SUBST_BY_FIRST (C macro) VRNA_TRIM_TRAILING (C macro) vrna_ud_add_motif (C function) vrna_ud_add_probs_f (C type) vrna_ud_exp_f (C type) vrna_ud_exp_production_f (C type) vrna_ud_f (C type) vrna_ud_get_probs_f (C type) vrna_ud_motifs_centroid (C function) vrna_ud_motifs_MEA (C function) vrna_ud_motifs_MFE (C function) vrna_ud_production_f (C type) vrna_ud_remove (C function) vrna_ud_set_data (C function) vrna_ud_set_exp_prod_rule_cb (C function) vrna_ud_set_prod_rule_cb (C function) vrna_ud_t (C type) vrna_unit_energy_e (C enum) vrna_unit_energy_e.VRNA_UNIT_CAL (C enumerator) vrna_unit_energy_e.VRNA_UNIT_CAL_IT (C enumerator) vrna_unit_energy_e.VRNA_UNIT_DACAL (C enumerator) vrna_unit_energy_e.VRNA_UNIT_DACAL_IT (C enumerator) vrna_unit_energy_e.VRNA_UNIT_EV (C enumerator) vrna_unit_energy_e.VRNA_UNIT_G_TNT (C enumerator) vrna_unit_energy_e.VRNA_UNIT_J (C enumerator) vrna_unit_energy_e.VRNA_UNIT_KCAL (C enumerator) vrna_unit_energy_e.VRNA_UNIT_KCAL_IT (C enumerator) vrna_unit_energy_e.VRNA_UNIT_KG_TNT (C enumerator) vrna_unit_energy_e.VRNA_UNIT_KJ (C enumerator) vrna_unit_energy_e.VRNA_UNIT_KWH (C enumerator) vrna_unit_energy_e.VRNA_UNIT_T_TNT (C enumerator) vrna_unit_energy_e.VRNA_UNIT_WH (C enumerator) vrna_unit_temperature_e (C enum) vrna_unit_temperature_e.VRNA_UNIT_DEG_C (C enumerator) vrna_unit_temperature_e.VRNA_UNIT_DEG_DE (C enumerator) vrna_unit_temperature_e.VRNA_UNIT_DEG_F (C enumerator) vrna_unit_temperature_e.VRNA_UNIT_DEG_N (C enumerator) vrna_unit_temperature_e.VRNA_UNIT_DEG_R (C enumerator) vrna_unit_temperature_e.VRNA_UNIT_DEG_RE (C enumerator) vrna_unit_temperature_e.VRNA_UNIT_DEG_RO (C enumerator) vrna_unit_temperature_e.VRNA_UNIT_K (C enumerator) VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS (C macro) VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP (C macro) VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP (C macro) VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP (C macro) VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP (C macro) VRNA_UNSTRUCTURED_DOMAIN_MOTIF (C macro) vrna_unstructured_domain_s (C struct) vrna_unstructured_domain_s.data (C var) vrna_unstructured_domain_s.energy_cb (C var) vrna_unstructured_domain_s.exp_energy_cb (C var) vrna_unstructured_domain_s.exp_prod_cb (C var) vrna_unstructured_domain_s.free_data (C var) vrna_unstructured_domain_s.motif (C var) vrna_unstructured_domain_s.motif_count (C var) vrna_unstructured_domain_s.motif_en (C var) vrna_unstructured_domain_s.motif_name (C var) vrna_unstructured_domain_s.motif_size (C var) vrna_unstructured_domain_s.motif_type (C var) vrna_unstructured_domain_s.probs_add (C var) vrna_unstructured_domain_s.probs_get (C var) vrna_unstructured_domain_s.prod_cb (C var) vrna_unstructured_domain_s.uniq_motif_count (C var) vrna_unstructured_domain_s.uniq_motif_size (C var) VRNA_UNUSED (C macro) vrna_urn (C function) VRNA_VERBOSITY_DEFAULT (C macro) VRNA_VERBOSITY_QUIET (C macro)

W

window_size (RNA.fold_compound attribute) (RNA.md attribute) (RNA.md property)

write_parameter_file (C function) write_parameter_file() (in module RNA)

X

X (RNA.COORDINATE attribute), [1] (RNA.COORDINATE property) xrna_plot (C function)

xrna_plot() (in module RNA) XSTR (C macro) xsubi (C var)

Y

Y (RNA.COORDINATE attribute), [1] (RNA.COORDINATE property)

Z

zsc_compute() (RNA.fold_compound method) zsc_compute_raw() (RNA.fold_compound method) zsc_filter_free() (RNA.fold_compound method) zsc_filter_init() (RNA.fold_compound method) zsc_filter_on() (RNA.fold_compound method)

zsc_filter_threshold() (RNA.fold_compound method) zsc_filter_update() (RNA.fold_compound method) zscore_data (RNA.fold_compound attribute) zukersubopt (C function) zukersubopt() (in module RNA) zukersubopt_par (C function)