\begin{theindex}

  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h}, \hyperpage{153}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h}, \hyperpage{155}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h}, \hyperpage{198}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/Lfold.h}, \hyperpage{190}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/MEA.h}, \hyperpage{200}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS\_\discretionary {-}{}{}dot.h}, \hyperpage{218}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/RNAstruct.h}, \hyperpage{224}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}, \hyperpage{156}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h}, \hyperpage{159}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\discretionary {-}{}{}epars.h}, \hyperpage{161}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\discretionary {-}{}{}structures.h}, \hyperpage{162}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/duplex.h}, \hyperpage{167}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/edit\_\discretionary {-}{}{}cost.h}, \hyperpage{168}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h}, \hyperpage{171}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h}, \hyperpage{173}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold\_\discretionary {-}{}{}vars.h}, \hyperpage{180}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h}, \hyperpage{186}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/inverse.h}, \hyperpage{189}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/loop\_\discretionary {-}{}{}energies.h}, \hyperpage{191}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/mm.h}, \hyperpage{201}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/naview.h}, \hyperpage{202}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h}, \hyperpage{203}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func.h}, \hyperpage{205}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{208}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h}, \hyperpage{211}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{212}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h}, \hyperpage{216}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/read\_\discretionary {-}{}{}epars.h}, \hyperpage{223}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/stringdist.h}, \hyperpage{229}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/subopt.h}, \hyperpage{231}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h}, \hyperpage{232}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/utils.h}, \hyperpage{234}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}epars.h}, \hyperpage{250}
  \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}intloops.h}, \hyperpage{251}

  \indexspace

  \item {add\_\discretionary {-}{}{}root}
    \subitem {RNAstruct.h}, \hyperpage{226}
  \item {alifold}
    \subitem {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{71}
  \item {alifold.h}
    \subitem {update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}, \hyperpage{158}
  \item {aliLfold}
    \subitem {local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}, \hyperpage{81}
  \item {alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
    \subitem {utils.h}, \hyperpage{246}
  \item {alipbacktrack}
    \subitem {consensus\_\discretionary {-}{}{}stochbt}, \hyperpage{75}
  \item {alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}
    \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{74}
  \item {alipf\_\discretionary {-}{}{}fold}
    \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{73}
  \item {alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
    \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{73}
  \item {aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
  \item {alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}
    \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{68}
  \item {alpha}
    \subitem {pf\_\discretionary {-}{}{}paramT}, \hyperpage{134}
  \item {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}
    \subitem {fold.h}, \hyperpage{177}
  \item {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}

  \indexspace

  \item {b2C}
    \subitem {RNAstruct.h}, \hyperpage{225}
  \item {b2HIT}
    \subitem {RNAstruct.h}, \hyperpage{225}
  \item {b2Shapiro}
    \subitem {RNAstruct.h}, \hyperpage{226}
  \item {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop}
    \subitem {gquad.h}, \hyperpage{187}
  \item {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L}
    \subitem {gquad.h}, \hyperpage{187}
  \item {backtrack\_\discretionary {-}{}{}type}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{185}
  \item {base\_\discretionary {-}{}{}pair}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
  \item {bondT}, \hyperpage{111}
  \item {bondTEn}, \hyperpage{112}
  \item {BONUS}
    \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}

  \indexspace

  \item {Calculate Partition Functions of a Distance Based Partitioning}, \hyperpage{104}
  \item {Calculate Secondary Structures of two RNAs upon Dimerization}, \hyperpage{54}
  \item {Calculating MFE representatives of a Distance Based Partitioning}, \hyperpage{101}
  \item {Calculating Minimum Free Energy (MFE) Structures}, \hyperpage{33}
  \item {Calculating Partition Functions and Pair Probabilities}, \hyperpage{37}
  \item {centroid}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
  \item {centroid\_\discretionary {-}{}{}fold}
    \subitem {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}, \hyperpage{46}
    \subitem {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}, \hyperpage{46}
  \item {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, \hyperpage{82}
  \item {circalifold}
    \subitem {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{71}
  \item {circfold}
    \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{35}
  \item {Classified Dynamic Programming}, \hyperpage{99}
  \item {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{59}
  \item {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
    \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{59}
  \item {cofold}
    \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{55}
  \item {cofold.h}
    \subitem {get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}, \hyperpage{160}
    \subitem {initialize\_\discretionary {-}{}{}cofold}, \hyperpage{160}
  \item {cofoldF}, \hyperpage{113}
  \item {Compute the centroid structure}, \hyperpage{46}
  \item {Compute the Density of States}, \hyperpage{109}
  \item {Compute the structure with maximum expected accuracy (MEA)}, \hyperpage{45}
  \item {compute\_\discretionary {-}{}{}probabilities}
    \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
  \item {ConcEnt}, \hyperpage{114}
  \item {consensus\_\discretionary {-}{}{}fold}
    \subitem {alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}, \hyperpage{68}
    \subitem {cv\_\discretionary {-}{}{}fact}, \hyperpage{70}
    \subitem {encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}, \hyperpage{68}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}, \hyperpage{67}
    \subitem {free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}, \hyperpage{69}
    \subitem {get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}, \hyperpage{69}
    \subitem {get\_\discretionary {-}{}{}mpi}, \hyperpage{67}
    \subitem {nc\_\discretionary {-}{}{}fact}, \hyperpage{70}
  \item {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}
    \subitem {alifold}, \hyperpage{71}
    \subitem {circalifold}, \hyperpage{71}
  \item {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}, \hyperpage{74}
    \subitem {alipf\_\discretionary {-}{}{}fold}, \hyperpage{73}
    \subitem {alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{73}
    \subitem {export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}, \hyperpage{74}
  \item {consensus\_\discretionary {-}{}{}stochbt}
    \subitem {alipbacktrack}, \hyperpage{75}
  \item {constrain}, \hyperpage{115}
  \item {constrain\_\discretionary {-}{}{}ptypes}
    \subitem {utils.h}, \hyperpage{248}
  \item {convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
  \item {Converting energy parameter files}, \hyperpage{88}
  \item {COORDINATE}, \hyperpage{116}
  \item {copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
    \subitem {utils.h}, \hyperpage{246}
  \item {cost\_\discretionary {-}{}{}matrix}
    \subitem {dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
  \item {cpair}, \hyperpage{117}
  \item {cut\_\discretionary {-}{}{}point}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
  \item {cv\_\discretionary {-}{}{}fact}
    \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{70}

  \indexspace

  \item {dangles}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
    \subitem {model\_\discretionary {-}{}{}detailsT}, \hyperpage{126}
  \item {density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}
    \subitem {dos}, \hyperpage{109}
  \item {destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
  \item {destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
  \item {dist\_\discretionary {-}{}{}vars.h}
    \subitem {cost\_\discretionary {-}{}{}matrix}, \hyperpage{165}
    \subitem {edit\_\discretionary {-}{}{}backtrack}, \hyperpage{165}
  \item {Distance based partitioning of the Secondary Structure Space}, \hyperpage{100}
  \item {do\_\discretionary {-}{}{}backtrack}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
  \item {dos}
    \subitem {density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}, \hyperpage{109}
  \item {duplexT}, \hyperpage{118}
  \item {dupVar}, \hyperpage{119}

  \indexspace

  \item {E\_\discretionary {-}{}{}Hairpin}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{193}
  \item {E\_\discretionary {-}{}{}IntLoop}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{192}
  \item {E\_\discretionary {-}{}{}Stem}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{194}
  \item {edit\_\discretionary {-}{}{}backtrack}
    \subitem {dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
  \item {encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}
    \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{68}
  \item {Energy evaluation}, \hyperpage{93}
  \item {energy\_\discretionary {-}{}{}const.h}
    \subitem {BONUS}, \hyperpage{170}
    \subitem {FORBIDDEN}, \hyperpage{169}
    \subitem {GASCONST}, \hyperpage{169}
    \subitem {INF}, \hyperpage{169}
    \subitem {K0}, \hyperpage{169}
    \subitem {MAXLOOP}, \hyperpage{170}
    \subitem {NBPAIRS}, \hyperpage{170}
    \subitem {TURN}, \hyperpage{170}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}
    \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{67}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}
    \subitem {fold.h}, \hyperpage{179}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}
    \subitem {eval}, \hyperpage{95}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}
    \subitem {eval}, \hyperpage{94}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}
    \subitem {fold.h}, \hyperpage{175}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}
    \subitem {fold.h}, \hyperpage{176}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}
    \subitem {fold.h}, \hyperpage{177}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}
    \subitem {eval}, \hyperpage{94}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}
    \subitem {fold.h}, \hyperpage{178}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}
    \subitem {eval}, \hyperpage{96}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}
    \subitem {eval}, \hyperpage{94}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}
    \subitem {eval}, \hyperpage{95}
  \item {energy\_\discretionary {-}{}{}parameters}
    \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}, \hyperpage{84}
    \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}, \hyperpage{84}
    \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}, \hyperpage{83}
    \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}, \hyperpage{83}
    \subitem {scale\_\discretionary {-}{}{}parameters}, \hyperpage{83}
  \item {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}
    \subitem {convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{91}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}, \hyperpage{91}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}, \hyperpage{91}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}, \hyperpage{90}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}, \hyperpage{89}
    \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}, \hyperpage{90}
  \item {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}
    \subitem {read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{86}
    \subitem {write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{86}
  \item {energy\_\discretionary {-}{}{}set}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
  \item {Enumerating Suboptimal Structures}, \hyperpage{48}
  \item {eval}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}, \hyperpage{95}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}, \hyperpage{94}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}, \hyperpage{94}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}, \hyperpage{96}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}, \hyperpage{94}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}, \hyperpage{95}
  \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{195}
  \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{196}
  \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{195}
  \item {expand\_\discretionary {-}{}{}Full}
    \subitem {RNAstruct.h}, \hyperpage{226}
  \item {expand\_\discretionary {-}{}{}Shapiro}
    \subitem {RNAstruct.h}, \hyperpage{226}
  \item {expHairpinEnergy}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
  \item {expLoopEnergy}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
  \item {export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}
    \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{74}
  \item {export\_\discretionary {-}{}{}bppm}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}
  \item {export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}
    \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{60}
  \item {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}
    \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{56}
  \item {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}
    \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{56}

  \indexspace

  \item {FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}
    \subitem {utils.h}, \hyperpage{240}
  \item {FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}
    \subitem {utils.h}, \hyperpage{240}
  \item {final\_\discretionary {-}{}{}cost}
    \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
  \item {find\_\discretionary {-}{}{}saddle}
    \subitem {findpath.h}, \hyperpage{171}
  \item {findpath.h}
    \subitem {find\_\discretionary {-}{}{}saddle}, \hyperpage{171}
    \subitem {free\_\discretionary {-}{}{}path}, \hyperpage{172}
    \subitem {get\_\discretionary {-}{}{}path}, \hyperpage{172}
  \item {fold}
    \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{35}
  \item {fold.h}
    \subitem {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}, \hyperpage{177}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}, \hyperpage{179}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}, \hyperpage{175}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}, \hyperpage{176}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}, \hyperpage{177}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}, \hyperpage{178}
    \subitem {HairpinE}, \hyperpage{177}
    \subitem {initialize\_\discretionary {-}{}{}fold}, \hyperpage{177}
    \subitem {loop\_\discretionary {-}{}{}energy}, \hyperpage{176}
    \subitem {LoopEnergy}, \hyperpage{177}
    \subitem {parenthesis\_\discretionary {-}{}{}structure}, \hyperpage{175}
    \subitem {parenthesis\_\discretionary {-}{}{}zuker}, \hyperpage{175}
  \item {fold\_\discretionary {-}{}{}par}
    \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{34}
  \item {fold\_\discretionary {-}{}{}vars.h}
    \subitem {backtrack\_\discretionary {-}{}{}type}, \hyperpage{185}
    \subitem {base\_\discretionary {-}{}{}pair}, \hyperpage{184}
    \subitem {cut\_\discretionary {-}{}{}point}, \hyperpage{183}
    \subitem {dangles}, \hyperpage{182}
    \subitem {do\_\discretionary {-}{}{}backtrack}, \hyperpage{184}
    \subitem {energy\_\discretionary {-}{}{}set}, \hyperpage{183}
    \subitem {iindx}, \hyperpage{184}
    \subitem {james\_\discretionary {-}{}{}rule}, \hyperpage{183}
    \subitem {logML}, \hyperpage{183}
    \subitem {noLonelyPairs}, \hyperpage{182}
    \subitem {nonstandards}, \hyperpage{183}
    \subitem {oldAliEn}, \hyperpage{183}
    \subitem {pf\_\discretionary {-}{}{}scale}, \hyperpage{184}
    \subitem {pr}, \hyperpage{184}
    \subitem {ribo}, \hyperpage{183}
    \subitem {RibosumFile}, \hyperpage{183}
    \subitem {set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}, \hyperpage{182}
    \subitem {temperature}, \hyperpage{183}
    \subitem {tetra\_\discretionary {-}{}{}loop}, \hyperpage{183}
  \item {folden}, \hyperpage{120}
  \item {FORBIDDEN}
    \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
  \item {free\_\discretionary {-}{}{}path}
    \subitem {findpath.h}, \hyperpage{172}
  \item {free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{41}
  \item {free\_\discretionary {-}{}{}profile}
    \subitem {profiledist.h}, \hyperpage{217}
  \item {free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}
    \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{69}
  \item {free\_\discretionary {-}{}{}tree}
    \subitem {treedist.h}, \hyperpage{233}

  \indexspace

  \item {GASCONST}
    \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
  \item {get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}
    \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{69}
  \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}
    \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{84}
  \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}
    \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{84}
  \item {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}
    \subitem {centroid\_\discretionary {-}{}{}fold}, \hyperpage{46}
  \item {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}
    \subitem {centroid\_\discretionary {-}{}{}fold}, \hyperpage{46}
  \item {get\_\discretionary {-}{}{}concentrations}
    \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
  \item {get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix}
    \subitem {gquad.h}, \hyperpage{186}
  \item {get\_\discretionary {-}{}{}iindx}
    \subitem {utils.h}, \hyperpage{248}
  \item {get\_\discretionary {-}{}{}indx}
    \subitem {utils.h}, \hyperpage{248}
  \item {get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}
    \subitem {utils.h}, \hyperpage{243}
  \item {get\_\discretionary {-}{}{}line}
    \subitem {utils.h}, \hyperpage{243}
  \item {get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}
    \subitem {cofold.h}, \hyperpage{160}
  \item {get\_\discretionary {-}{}{}mpi}
    \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{67}
  \item {get\_\discretionary {-}{}{}path}
    \subitem {findpath.h}, \hyperpage{172}
  \item {get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
  \item {get\_\discretionary {-}{}{}plist}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{209}
  \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}
    \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
  \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}
    \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
  \item {get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
  \item {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
  \item {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
  \item {give\_\discretionary {-}{}{}up}
    \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
  \item {gmlRNA}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
  \item {gquad.h}
    \subitem {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop}, \hyperpage{187}
    \subitem {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L}, \hyperpage{187}
    \subitem {get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix}, \hyperpage{186}
    \subitem {parse\_\discretionary {-}{}{}gquad}, \hyperpage{187}

  \indexspace

  \item {HairpinE}
    \subitem {fold.h}, \hyperpage{177}
  \item {hamming}
    \subitem {utils.h}, \hyperpage{242}
  \item {hamming\_\discretionary {-}{}{}bound}
    \subitem {utils.h}, \hyperpage{242}

  \indexspace

  \item {iindx}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
  \item {INF}
    \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
  \item {init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{209}
  \item {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
  \item {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}
    \subitem {LPfold.h}, \hyperpage{199}
  \item {initialize\_\discretionary {-}{}{}cofold}
    \subitem {cofold.h}, \hyperpage{160}
  \item {initialize\_\discretionary {-}{}{}fold}
    \subitem {fold.h}, \hyperpage{177}
  \item {int\_\discretionary {-}{}{}urn}
    \subitem {utils.h}, \hyperpage{241}
  \item {interact}, \hyperpage{121}
  \item {intermediate\_\discretionary {-}{}{}t}, \hyperpage{122}
  \item {INTERVAL}, \hyperpage{123}
  \item {inv\_\discretionary {-}{}{}verbose}
    \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
  \item {inverse\_\discretionary {-}{}{}fold}
    \subitem {final\_\discretionary {-}{}{}cost}, \hyperpage{98}
    \subitem {give\_\discretionary {-}{}{}up}, \hyperpage{98}
    \subitem {inv\_\discretionary {-}{}{}verbose}, \hyperpage{98}
    \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{97}
    \subitem {inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{98}
    \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{97}
  \item {inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}

  \indexspace

  \item {james\_\discretionary {-}{}{}rule}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}

  \indexspace

  \item {K0}
    \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
  \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}
    \subitem {destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}, \hyperpage{102}
    \subitem {get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}, \hyperpage{102}
    \subitem {TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}, \hyperpage{103}
    \subitem {TwoDfoldList}, \hyperpage{102}
  \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}
    \subitem {destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}, \hyperpage{105}
    \subitem {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}, \hyperpage{105}
    \subitem {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}, \hyperpage{105}
    \subitem {TwoDpfoldList}, \hyperpage{106}
  \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}
    \subitem {TwoDpfold\_\discretionary {-}{}{}pbacktrack}, \hyperpage{107}
    \subitem {TwoDpfold\_\discretionary {-}{}{}pbacktrack5}, \hyperpage{108}

  \indexspace

  \item {Lfold}
    \subitem {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{77}
  \item {Lfoldz}
    \subitem {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{77}
  \item {LIST}, \hyperpage{124}
  \item {Local MFE consensus structures for Sequence Alignments}, \hyperpage{81}
  \item {Local MFE structure Prediction and Z-\/scores}, \hyperpage{77}
  \item {local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}
    \subitem {aliLfold}, \hyperpage{81}
  \item {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}
    \subitem {Lfold}, \hyperpage{77}
    \subitem {Lfoldz}, \hyperpage{77}
  \item {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {pfl\_\discretionary {-}{}{}fold}, \hyperpage{78}
    \subitem {putoutpU\_\discretionary {-}{}{}prob}, \hyperpage{79}
    \subitem {putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}, \hyperpage{79}
    \subitem {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}, \hyperpage{78}
  \item {logML}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
  \item {loop\_\discretionary {-}{}{}energies.h}
    \subitem {E\_\discretionary {-}{}{}Hairpin}, \hyperpage{193}
    \subitem {E\_\discretionary {-}{}{}IntLoop}, \hyperpage{192}
    \subitem {E\_\discretionary {-}{}{}Stem}, \hyperpage{194}
    \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}, \hyperpage{195}
    \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}, \hyperpage{196}
    \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}, \hyperpage{195}
  \item {loop\_\discretionary {-}{}{}energy}
    \subitem {fold.h}, \hyperpage{176}
  \item {LoopEnergy}
    \subitem {fold.h}, \hyperpage{177}
  \item {LPfold.h}
    \subitem {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}, \hyperpage{199}
  \item {LST\_\discretionary {-}{}{}BUCKET}, \hyperpage{125}

  \indexspace

  \item {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}
    \subitem {profiledist.h}, \hyperpage{217}
  \item {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}
    \subitem {profiledist.h}, \hyperpage{216}
  \item {make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt}
    \subitem {utils.h}, \hyperpage{246}
  \item {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
    \subitem {utils.h}, \hyperpage{246}
  \item {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}
    \subitem {utils.h}, \hyperpage{246}
  \item {Make\_\discretionary {-}{}{}swString}
    \subitem {stringdist.h}, \hyperpage{229}
  \item {make\_\discretionary {-}{}{}tree}
    \subitem {treedist.h}, \hyperpage{232}
  \item {MAX2}
    \subitem {utils.h}, \hyperpage{239}
  \item {MAX3}
    \subitem {utils.h}, \hyperpage{240}
  \item {MAXLOOP}
    \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
  \item {MEA}
    \subitem {MEA.h}, \hyperpage{200}
  \item {MEA.h}
    \subitem {MEA}, \hyperpage{200}
  \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
  \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
  \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
  \item {MFE Consensus Structures for Sequence Alignment(s)}, \hyperpage{71}
  \item {MFE Structures of two hybridized Sequences}, \hyperpage{55}
  \item {mfe\_\discretionary {-}{}{}cofold}
    \subitem {cofold}, \hyperpage{55}
    \subitem {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}, \hyperpage{56}
    \subitem {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}, \hyperpage{56}
  \item {mfe\_\discretionary {-}{}{}fold}
    \subitem {circfold}, \hyperpage{35}
    \subitem {fold}, \hyperpage{35}
    \subitem {fold\_\discretionary {-}{}{}par}, \hyperpage{34}
  \item {MIN2}
    \subitem {utils.h}, \hyperpage{239}
  \item {MIN3}
    \subitem {utils.h}, \hyperpage{239}
  \item {model\_\discretionary {-}{}{}detailsT}, \hyperpage{126}
    \subitem {dangles}, \hyperpage{126}
  \item {move\_\discretionary {-}{}{}t}, \hyperpage{128}

  \indexspace

  \item {NBPAIRS}
    \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
  \item {nc\_\discretionary {-}{}{}fact}
    \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{70}
  \item {noLonelyPairs}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
  \item {nonstandards}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
  \item {nrerror}
    \subitem {utils.h}, \hyperpage{241}

  \indexspace

  \item {oldAliEn}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}

  \indexspace

  \item {pack\_\discretionary {-}{}{}structure}
    \subitem {utils.h}, \hyperpage{245}
  \item {PAIR}, \hyperpage{129}
  \item {pair\_\discretionary {-}{}{}info}, \hyperpage{130}
  \item {pairpro}, \hyperpage{131}
  \item {paramT}, \hyperpage{132}
  \item {parenthesis\_\discretionary {-}{}{}structure}
    \subitem {fold.h}, \hyperpage{175}
  \item {parenthesis\_\discretionary {-}{}{}zuker}
    \subitem {fold.h}, \hyperpage{175}
  \item {parse\_\discretionary {-}{}{}gquad}
    \subitem {gquad.h}, \hyperpage{187}
  \item {parse\_\discretionary {-}{}{}structure}
    \subitem {RNAstruct.h}, \hyperpage{227}
  \item {Parsing and Comparing -\/ Functions to Manipulate Structures}, \hyperpage{110}
  \item {part\_\discretionary {-}{}{}func.h}
    \subitem {centroid}, \hyperpage{207}
    \subitem {expHairpinEnergy}, \hyperpage{207}
    \subitem {expLoopEnergy}, \hyperpage{207}
    \subitem {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{207}
    \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}, \hyperpage{207}
  \item {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}
    \subitem {get\_\discretionary {-}{}{}plist}, \hyperpage{209}
    \subitem {init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{209}
  \item {Partition Function and Base Pair Probabilities for Sequence Alignment(s)}, \hyperpage{73}
  \item {Partition Function for two hybridized Sequences}, \hyperpage{58}
  \item {Partition Function for two hybridized Sequences as a stepwise Process}, \hyperpage{63}
  \item {Partition functions for locally stable secondary structures}, \hyperpage{78}
  \item {path\_\discretionary {-}{}{}t}, \hyperpage{133}
  \item {pbacktrack}
    \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{52}
  \item {pbacktrack\_\discretionary {-}{}{}circ}
    \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{53}
  \item {pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{40}
  \item {pf\_\discretionary {-}{}{}cofold}
    \subitem {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{59}
    \subitem {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{59}
    \subitem {compute\_\discretionary {-}{}{}probabilities}, \hyperpage{61}
    \subitem {export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}, \hyperpage{60}
    \subitem {get\_\discretionary {-}{}{}concentrations}, \hyperpage{61}
    \subitem {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}, \hyperpage{60}
    \subitem {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}, \hyperpage{61}
  \item {pf\_\discretionary {-}{}{}fold}
    \subitem {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}, \hyperpage{42}
    \subitem {export\_\discretionary {-}{}{}bppm}, \hyperpage{42}
    \subitem {free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}, \hyperpage{41}
    \subitem {get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}, \hyperpage{43}
    \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}, \hyperpage{43}
    \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}, \hyperpage{43}
    \subitem {pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}, \hyperpage{40}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
    \subitem {pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{39}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
    \subitem {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}, \hyperpage{42}
  \item {pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
  \item {pf\_\discretionary {-}{}{}interact}
    \subitem {up\_\discretionary {-}{}{}cofold}, \hyperpage{64}
  \item {pf\_\discretionary {-}{}{}paramT}, \hyperpage{134}
    \subitem {alpha}, \hyperpage{134}
  \item {pf\_\discretionary {-}{}{}scale}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
  \item {pf\_\discretionary {-}{}{}unstru}
    \subitem {up\_\discretionary {-}{}{}cofold}, \hyperpage{63}
  \item {pfl\_\discretionary {-}{}{}fold}
    \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{78}
  \item {plist}, \hyperpage{136}
  \item {plot\_\discretionary {-}{}{}layouts.h}
    \subitem {rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}, \hyperpage{215}
    \subitem {simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}, \hyperpage{214}
    \subitem {simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}, \hyperpage{214}
    \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}, \hyperpage{213}
    \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}, \hyperpage{213}
    \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}, \hyperpage{213}
  \item {Postorder\_\discretionary {-}{}{}list}, \hyperpage{137}
  \item {pr}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
  \item {Predicting Consensus Structures from Alignment(s)}, \hyperpage{66}
  \item {Predicting Locally stable structures of large sequences}, \hyperpage{76}
  \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}
    \subitem {utils.h}, \hyperpage{247}
  \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}
    \subitem {utils.h}, \hyperpage{247}
  \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}
    \subitem {utils.h}, \hyperpage{247}
  \item {profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
    \subitem {profiledist.h}, \hyperpage{216}
  \item {profiledist.h}
    \subitem {free\_\discretionary {-}{}{}profile}, \hyperpage{217}
    \subitem {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}, \hyperpage{217}
    \subitem {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}, \hyperpage{216}
    \subitem {profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{216}
  \item {PS\_\discretionary {-}{}{}dot.h}
    \subitem {aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln}, \hyperpage{221}
    \subitem {gmlRNA}, \hyperpage{220}
    \subitem {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}, \hyperpage{222}
    \subitem {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}, \hyperpage{221}
    \subitem {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{219}
    \subitem {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}, \hyperpage{219}
    \subitem {ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{220}
    \subitem {svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{220}
    \subitem {xrna\_\discretionary {-}{}{}plot}, \hyperpage{221}
  \item {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{222}
  \item {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
  \item {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{219}
  \item {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{219}
  \item {pu\_\discretionary {-}{}{}contrib}, \hyperpage{138}
  \item {pu\_\discretionary {-}{}{}out}, \hyperpage{139}
  \item {putoutpU\_\discretionary {-}{}{}prob}
    \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{79}
  \item {putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}
    \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{79}

  \indexspace

  \item {random\_\discretionary {-}{}{}string}
    \subitem {utils.h}, \hyperpage{242}
  \item {read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}, \hyperpage{86}
  \item {read\_\discretionary {-}{}{}record}
    \subitem {utils.h}, \hyperpage{244}
  \item {Reading/Writing energy parameter sets from/to File}, \hyperpage{86}
  \item {ribo}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
  \item {RibosumFile}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
  \item {RNA Secondary Structure Folding}, \hyperpage{31}
  \item {rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{215}
  \item {RNAstruct.h}
    \subitem {add\_\discretionary {-}{}{}root}, \hyperpage{226}
    \subitem {b2C}, \hyperpage{225}
    \subitem {b2HIT}, \hyperpage{225}
    \subitem {b2Shapiro}, \hyperpage{226}
    \subitem {expand\_\discretionary {-}{}{}Full}, \hyperpage{226}
    \subitem {expand\_\discretionary {-}{}{}Shapiro}, \hyperpage{226}
    \subitem {parse\_\discretionary {-}{}{}structure}, \hyperpage{227}
    \subitem {unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}, \hyperpage{227}
    \subitem {unexpand\_\discretionary {-}{}{}Full}, \hyperpage{227}
    \subitem {unweight}, \hyperpage{227}

  \indexspace

  \item {scale\_\discretionary {-}{}{}parameters}
    \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
  \item {Searching Sequences for Predefined Structures}, \hyperpage{97}
  \item {sect}, \hyperpage{140}
  \item {set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
  \item {simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{214}
  \item {simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{214}
  \item {snoopT}, \hyperpage{141}
  \item {SOLUTION}, \hyperpage{142}
  \item {space}
    \subitem {utils.h}, \hyperpage{240}
  \item {ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
  \item {st\_\discretionary {-}{}{}back}
    \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{53}
  \item {Stochastic backtracking in the Ensemble}, \hyperpage{52}
  \item {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}, \hyperpage{75}
  \item {Stochastic Backtracking of Structures from Distance Based Partitioning}, \hyperpage{107}
  \item {STR}
    \subitem {utils.h}, \hyperpage{240}
  \item {str\_\discretionary {-}{}{}DNA2RNA}
    \subitem {utils.h}, \hyperpage{247}
  \item {str\_\discretionary {-}{}{}uppercase}
    \subitem {utils.h}, \hyperpage{247}
  \item {string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
    \subitem {stringdist.h}, \hyperpage{229}
  \item {stringdist.h}
    \subitem {Make\_\discretionary {-}{}{}swString}, \hyperpage{229}
    \subitem {string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{229}
  \item {struct\_\discretionary {-}{}{}en}, \hyperpage{143}
  \item {subopt}
    \subitem {subopt\_\discretionary {-}{}{}wuchty}, \hyperpage{50}
  \item {subopt\_\discretionary {-}{}{}circ}
    \subitem {subopt\_\discretionary {-}{}{}wuchty}, \hyperpage{51}
  \item {subopt\_\discretionary {-}{}{}stochbt}
    \subitem {pbacktrack}, \hyperpage{52}
    \subitem {pbacktrack\_\discretionary {-}{}{}circ}, \hyperpage{53}
    \subitem {st\_\discretionary {-}{}{}back}, \hyperpage{53}
  \item {subopt\_\discretionary {-}{}{}wuchty}
    \subitem {subopt}, \hyperpage{50}
    \subitem {subopt\_\discretionary {-}{}{}circ}, \hyperpage{51}
  \item {subopt\_\discretionary {-}{}{}zuker}
    \subitem {zukersubopt}, \hyperpage{49}
  \item {Suboptimal structures according to Zuker et al. 1989}, \hyperpage{49}
  \item {Suboptimal structures within an energy band arround the MFE}, \hyperpage{50}
  \item {svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
  \item {svm\_\discretionary {-}{}{}model}, \hyperpage{144}
  \item {swString}, \hyperpage{145}

  \indexspace

  \item {temperature}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
  \item {tetra\_\discretionary {-}{}{}loop}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
  \item {time\_\discretionary {-}{}{}stamp}
    \subitem {utils.h}, \hyperpage{242}
  \item {Tree}, \hyperpage{146}
  \item {tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
    \subitem {treedist.h}, \hyperpage{232}
  \item {treedist.h}
    \subitem {free\_\discretionary {-}{}{}tree}, \hyperpage{233}
    \subitem {make\_\discretionary {-}{}{}tree}, \hyperpage{232}
    \subitem {tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{232}
  \item {TURN}
    \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
  \item {TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{103}
  \item {TwoDfold\_\discretionary {-}{}{}solution}, \hyperpage{147}
  \item {TwoDfold\_\discretionary {-}{}{}vars}, \hyperpage{148}
  \item {TwoDfoldList}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
  \item {TwoDpfold\_\discretionary {-}{}{}pbacktrack}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}, \hyperpage{107}
  \item {TwoDpfold\_\discretionary {-}{}{}pbacktrack5}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}, \hyperpage{108}
  \item {TwoDpfold\_\discretionary {-}{}{}solution}, \hyperpage{150}
  \item {TwoDpfold\_\discretionary {-}{}{}vars}, \hyperpage{151}
  \item {TwoDpfoldList}
    \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{106}

  \indexspace

  \item {unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}
    \subitem {RNAstruct.h}, \hyperpage{227}
  \item {unexpand\_\discretionary {-}{}{}Full}
    \subitem {RNAstruct.h}, \hyperpage{227}
  \item {unpack\_\discretionary {-}{}{}structure}
    \subitem {utils.h}, \hyperpage{245}
  \item {unweight}
    \subitem {RNAstruct.h}, \hyperpage{227}
  \item {up\_\discretionary {-}{}{}cofold}
    \subitem {pf\_\discretionary {-}{}{}interact}, \hyperpage{64}
    \subitem {pf\_\discretionary {-}{}{}unstru}, \hyperpage{63}
  \item {update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}
    \subitem {alifold.h}, \hyperpage{158}
  \item {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}
    \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{60}
  \item {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}
    \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
  \item {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}
  \item {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}
    \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{78}
  \item {urn}
    \subitem {utils.h}, \hyperpage{241}
  \item {utils.h}
    \subitem {alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
    \subitem {constrain\_\discretionary {-}{}{}ptypes}, \hyperpage{248}
    \subitem {copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
    \subitem {FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}, \hyperpage{240}
    \subitem {FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}, \hyperpage{240}
    \subitem {get\_\discretionary {-}{}{}iindx}, \hyperpage{248}
    \subitem {get\_\discretionary {-}{}{}indx}, \hyperpage{248}
    \subitem {get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}, \hyperpage{243}
    \subitem {get\_\discretionary {-}{}{}line}, \hyperpage{243}
    \subitem {hamming}, \hyperpage{242}
    \subitem {hamming\_\discretionary {-}{}{}bound}, \hyperpage{242}
    \subitem {int\_\discretionary {-}{}{}urn}, \hyperpage{241}
    \subitem {make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt}, \hyperpage{246}
    \subitem {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
    \subitem {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}, \hyperpage{246}
    \subitem {MAX2}, \hyperpage{239}
    \subitem {MAX3}, \hyperpage{240}
    \subitem {MIN2}, \hyperpage{239}
    \subitem {MIN3}, \hyperpage{239}
    \subitem {nrerror}, \hyperpage{241}
    \subitem {pack\_\discretionary {-}{}{}structure}, \hyperpage{245}
    \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}, \hyperpage{247}
    \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}, \hyperpage{247}
    \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}, \hyperpage{247}
    \subitem {random\_\discretionary {-}{}{}string}, \hyperpage{242}
    \subitem {read\_\discretionary {-}{}{}record}, \hyperpage{244}
    \subitem {space}, \hyperpage{240}
    \subitem {STR}, \hyperpage{240}
    \subitem {str\_\discretionary {-}{}{}DNA2RNA}, \hyperpage{247}
    \subitem {str\_\discretionary {-}{}{}uppercase}, \hyperpage{247}
    \subitem {time\_\discretionary {-}{}{}stamp}, \hyperpage{242}
    \subitem {unpack\_\discretionary {-}{}{}structure}, \hyperpage{245}
    \subitem {urn}, \hyperpage{241}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL}, \hyperpage{239}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G}, \hyperpage{239}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE}, \hyperpage{239}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER}, \hyperpage{239}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK}, \hyperpage{239}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}, \hyperpage{237}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR}, \hyperpage{237}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}, \hyperpage{237}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC}, \hyperpage{237}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION}, \hyperpage{237}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS}, \hyperpage{238}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT}, \hyperpage{237}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}, \hyperpage{237}
    \subitem {VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}, \hyperpage{239}
    \subitem {warn\_\discretionary {-}{}{}user}, \hyperpage{241}
    \subitem {xrealloc}, \hyperpage{240}
    \subitem {XSTR}, \hyperpage{240}
    \subitem {xsubi}, \hyperpage{249}

  \indexspace

  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL}
    \subitem {utils.h}, \hyperpage{239}
  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G}
    \subitem {utils.h}, \hyperpage{239}
  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE}
    \subitem {utils.h}, \hyperpage{239}
  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER}
    \subitem {utils.h}, \hyperpage{239}
  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK}
    \subitem {utils.h}, \hyperpage{239}
  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
  \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}
    \subitem {utils.h}, \hyperpage{237}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR}
    \subitem {utils.h}, \hyperpage{237}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}
    \subitem {utils.h}, \hyperpage{237}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC}
    \subitem {utils.h}, \hyperpage{237}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION}
    \subitem {utils.h}, \hyperpage{237}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS}
    \subitem {utils.h}, \hyperpage{238}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT}
    \subitem {utils.h}, \hyperpage{237}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}
    \subitem {utils.h}, \hyperpage{237}
  \item {VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}
    \subitem {utils.h}, \hyperpage{239}
  \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}
  \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}
  \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}

  \indexspace

  \item {warn\_\discretionary {-}{}{}user}
    \subitem {utils.h}, \hyperpage{241}
  \item {write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
    \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}, \hyperpage{86}

  \indexspace

  \item {xrealloc}
    \subitem {utils.h}, \hyperpage{240}
  \item {xrna\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
  \item {XSTR}
    \subitem {utils.h}, \hyperpage{240}
  \item {xsubi}
    \subitem {utils.h}, \hyperpage{249}

  \indexspace

  \item {zukersubopt}
    \subitem {subopt\_\discretionary {-}{}{}zuker}, \hyperpage{49}

\end{theindex}
