Index

Symbols

( command line option () command line option (possible values="conjugate_fr", command line option , command line option, [1] --absolute-concentrations Report absolute instead of relative command line option --accessibility-dir=STRING command line option --alignment-mode command line option, [1] --alignmentLength=INT command line option --all_pf[=INT] command line option, [1] --allowFlipping command line option --aln command line option, [1] --aln-EPS-cols=INT command line option, [1], [2] --aln-EPS-ss[=prefix] command line option --aln-EPS[=prefix] command line option --aln-stk[=prefix] command line option, [1] --aln[=prefix] command line option --alphabet=ALPHABET command line option --auto-id command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --backbone-length=FLOAT command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --backtrack-global command line option --backtrack[=<filename>] command line option, [1] --batch command line option, [1], [2], [3] --betaScale=DOUBLE command line option, [1], [2], [3], [4], [5] --binaries command line option --binary command line option --bppmThreshold=cutoff command line option, [1], [2], [3] --canonicalBPonly command line option, [1], [2] --centroid command line option --cfactor=DOUBLE command line option, [1], [2] --circ command line option, [1], [2], [3], [4], [5] --color command line option --commands=filename command line option, [1], [2], [3], [4], [5] --compare=p|m|f|c command line option, [1] --concentrations command line option, [1] --concfile=filename command line option, [1] --constraint command line option, [1], [2] --constraint[=filename] command line option, [1], [2], [3] --continuous-ids command line option --contributions=SHIME command line option --convert-to-bin command line option --covar command line option --csv command line option --csv-delim=delimiter command line option --csv-noheader command line option --cutoff=FLOAT command line option, [1] --dangles=INT command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] --deltaEnergy=range command line option, [1], [2] --deltaEnergyPost=range 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] --direct-redraw command line option --distance=fhwcFHWCP command line option --dos command line option --dump command line option --duplex-distance=INT command line option, [1] --en-only command line option --endgaps command line option, [1] --energy-threshold=DOUBLE Maximal energy difference between the mfe and command line option --energy-threshold=DOUBLE Minimal energy for a duplex to be returned command line option --energyCutoff=DOUBLE command line option --energyModel=INT 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=INT command line option --extend5=INT command line option --extension-cost=INT command line option, [1] --fast-folding=INT command line option, [1] --filename-delim=CHAR command line option, [1], [2], [3], [4], [5], [6], [7], [8] --filename-full command line option, [1], [2], [3], [4], [5], [6] --final=FLOAT command line option --from-RNAplfold=STRING command line option --from-RNAup=STRING 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] --function=mp command line option --gape=ext command line option --gapo=open command line option --gquad command line option, [1], [2], [3], [4], [5], [6], [7], [8] --hashtable-bits=INT command line option --helical-rise=FLOAT 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=CHAR command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-digits=INT command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-prefix=STRING command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-start=LONG 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=<filename> command line option --infile=filename command line option, [1], [2], [3], [4] --initialStepSize=DOUBLE command line option --initialVector=DOUBLE command line option --input-format=C|S|F|M command line option, [1] --input=filename command line option --interaction-length=INT command line option --interaction_first command line option --interaction_pairwise command line option --intermediatePath=STRING Write an output file for each iteration of the command line option --ipoints=ipoints command line option --jobs[=number] command line option, [1], [2], [3], [4], [5], [6] --k-concentration=DOUBLE command line option --layout-type=INT command line option, [1], [2] --logML command line option, [1] --max-energy=INT command line option --maxBPspan=INT command line option, [1], [2], [3], [4], [5], [6], [7] --maxDist1=INT command line option --maxDist2=INT command line option --maximal-duplex-box-length=INT command line option --maximal-snoRNA-duplex-length=INT command line option --maximal-snoRNA-stem-loop-length=INT command line option --maximal-stem-asymmetry=INT command line option --MEA[=gamma] command line option, [1], [2] --mg-concentration=DOUBLE Set the Mg2+ concentration for the Tm command line option --minimal-duplex-box-length=INT command line option --minimal-duplex-stem-energy=INT command line option --minimal-duplex=INT command line option --minimal-loop-energy=INT Minimal Right Duplex Energy. command line option --minimal-lower-stem-energy=INT command line option --minimal-right-duplex=INT command line option --minimal-snoRNA-duplex-length=INT command line option --minimal-snoRNA-stem-loop-length=INT command line option --minimal-total-energy=INT command line option --minimizer=ENUM command line option --minimizerTolerance=DOUBLE command line option --minImprovement=DOUBLE command line option --minStepSize=DOUBLE command line option --mis command line option, [1], [2], [3] --mod-file=STRING command line option, [1], [2], [3], [4] --mode=pmfc command line option --modifications[=STRING] command line option, [1], [2], [3], [4] --motif=SEQUENCE,STRUCTURE,ENERGY command line option --msa command line option, [1] --na-concentration=DOUBLE Set the Na+ concentration for the Tm command line option --neighborhood=<k>:<l> command line option --nfactor=DOUBLE 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=STRING command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --numThreads=INT command line option, [1], [2] --objectiveFunction=INT command line option --old command line option, [1] --opening_energies command line option --outfile[=filename] command line option, [1], [2] --output-format=format-character command line option --output-format=ps|gml|xrna|svg command line option --output=filename command line option --output_directory=STRING Set where the generated figures should be command line option --paramFile=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 --partfunc[=INT] command line option, [1], [2], [3] --pfScale=DOUBLE command line option, [1], [2], [3], [4], [5], [6], [7], [8] --plex_output command line option --post=string command line option --pre=string command line option --print_onthefly command line option --printAlignment[=filename] command line option --probe-concentration=DOUBLE command line option --probe-mode command line option --produce-ps command line option --produce-ps=STRING command line option --query=STRING command line option, [1] --quiet command line option, [1] --repeat[=INT] command line option --ribosum_file=ribosumfile command line option, [1], [2] --ribosum_scoring command line option, [1], [2] --salt=DOUBLE command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --saltInit=DOUBLE command line option, [1], [2], [3], [4] --sampleSize=INT command line option --scale-accessibility=DOUBLE command line option --sci command line option --sequence=STRING command line option --seqw=w command line option --shape=file1,file2 command line option, [1] --shape=filename command line option, [1], [2], [3], [4], [5] --shapeConversion=method command line option, [1], [2], [3], [4], [5] --shapeConversion=STRING command line option --shapeMethod=D[mX][bY] command line option, [1] --shapeMethod=method command line option, [1], [2], [3], [4], [5] --shapiro command line option --silent command line option --sorted command line option, [1], [2] --span=INT command line option --span=size command line option --split-contributions command line option --SS_cons command line option --stepsize=FLOAT command line option --stochBT=INT command line option, [1] --stochBT=number command line option --stochBT_en=INT command line option --stochBT_en=number command line option --subopts=DOUBLE command line option --suffix=STRING command line option --target=STRING command line option, [1] --tauSigmaRatio=DOUBLE command line option --temp=DOUBLE command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] --threshold=DOUBLE command line option --Tmax=t2 command line option --Tmin=t1 command line option --tris-concentration=DOUBLE command line option --ulength=length 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] --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=INT command line option --WindowLength=INT command line option --winsize=size 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-pre-filter command line option --zscore-report-subsumed command line option --zscore[=DOUBLE] 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], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] -F command line option -f command line option, [1], [2], [3], [4], [5], [6] -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], [7] -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] -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] -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]

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) 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) (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.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.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)

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.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 (C function) backtrack_GQuad_IntLoop_comparative (C function) backtrack_GQuad_IntLoop_L (C function) backtrack_GQuad_IntLoop_L_comparative (C function) 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.UIntVector method) beginning of stem loop and command line option, [1] 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) (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.UIntVector method) cast() (RNA.doubleArray method) (RNA.floatArray method) (RNA.intArray method) cdata() (in module RNA) centroid() (in module RNA) (RNA.fold_compound method) circ (C var) (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.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 values="conjugate_fr", ,, [1] --absolute-concentrations Report absolute instead of relative --accessibility-dir=STRING --alignment-mode, [1] --alignmentLength=INT --all_pf[=INT], [1] --allowFlipping --aln, [1] --aln-EPS-cols=INT, [1], [2] --aln-EPS-ss[=prefix] --aln-EPS[=prefix] --aln-stk[=prefix], [1] --aln[=prefix] --alphabet=ALPHABET --auto-id, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --backbone-length=FLOAT, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --backtrack-global --backtrack[=<filename>], [1] --batch, [1], [2], [3] --betaScale=DOUBLE, [1], [2], [3], [4], [5] --binaries --binary --bppmThreshold=cutoff, [1], [2], [3] --canonicalBPonly, [1], [2] --centroid --cfactor=DOUBLE, [1], [2] --circ, [1], [2], [3], [4], [5] --color --commands=filename, [1], [2], [3], [4], [5] --compare=p|m|f|c, [1] --concentrations, [1] --concfile=filename, [1] --constraint, [1], [2] --constraint[=filename], [1], [2], [3] --continuous-ids --contributions=SHIME --convert-to-bin --covar --csv --csv-delim=delimiter --csv-noheader --cutoff=FLOAT, [1] --dangles=INT, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] --deltaEnergy=range, [1], [2] --deltaEnergyPost=range --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] --direct-redraw --distance=fhwcFHWCP --dos --dump --duplex-distance=INT, [1] --en-only --endgaps, [1] --energy-threshold=DOUBLE Maximal energy difference between the mfe and --energy-threshold=DOUBLE Minimal energy for a duplex to be returned --energyCutoff=DOUBLE --energyModel=INT, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] --enforceConstraint, [1], [2], [3] --extend3=INT --extend5=INT --extension-cost=INT, [1] --fast-folding=INT, [1] --filename-delim=CHAR, [1], [2], [3], [4], [5], [6], [7], [8] --filename-full, [1], [2], [3], [4], [5], [6] --final=FLOAT --from-RNAplfold=STRING --from-RNAup=STRING --full-help, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22] --function=mp --gape=ext --gapo=open --gquad, [1], [2], [3], [4], [5], [6], [7], [8] --hashtable-bits=INT --helical-rise=FLOAT, [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=CHAR, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-digits=INT, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-prefix=STRING, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --id-start=LONG, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] --ignoreAncestorIntersections --ignoreExteriorIntersections --ignoreSiblingIntersections --ImFeelingLucky --include_both --infile=<filename> --infile=filename, [1], [2], [3], [4] --initialStepSize=DOUBLE --initialVector=DOUBLE --input-format=C|S|F|M, [1] --input=filename --interaction-length=INT --interaction_first --interaction_pairwise --intermediatePath=STRING Write an output file for each iteration of the --ipoints=ipoints --jobs[=number], [1], [2], [3], [4], [5], [6] --k-concentration=DOUBLE --layout-type=INT, [1], [2] --logML, [1] --max-energy=INT --maxBPspan=INT, [1], [2], [3], [4], [5], [6], [7] --maxDist1=INT --maxDist2=INT --maximal-duplex-box-length=INT --maximal-snoRNA-duplex-length=INT --maximal-snoRNA-stem-loop-length=INT --maximal-stem-asymmetry=INT --MEA[=gamma], [1], [2] --mg-concentration=DOUBLE Set the Mg2+ concentration for the Tm --minimal-duplex-box-length=INT --minimal-duplex-stem-energy=INT --minimal-duplex=INT --minimal-loop-energy=INT Minimal Right Duplex Energy. --minimal-lower-stem-energy=INT --minimal-right-duplex=INT --minimal-snoRNA-duplex-length=INT --minimal-snoRNA-stem-loop-length=INT --minimal-total-energy=INT --minimizer=ENUM --minimizerTolerance=DOUBLE --minImprovement=DOUBLE --minStepSize=DOUBLE --mis, [1], [2], [3] --mod-file=STRING, [1], [2], [3], [4] --mode=pmfc --modifications[=STRING], [1], [2], [3], [4] --motif=SEQUENCE,STRUCTURE,ENERGY --msa, [1] --na-concentration=DOUBLE Set the Na+ concentration for the Tm --neighborhood=<k>:<l> --nfactor=DOUBLE, [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=STRING, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --numThreads=INT, [1], [2] --objectiveFunction=INT --old, [1] --opening_energies --outfile[=filename], [1], [2] --output-format=format-character --output-format=ps|gml|xrna|svg --output=filename --output_directory=STRING Set where the generated figures should be --paramFile=paramfile, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --partfunc --partfunc[=INT], [1], [2], [3] --pfScale=DOUBLE, [1], [2], [3], [4], [5], [6], [7], [8] --plex_output --post=string --pre=string --print_onthefly --printAlignment[=filename] --probe-concentration=DOUBLE --probe-mode --produce-ps --produce-ps=STRING --query=STRING, [1] --quiet, [1] --repeat[=INT] --ribosum_file=ribosumfile, [1], [2] --ribosum_scoring, [1], [2] --salt=DOUBLE, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] --saltInit=DOUBLE, [1], [2], [3], [4] --sampleSize=INT --scale-accessibility=DOUBLE --sci --sequence=STRING --seqw=w --shape=file1,file2, [1] --shape=filename, [1], [2], [3], [4], [5] --shapeConversion=method, [1], [2], [3], [4], [5] --shapeConversion=STRING --shapeMethod=D[mX][bY], [1] --shapeMethod=method, [1], [2], [3], [4], [5] --shapiro --silent --sorted, [1], [2] --span=INT --span=size --split-contributions --SS_cons --stepsize=FLOAT --stochBT=INT, [1] --stochBT=number --stochBT_en=INT --stochBT_en=number --subopts=DOUBLE --suffix=STRING --target=STRING, [1] --tauSigmaRatio=DOUBLE --temp=DOUBLE, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] --threshold=DOUBLE --Tmax=t2 --Tmin=t1 --tris-concentration=DOUBLE --ulength=length, [1] --unordered, [1], [2], [3], [4], [5] --vanilla --verbose, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --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=INT --WindowLength=INT --winsize=size --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-pre-filter --zscore-report-subsumed --zscore[=DOUBLE] --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], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] -E -f, [1], [2], [3], [4], [5], [6] -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], [7] -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] -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] -W -w, [1] -X, [1], [2] -x -y -z, [1], [2] ., [1] ``m`` { {} |, [1] beginning of stem loop and, [1] profiles

commands_apply() (RNA.fold_compound method) compare() (RNA.move method) compute_BPdifferences (C function) compute_bpp (RNA.md attribute) (RNA.md property) compute_probabilities (C function) ConcEnt (C type) 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) (RNA.param property) dangle3_dG (RNA.sc_mod_param attribute) dangle3_dH (RNA.sc_mod_param attribute) dangle5 (RNA.param attribute) (RNA.param property) dangle5_dG (RNA.sc_mod_param attribute) dangle5_dH (RNA.sc_mod_param attribute) dangles (C var) (RNA.md attribute) (RNA.md property) data (RNA.hc attribute) 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) 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) DEPRECATED (C macro) deref_any() (in module RNA) destroy_TwoDfold_variables (C function) 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) duplex_list_t (class in RNA) duplex_subopt() (in module RNA) duplexfold() (in module RNA) DuplexInit (RNA.param attribute) (RNA.param property) duplexT (C struct) 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_ext_stem() (in module RNA) E_ExtLoop (C function) E_ExtLoop() (in module RNA) E_gquad (C function) E_gquad_ali_en (C function) E_GQuad_IntLoop (C function) E_GQuad_IntLoop_comparative (C function) E_GQuad_IntLoop_exhaustive (C function) E_GQuad_IntLoop_L (C function) E_GQuad_IntLoop_L_comparative (C function) 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 (C function) 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.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.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.UIntVector method) energy (RNA.duplex_list_t property) (RNA.SOLUTION property) (RNA.struct_en attribute) (RNA.struct_en property) (RNA.subopt_solution 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.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() (in module RNA) (RNA.fold_compound method) exp_E_ExtLoop (C function) exp_E_ExtLoop() (in module RNA) exp_E_gquad (C function) exp_E_GQuad_IntLoop (C function) exp_E_GQuad_IntLoop_comparative (C function) 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) (RNA.exp_param property) expdangle3 (RNA.exp_param attribute) (RNA.exp_param property) expdangle5 (RNA.exp_param attribute) (RNA.exp_param property) expDuplexInit (RNA.exp_param attribute) (RNA.exp_param property) expgquad (RNA.exp_param attribute) (RNA.exp_param property) expgquadLayerMismatch (RNA.exp_param attribute) (RNA.exp_param property) exphairpin (RNA.exp_param attribute) (RNA.exp_param property) exphex (RNA.exp_param attribute) (RNA.exp_param property) expint11 (RNA.exp_param attribute) (RNA.exp_param property) expint21 (RNA.exp_param attribute) (RNA.exp_param property) expint22 (RNA.exp_param attribute) (RNA.exp_param property) expinternal (RNA.exp_param attribute) (RNA.exp_param property) expmismatch1nI (RNA.exp_param attribute) (RNA.exp_param property) expmismatch23I (RNA.exp_param attribute) (RNA.exp_param property) expmismatchExt (RNA.exp_param attribute) (RNA.exp_param property) expmismatchH (RNA.exp_param attribute) (RNA.exp_param property) expmismatchI (RNA.exp_param attribute) (RNA.exp_param property) expmismatchM (RNA.exp_param attribute) (RNA.exp_param property) expMLbase (RNA.exp_param attribute) (RNA.exp_param property) (RNA.mx_pf property) expMLclosing (RNA.exp_param attribute) (RNA.exp_param property) expMLintern (RNA.exp_param attribute) (RNA.exp_param property) expMultipleCA (RNA.exp_param attribute) (RNA.exp_param property) expMultipleCB (RNA.exp_param attribute) (RNA.exp_param property) expninio (RNA.exp_param attribute) (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) (RNA.exp_param property) expSaltStack (RNA.exp_param attribute) (RNA.exp_param property) expstack (RNA.exp_param attribute) (RNA.exp_param property) expTermAU (RNA.exp_param attribute) (RNA.exp_param property) exptetra (RNA.exp_param attribute) (RNA.exp_param property) exptri (RNA.exp_param attribute) (RNA.exp_param property) expTriloop (RNA.exp_param attribute) (RNA.exp_param property) expTripleC (RNA.exp_param attribute) (RNA.exp_param property) extract_record_rest_structure (C function) extract_record_rest_structure() (in module RNA)

F

f (RNA.hc attribute) f3 (RNA.mx_mfe property) f5 (RNA.mx_mfe property) F_monomer (C var) fallback (RNA.sc_mod_param attribute) fallback_encoding (RNA.sc_mod_param attribute) 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) 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_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) fold (C function) fold() (in module RNA)

fold_compound (class in RNA) fold_par (C function) folden (C type) 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) 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.UIntVector method)

G

G (RNA.mx_pf property) 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.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 (C function) get_gquad_count (C function) get_gquad_L_matrix (C function) get_gquad_layer_count (C function) get_gquad_matrix (C function) get_gquad_pattern_exhaustive (C function) get_gquad_pattern_mfe (C function)

get_gquad_pattern_mfe_ali (C function) get_gquad_pattern_pf (C function) get_gquad_pf_matrix (C function) get_gquad_pf_matrix_comparative (C function) 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_pr (C function) get_plist_gquad_from_pr_max (C function) 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) ggg (RNA.mx_mfe property) give_up (C var) gmlRNA (C function) gmlRNA() (in module RNA) gquad (C var) (RNA.md attribute) (RNA.md property) (RNA.param attribute) (RNA.param property) gquadLayerMismatch (RNA.param attribute) (RNA.param property) gquadLayerMismatchMax (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (RNA.param property)

H

hairpin (RNA.param attribute) (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_from_db() (RNA.fold_compound method) hc_add_up() (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) (RNA.param property) Hexaloops (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (RNA.param property) hx (class in RNA) hx_from_ptable() (in module RNA)

I

i (RNA.basepair property) (RNA.duplex_list_t property) (RNA.ep attribute) (RNA.ep property) id (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (RNA.param property) iindx (RNA.fold_compound attribute) (RNA.fold_compound property) incr() (RNA.SwigPyIterator method) init_co_pf_fold (C function) 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.UIntVector method) int11 (RNA.param attribute) (RNA.param property) int21 (RNA.param attribute) (RNA.param property) int22 (RNA.param attribute) (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) (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.UIntVector method)

J

j (RNA.basepair property) (RNA.duplex_list_t property) (RNA.ep attribute) (RNA.ep property)

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

K

kT (RNA.exp_param attribute) (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) letter_structure (C function) Lfold (C function) Lfold() (in module RNA) Lfold_cb() (in module RNA) Lfoldz (C function) Lfoldz() (in module RNA) Lfoldz_cb() (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) (RNA.exp_param property) (RNA.param attribute) (RNA.param property)

M

Make_bp_profile() (in module RNA) Make_bp_profile_bppm() (in module RNA) make_loop_index() (in module RNA) make_loop_index_pt (C function) make_pair_table (C function) make_pair_table_pk (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) 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) maxmimum_matching() (RNA.fold_compound method) md (class in RNA) 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) (RNA.param property) mismatch23I (RNA.param attribute) (RNA.param property) mismatch_dG (RNA.sc_mod_param attribute) mismatch_dH (RNA.sc_mod_param attribute) mismatchExt (RNA.param attribute) (RNA.param property) mismatchH (RNA.param attribute) (RNA.param property) mismatchI (RNA.param attribute) (RNA.param property) mismatchM (RNA.param attribute) (RNA.param property) MLbase (RNA.param attribute) (RNA.param property) MLclosing (RNA.param attribute) (RNA.param property) MLintern (RNA.param attribute) (RNA.param property) mm1 (RNA.fold_compound attribute) mm2 (RNA.fold_compound attribute) model_details (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (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) (RNA.param property) MultipleCB (RNA.param attribute) (RNA.param property) mx (RNA.hc attribute) (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) (RNA.hc property) n_seq (RNA.fold_compound attribute) name (RNA.sc_mod_param attribute) 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) next() (RNA.SwigPyIterator method) (RNA.var_array_Iterator method) ninio (RNA.param attribute) (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) nucleotides (RNA.fold_compound attribute) num_ptypes (RNA.sc_mod_param attribute)

O

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) option_string (C function) option_string() (RNA.md method)

P

p (RNA.ep attribute) (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) pairing_partners (RNA.sc_mod_param attribute) pairing_partners_encoding (RNA.sc_mod_param attribute) pairs (C var) param (class in RNA) param_file (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (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_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) (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_dp_EPS() (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.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.UIntVector method) pos_3 (RNA.move attribute) (RNA.move property) pos_5 (RNA.move attribute) (RNA.move property) positional_entropy() (RNA.fold_compound method) pr_energy() (RNA.fold_compound method) pr_structure() (RNA.fold_compound method) previous() (RNA.SwigPyIterator method) print_bppm() (in module RNA) print_energy (C var) print_tree() (in module RNA) PRIVATE (C macro) 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) 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) 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.UIntVector method) putoutpU_prob (C function) putoutpU_prob_bin (C function)

Q

q (RNA.mx_pf property) q1k (RNA.mx_pf property) qb (RNA.mx_pf 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.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.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.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.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) (RNA.exp_param property) saltDPXInit (RNA.md attribute) (RNA.md property) SaltDPXInit (RNA.param attribute) (RNA.param property) saltDPXInitFact (RNA.md attribute) (RNA.md property) SaltLoop (RNA.param attribute) (RNA.param property) SaltLoopDbl (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (RNA.param property) SaltMLbase (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (RNA.param property) SaltMLclosing (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (RNA.param property) SaltMLintern (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (RNA.param property) saltMLLower (RNA.md attribute) (RNA.md property) saltMLUpper (RNA.md attribute) (RNA.md property) SaltStack (RNA.param attribute) (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_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_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) 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.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) (RNA.param property) stack_dG (RNA.sc_mod_param attribute) stack_dH (RNA.sc_mod_param attribute) stackProb (C function) start (RNA.hx property) stat_cb (RNA.fold_compound attribute) state (RNA.hc attribute) 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.SOLUTION property) (RNA.struct_en attribute) (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.UIntVector method) SwigPyIterator (class in RNA) symbolset (C var)

T

temperature (C var) (RNA.exp_param attribute) (RNA.exp_param property) (RNA.heat_capacity_result property) (RNA.md attribute) (RNA.md property) (RNA.param attribute) (RNA.param property) terminal_dG (RNA.sc_mod_param attribute) terminal_dH (RNA.sc_mod_param attribute) TerminalAU (RNA.param attribute) (RNA.param property) tetra_loop (C var) Tetraloop_E (RNA.param attribute) (RNA.param property) Tetraloops (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (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.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.sc_mod_param 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.UIntVector property) (RNA.varArrayChar property) (RNA.varArrayFLTorDBL property) (RNA.varArrayInt property) (RNA.varArrayMove property) (RNA.varArrayShort property) (RNA.varArrayUChar property) (RNA.varArrayUInt 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) (RNA.param property) Triloops (RNA.exp_param attribute) (RNA.exp_param property) (RNA.param attribute) (RNA.param property) TripleC (RNA.param attribute) (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) (RNA.ep property) (RNA.fold_compound attribute) (RNA.fold_compound property) (RNA.hc attribute) (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) 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) unmodified_encoding (RNA.sc_mod_param attribute) unpack_structure (C function) unpack_structure() (in module RNA) unpaired (C var)

unweight (C function) unweight() (in module RNA) up3 (RNA.hx property) up5 (RNA.hx property) up_ext (RNA.hc attribute) (RNA.hc property) up_hp (RNA.hc attribute) (RNA.hc property) up_int (RNA.hc attribute) (RNA.hc property) up_ml (RNA.hc attribute) (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), [1] 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_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_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), [1] vrna_backtrack5_TwoD (C function) vrna_backtrack_from_intervals (C function), [1] vrna_backtrack_window (C function), [1] vrna_basename (C function) vrna_basepair_s (C struct) vrna_basepair_s.i (C var) vrna_basepair_s.j (C var) vrna_basepair_t (C type) vrna_boustrophedon (C function) vrna_boustrophedon_pos (C function) vrna_bp_distance (C function) vrna_bp_distance_pt (C function) vrna_bp_stack_s (C struct) vrna_bp_stack_s.i (C var) vrna_bp_stack_s.j (C var) vrna_bp_stack_t (C type) vrna_bpp_symbol (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_ext_loop_f3 (C function) vrna_BT_ext_loop_f3_pp (C function) vrna_BT_ext_loop_f5 (C function) vrna_BT_gquad_int (C function) vrna_BT_gquad_mfe (C function) vrna_BT_hp_loop (C function) vrna_BT_int_loop (C function) vrna_BT_mb_loop (C function) vrna_BT_mb_loop_split (C function) vrna_BT_stack (C function) vrna_C11_features (C function) vrna_centroid (C function) vrna_centroid_from_plist (C function) vrna_centroid_from_probs (C function) vrna_circalifold (C function), [1] vrna_circfold (C function), [1] 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), [1] vrna_color_s (C struct) vrna_color_s.bri (C var) vrna_color_s.hue (C var) vrna_color_s.sat (C var) vrna_color_t (C type) vrna_commands_apply (C function) vrna_commands_free (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_s (C struct) vrna_cpair_s.hue (C var) vrna_cpair_s.i (C var) vrna_cpair_s.j (C var) vrna_cpair_s.mfe (C var) vrna_cpair_s.p (C var) vrna_cpair_s.sat (C var) vrna_cpair_s.type (C var) 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_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_data_linear_s (C struct) vrna_data_linear_s.color (C var) vrna_data_linear_s.position (C var) vrna_data_linear_s.value (C var) vrna_db_flatten (C function) vrna_db_flatten_to (C function) vrna_db_from_bp_stack (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_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_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_hp_loop (C function) vrna_E_int_loop (C function) vrna_E_mb_loop_fast (C function) vrna_E_mb_loop_stack (C function) vrna_E_ml_stems_fast (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_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_hp_loop (C function) vrna_eval_int_loop (C function) 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_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_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_hp_loop (C function) vrna_exp_E_int_loop (C function) vrna_exp_E_interior_loop (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_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_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_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_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), [1] 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_plist_gquad_from_pr (C function) vrna_get_plist_gquad_from_pr_max (C function) vrna_get_ptype (C function) vrna_get_ptype_md (C function) vrna_get_ptype_window (C function) 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_gquad_mx_local_update (C function) vrna_gr_aux_s (C struct) vrna_gr_aux_s.cb_aux (C var) vrna_gr_aux_s.cb_aux_c (C var) vrna_gr_aux_s.cb_aux_exp (C var) vrna_gr_aux_s.cb_aux_exp_c (C var) vrna_gr_aux_s.cb_aux_exp_f (C var) vrna_gr_aux_s.cb_aux_exp_m (C var) vrna_gr_aux_s.cb_aux_exp_m1 (C var) vrna_gr_aux_s.cb_aux_f (C var) vrna_gr_aux_s.cb_aux_m (C var) vrna_gr_aux_s.cb_aux_m1 (C var) vrna_gr_aux_s.cb_proc (C var) vrna_gr_aux_s.data (C var) vrna_gr_aux_s.free_data (C var) vrna_gr_aux_t (C type) vrna_gr_reset (C function) vrna_gr_set_aux (C function) vrna_gr_set_aux_c (C function) vrna_gr_set_aux_exp (C function) vrna_gr_set_aux_exp_c (C function) vrna_gr_set_aux_exp_f (C function) vrna_gr_set_aux_exp_m (C function) vrna_gr_set_aux_exp_m1 (C function) vrna_gr_set_aux_f (C function) vrna_gr_set_aux_m (C function) vrna_gr_set_aux_m1 (C function) vrna_gr_set_cond (C function) vrna_gr_set_data (C function) vrna_grammar_cond_f (C type) vrna_grammar_data_free_f (C type) vrna_grammar_rule_f (C type) vrna_grammar_rule_f_aux (C type) vrna_grammar_rule_f_aux_exp (C type) vrna_grammar_rule_f_exp (C type) 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_from_db (C function) vrna_hc_add_up (C function) vrna_hc_add_up_batch (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.[anonymous] (C var) 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_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_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.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), [1] vrna_mfe_dimer (C function), [1] 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_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_mfe_add (C function) 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.fM2 (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 (C var) vrna_mx_mfe_s.ggg_local (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 (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.qm2 (C var) vrna_mx_pf_s.qm2_local (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_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_from_probs (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_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.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_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_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_bp (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_zarringhalam (C function) vrna_sc_add_up (C function) vrna_sc_bt_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_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_bp (C function) vrna_sc_set_up (C function) vrna_sc_SHAPE_to_pr (C function) vrna_sc_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_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_make (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_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) (RNA.COORDINATE property) xrna_plot (C function)

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

Y

Y (RNA.COORDINATE attribute) (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)