\begin{theindex}

  \item {2Dfold.h}
    \subitem {destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}, \hyperpage{82}
    \subitem {get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}, \hyperpage{82}
    \subitem {TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}, \hyperpage{83}
    \subitem {TwoDfoldList}, \hyperpage{82}
  \item {2Dpfold.h}
    \subitem {destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}, \hyperpage{85}
    \subitem {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}, \hyperpage{84}
    \subitem {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}, \hyperpage{85}
    \subitem {TwoDpfold\_\discretionary {-}{}{}pbacktrack}, \hyperpage{86}
    \subitem {TwoDpfold\_\discretionary {-}{}{}pbacktrack5}, \hyperpage{86}
    \subitem {TwoDpfoldList}, \hyperpage{85}

  \indexspace

  \item {add\_\discretionary {-}{}{}root}
    \subitem {RNAstruct.h}, \hyperpage{174}
  \item {alifold}
    \subitem {alifold.h}, \hyperpage{89}
  \item {alifold.h}
    \subitem {alifold}, \hyperpage{89}
    \subitem {alipbacktrack}, \hyperpage{93}
    \subitem {alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}, \hyperpage{93}
    \subitem {alipf\_\discretionary {-}{}{}fold}, \hyperpage{92}
    \subitem {alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{92}
    \subitem {alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}, \hyperpage{91}
    \subitem {circalifold}, \hyperpage{90}
    \subitem {cv\_\discretionary {-}{}{}fact}, \hyperpage{94}
    \subitem {encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}, \hyperpage{91}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}, \hyperpage{90}
    \subitem {export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}, \hyperpage{93}
    \subitem {free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}, \hyperpage{91}
    \subitem {get\_\discretionary {-}{}{}mpi}, \hyperpage{90}
    \subitem {nc\_\discretionary {-}{}{}fact}, \hyperpage{94}
    \subitem {update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}, \hyperpage{89}
  \item {aliLfold}
    \subitem {Lfold.h}, \hyperpage{125}
  \item {alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
    \subitem {utils.h}, \hyperpage{193}
  \item {alipbacktrack}
    \subitem {alifold.h}, \hyperpage{93}
  \item {alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}
    \subitem {alifold.h}, \hyperpage{93}
  \item {alipf\_\discretionary {-}{}{}fold}
    \subitem {alifold.h}, \hyperpage{92}
  \item {alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
    \subitem {alifold.h}, \hyperpage{92}
  \item {alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}
    \subitem {alifold.h}, \hyperpage{91}
  \item {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}
    \subitem {fold.h}, \hyperpage{115}
  \item {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{147}

  \indexspace

  \item {b2C}
    \subitem {RNAstruct.h}, \hyperpage{173}
  \item {b2HIT}
    \subitem {RNAstruct.h}, \hyperpage{173}
  \item {b2Shapiro}
    \subitem {RNAstruct.h}, \hyperpage{174}
  \item {backtrack\_\discretionary {-}{}{}type}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{122}
  \item {base\_\discretionary {-}{}{}pair}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{121}
  \item {bondT}, \hyperpage{43}
  \item {bondTEn}, \hyperpage{44}
  \item {bp\_\discretionary {-}{}{}distance}
    \subitem {utils.h}, \hyperpage{193}

  \indexspace

  \item {centroid}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{150}
  \item {circ}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{121}
  \item {circalifold}
    \subitem {alifold.h}, \hyperpage{90}
  \item {circfold}
    \subitem {fold.h}, \hyperpage{111}
  \item {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{153}
  \item {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{154}
  \item {cofold}
    \subitem {cofold.h}, \hyperpage{95}
  \item {cofold.h}
    \subitem {cofold}, \hyperpage{95}
    \subitem {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}, \hyperpage{96}
    \subitem {get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}, \hyperpage{96}
    \subitem {initialize\_\discretionary {-}{}{}cofold}, \hyperpage{97}
    \subitem {zukersubopt}, \hyperpage{96}
  \item {cofoldF}, \hyperpage{45}
  \item {compute\_\discretionary {-}{}{}probabilities}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{155}
  \item {ConcEnt}, \hyperpage{46}
  \item {constrain}, \hyperpage{47}
  \item {constrain\_\discretionary {-}{}{}ptypes}
    \subitem {utils.h}, \hyperpage{195}
  \item {convert\_\discretionary {-}{}{}epars.h}
    \subitem {convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{100}
  \item {convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
    \subitem {convert\_\discretionary {-}{}{}epars.h}, \hyperpage{100}
  \item {COORDINATE}, \hyperpage{48}
  \item {copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
    \subitem {utils.h}, \hyperpage{192}
  \item {cost\_\discretionary {-}{}{}matrix}
    \subitem {dist\_\discretionary {-}{}{}vars.h}, \hyperpage{103}
  \item {cpair}, \hyperpage{49}
  \item {cut\_\discretionary {-}{}{}point}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{121}
  \item {cv\_\discretionary {-}{}{}fact}
    \subitem {alifold.h}, \hyperpage{94}

  \indexspace

  \item {dangles}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{120}
  \item {destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}
    \subitem {2Dfold.h}, \hyperpage{82}
  \item {destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}
    \subitem {2Dpfold.h}, \hyperpage{85}
  \item {dist\_\discretionary {-}{}{}vars.h}
    \subitem {cost\_\discretionary {-}{}{}matrix}, \hyperpage{103}
    \subitem {edit\_\discretionary {-}{}{}backtrack}, \hyperpage{103}
  \item {do\_\discretionary {-}{}{}backtrack}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{122}
  \item {duplexT}, \hyperpage{50}
  \item {dupVar}, \hyperpage{51}

  \indexspace

  \item {E\_\discretionary {-}{}{}Hairpin}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{128}
  \item {E\_\discretionary {-}{}{}IntLoop}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{127}
  \item {E\_\discretionary {-}{}{}Stem}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{129}
  \item {edit\_\discretionary {-}{}{}backtrack}
    \subitem {dist\_\discretionary {-}{}{}vars.h}, \hyperpage{103}
  \item {encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}
    \subitem {alifold.h}, \hyperpage{91}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}
    \subitem {alifold.h}, \hyperpage{90}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}
    \subitem {fold.h}, \hyperpage{117}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}
    \subitem {fold.h}, \hyperpage{113}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}
    \subitem {fold.h}, \hyperpage{112}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}
    \subitem {fold.h}, \hyperpage{116}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}
    \subitem {fold.h}, \hyperpage{112}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}
    \subitem {fold.h}, \hyperpage{116}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}
    \subitem {fold.h}, \hyperpage{114}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}
    \subitem {fold.h}, \hyperpage{112}
  \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}
    \subitem {fold.h}, \hyperpage{113}
  \item {energy\_\discretionary {-}{}{}set}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{120}
  \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{131}
  \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{132}
  \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}
    \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{131}
  \item {expand\_\discretionary {-}{}{}Full}
    \subitem {RNAstruct.h}, \hyperpage{174}
  \item {expand\_\discretionary {-}{}{}Shapiro}
    \subitem {RNAstruct.h}, \hyperpage{174}
  \item {expHairpinEnergy}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{150}
  \item {expLoopEnergy}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{150}
  \item {export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}
    \subitem {alifold.h}, \hyperpage{93}
  \item {export\_\discretionary {-}{}{}bppm}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{147}
  \item {export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{154}
  \item {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}
    \subitem {cofold.h}, \hyperpage{96}

  \indexspace

  \item {FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}
    \subitem {utils.h}, \hyperpage{187}
  \item {FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}
    \subitem {utils.h}, \hyperpage{187}
  \item {fold}
    \subitem {fold.h}, \hyperpage{111}
  \item {fold.h}
    \subitem {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}, \hyperpage{115}
    \subitem {circfold}, \hyperpage{111}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}, \hyperpage{117}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}, \hyperpage{113}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}, \hyperpage{112}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}, \hyperpage{116}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}, \hyperpage{112}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}, \hyperpage{116}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}, \hyperpage{114}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}, \hyperpage{112}
    \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}, \hyperpage{113}
    \subitem {fold}, \hyperpage{111}
    \subitem {fold\_\discretionary {-}{}{}par}, \hyperpage{110}
    \subitem {HairpinE}, \hyperpage{115}
    \subitem {initialize\_\discretionary {-}{}{}fold}, \hyperpage{115}
    \subitem {LoopEnergy}, \hyperpage{115}
    \subitem {parenthesis\_\discretionary {-}{}{}structure}, \hyperpage{114}
    \subitem {parenthesis\_\discretionary {-}{}{}zuker}, \hyperpage{115}
  \item {fold\_\discretionary {-}{}{}par}
    \subitem {fold.h}, \hyperpage{110}
  \item {fold\_\discretionary {-}{}{}vars.h}
    \subitem {backtrack\_\discretionary {-}{}{}type}, \hyperpage{122}
    \subitem {base\_\discretionary {-}{}{}pair}, \hyperpage{121}
    \subitem {circ}, \hyperpage{121}
    \subitem {cut\_\discretionary {-}{}{}point}, \hyperpage{121}
    \subitem {dangles}, \hyperpage{120}
    \subitem {do\_\discretionary {-}{}{}backtrack}, \hyperpage{122}
    \subitem {energy\_\discretionary {-}{}{}set}, \hyperpage{120}
    \subitem {iindx}, \hyperpage{121}
    \subitem {noLonelyPairs}, \hyperpage{120}
    \subitem {nonstandards}, \hyperpage{121}
    \subitem {pf\_\discretionary {-}{}{}scale}, \hyperpage{122}
    \subitem {pr}, \hyperpage{121}
    \subitem {set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}, \hyperpage{120}
    \subitem {temperature}, \hyperpage{121}
    \subitem {tetra\_\discretionary {-}{}{}loop}, \hyperpage{120}
  \item {folden}, \hyperpage{52}
  \item {free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{146}
  \item {free\_\discretionary {-}{}{}profile}
    \subitem {profiledist.h}, \hyperpage{164}
  \item {free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}
    \subitem {alifold.h}, \hyperpage{91}
  \item {free\_\discretionary {-}{}{}tree}
    \subitem {treedist.h}, \hyperpage{181}

  \indexspace

  \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}
    \subitem {params.h}, \hyperpage{141}
  \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}
    \subitem {params.h}, \hyperpage{140}
  \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors\_\discretionary {-}{}{}ali}
    \subitem {params.h}, \hyperpage{141}
  \item {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{148}
  \item {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{148}
  \item {get\_\discretionary {-}{}{}concentrations}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{156}
  \item {get\_\discretionary {-}{}{}iindx}
    \subitem {utils.h}, \hyperpage{194}
  \item {get\_\discretionary {-}{}{}indx}
    \subitem {utils.h}, \hyperpage{195}
  \item {get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}
    \subitem {utils.h}, \hyperpage{190}
  \item {get\_\discretionary {-}{}{}line}
    \subitem {utils.h}, \hyperpage{189}
  \item {get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}
    \subitem {cofold.h}, \hyperpage{96}
  \item {get\_\discretionary {-}{}{}mpi}
    \subitem {alifold.h}, \hyperpage{90}
  \item {get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{147}
  \item {get\_\discretionary {-}{}{}plist}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{156}
  \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}parameters}
    \subitem {params.h}, \hyperpage{141}
  \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}
    \subitem {params.h}, \hyperpage{140}
  \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}
    \subitem {params.h}, \hyperpage{140}
  \item {get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}
    \subitem {2Dfold.h}, \hyperpage{82}
  \item {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}
    \subitem {2Dpfold.h}, \hyperpage{84}
  \item {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}
    \subitem {2Dpfold.h}, \hyperpage{85}
  \item {gmlRNA}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{167}

  \indexspace

  \item {H/2Dfold.h}, \hyperpage{81}
  \item {H/2Dpfold.h}, \hyperpage{84}
  \item {H/alifold.h}, \hyperpage{88}
  \item {H/cofold.h}, \hyperpage{95}
  \item {H/convert\_\discretionary {-}{}{}epars.h}, \hyperpage{98}
  \item {H/data\_\discretionary {-}{}{}structures.h}, \hyperpage{101}
  \item {H/dist\_\discretionary {-}{}{}vars.h}, \hyperpage{103}
  \item {H/duplex.h}, \hyperpage{104}
  \item {H/edit\_\discretionary {-}{}{}cost.h}, \hyperpage{105}
  \item {H/energy\_\discretionary {-}{}{}const.h}, \hyperpage{106}
  \item {H/findpath.h}, \hyperpage{107}
  \item {H/fold.h}, \hyperpage{108}
  \item {H/fold\_\discretionary {-}{}{}vars.h}, \hyperpage{118}
  \item {H/inverse.h}, \hyperpage{123}
  \item {H/Lfold.h}, \hyperpage{125}
  \item {H/loop\_\discretionary {-}{}{}energies.h}, \hyperpage{127}
  \item {H/LPfold.h}, \hyperpage{133}
  \item {H/MEA.h}, \hyperpage{136}
  \item {H/mm.h}, \hyperpage{137}
  \item {H/naview.h}, \hyperpage{138}
  \item {H/params.h}, \hyperpage{139}
  \item {H/part\_\discretionary {-}{}{}func.h}, \hyperpage{142}
  \item {H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{152}
  \item {H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h}, \hyperpage{158}
  \item {H/plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{161}
  \item {H/profiledist.h}, \hyperpage{164}
  \item {H/PS\_\discretionary {-}{}{}dot.h}, \hyperpage{166}
  \item {H/read\_\discretionary {-}{}{}epars.h}, \hyperpage{171}
  \item {H/RNAstruct.h}, \hyperpage{172}
  \item {H/stringdist.h}, \hyperpage{177}
  \item {H/subopt.h}, \hyperpage{178}
  \item {H/treedist.h}, \hyperpage{180}
  \item {H/utils.h}, \hyperpage{182}
  \item {HairpinE}
    \subitem {fold.h}, \hyperpage{115}
  \item {hamming}
    \subitem {utils.h}, \hyperpage{189}
  \item {hamming\_\discretionary {-}{}{}bound}
    \subitem {utils.h}, \hyperpage{189}

  \indexspace

  \item {iindx}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{121}
  \item {init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{156}
  \item {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{150}
  \item {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}
    \subitem {LPfold.h}, \hyperpage{135}
  \item {initialize\_\discretionary {-}{}{}cofold}
    \subitem {cofold.h}, \hyperpage{97}
  \item {initialize\_\discretionary {-}{}{}fold}
    \subitem {fold.h}, \hyperpage{115}
  \item {int\_\discretionary {-}{}{}urn}
    \subitem {utils.h}, \hyperpage{188}
  \item {interact}, \hyperpage{53}
  \item {intermediate\_\discretionary {-}{}{}t}, \hyperpage{54}
  \item {INTERVAL}, \hyperpage{55}
  \item {inverse.h}
    \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{123}
    \subitem {inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{124}
    \subitem {symbolset}, \hyperpage{124}
  \item {inverse\_\discretionary {-}{}{}fold}
    \subitem {inverse.h}, \hyperpage{123}
  \item {inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
    \subitem {inverse.h}, \hyperpage{124}

  \indexspace

  \item {Lfold}
    \subitem {Lfold.h}, \hyperpage{125}
  \item {Lfold.h}
    \subitem {aliLfold}, \hyperpage{125}
    \subitem {Lfold}, \hyperpage{125}
    \subitem {Lfoldz}, \hyperpage{125}
  \item {Lfoldz}
    \subitem {Lfold.h}, \hyperpage{125}
  \item {lib/1.8.4\_\discretionary {-}{}{}epars.h}, \hyperpage{197}
  \item {lib/1.8.4\_\discretionary {-}{}{}intloops.h}, \hyperpage{198}
  \item {LIST}, \hyperpage{56}
  \item {loop\_\discretionary {-}{}{}energies.h}
    \subitem {E\_\discretionary {-}{}{}Hairpin}, \hyperpage{128}
    \subitem {E\_\discretionary {-}{}{}IntLoop}, \hyperpage{127}
    \subitem {E\_\discretionary {-}{}{}Stem}, \hyperpage{129}
    \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}, \hyperpage{131}
    \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}, \hyperpage{132}
    \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}, \hyperpage{131}
  \item {loop\_\discretionary {-}{}{}size}
    \subitem {RNAstruct.h}, \hyperpage{176}
  \item {LoopEnergy}
    \subitem {fold.h}, \hyperpage{115}
  \item {LPfold.h}
    \subitem {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}, \hyperpage{135}
    \subitem {pfl\_\discretionary {-}{}{}fold}, \hyperpage{133}
    \subitem {putoutpU\_\discretionary {-}{}{}prob}, \hyperpage{134}
    \subitem {putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}, \hyperpage{134}
    \subitem {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}, \hyperpage{133}
  \item {LST\_\discretionary {-}{}{}BUCKET}, \hyperpage{57}

  \indexspace

  \item {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}
    \subitem {profiledist.h}, \hyperpage{165}
  \item {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}
    \subitem {profiledist.h}, \hyperpage{164}
  \item {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
    \subitem {utils.h}, \hyperpage{192}
  \item {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}
    \subitem {utils.h}, \hyperpage{193}
  \item {Make\_\discretionary {-}{}{}swString}
    \subitem {stringdist.h}, \hyperpage{177}
  \item {make\_\discretionary {-}{}{}tree}
    \subitem {treedist.h}, \hyperpage{180}
  \item {MEA}
    \subitem {MEA.h}, \hyperpage{136}
  \item {MEA.h}
    \subitem {MEA}, \hyperpage{136}
  \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{150}
  \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{149}
  \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{149}
  \item {model\_\discretionary {-}{}{}detailsT}, \hyperpage{58}
  \item {move\_\discretionary {-}{}{}t}, \hyperpage{59}

  \indexspace

  \item {nc\_\discretionary {-}{}{}fact}
    \subitem {alifold.h}, \hyperpage{94}
  \item {noLonelyPairs}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{120}
  \item {nonstandards}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{121}
  \item {nrerror}
    \subitem {utils.h}, \hyperpage{188}

  \indexspace

  \item {pack\_\discretionary {-}{}{}structure}
    \subitem {utils.h}, \hyperpage{192}
  \item {PAIR}, \hyperpage{60}
  \item {pair\_\discretionary {-}{}{}info}, \hyperpage{61}
  \item {pairpro}, \hyperpage{62}
  \item {params.h}
    \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}, \hyperpage{141}
    \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}, \hyperpage{140}
    \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors\_\discretionary {-}{}{}ali}, \hyperpage{141}
    \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}parameters}, \hyperpage{141}
    \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}, \hyperpage{140}
    \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}, \hyperpage{140}
    \subitem {scale\_\discretionary {-}{}{}parameters}, \hyperpage{139}
  \item {paramT}, \hyperpage{63}
  \item {parenthesis\_\discretionary {-}{}{}structure}
    \subitem {fold.h}, \hyperpage{114}
  \item {parenthesis\_\discretionary {-}{}{}zuker}
    \subitem {fold.h}, \hyperpage{115}
  \item {parse\_\discretionary {-}{}{}structure}
    \subitem {RNAstruct.h}, \hyperpage{175}
  \item {part\_\discretionary {-}{}{}func.h}
    \subitem {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}, \hyperpage{147}
    \subitem {centroid}, \hyperpage{150}
    \subitem {expHairpinEnergy}, \hyperpage{150}
    \subitem {expLoopEnergy}, \hyperpage{150}
    \subitem {export\_\discretionary {-}{}{}bppm}, \hyperpage{147}
    \subitem {free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}, \hyperpage{146}
    \subitem {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}, \hyperpage{148}
    \subitem {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}, \hyperpage{148}
    \subitem {get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}, \hyperpage{147}
    \subitem {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{150}
    \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}, \hyperpage{150}
    \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}, \hyperpage{149}
    \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}, \hyperpage{149}
    \subitem {pbacktrack}, \hyperpage{145}
    \subitem {pbacktrack\_\discretionary {-}{}{}circ}, \hyperpage{146}
    \subitem {pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}, \hyperpage{145}
    \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{144}
    \subitem {pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{144}
    \subitem {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}, \hyperpage{147}
  \item {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}
    \subitem {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{153}
    \subitem {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{154}
    \subitem {compute\_\discretionary {-}{}{}probabilities}, \hyperpage{155}
    \subitem {export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}, \hyperpage{154}
    \subitem {get\_\discretionary {-}{}{}concentrations}, \hyperpage{156}
    \subitem {get\_\discretionary {-}{}{}plist}, \hyperpage{156}
    \subitem {init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{156}
    \subitem {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}, \hyperpage{154}
    \subitem {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}, \hyperpage{155}
  \item {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h}
    \subitem {pf\_\discretionary {-}{}{}interact}, \hyperpage{159}
    \subitem {pf\_\discretionary {-}{}{}unstru}, \hyperpage{158}
  \item {path\_\discretionary {-}{}{}t}, \hyperpage{64}
  \item {pbacktrack}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{145}
  \item {pbacktrack\_\discretionary {-}{}{}circ}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{146}
  \item {pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{145}
  \item {pf\_\discretionary {-}{}{}fold}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{144}
  \item {pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{144}
  \item {pf\_\discretionary {-}{}{}interact}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h}, \hyperpage{159}
  \item {pf\_\discretionary {-}{}{}paramT}, \hyperpage{65}
  \item {pf\_\discretionary {-}{}{}scale}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{122}
  \item {pf\_\discretionary {-}{}{}unstru}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h}, \hyperpage{158}
  \item {pfl\_\discretionary {-}{}{}fold}
    \subitem {LPfold.h}, \hyperpage{133}
  \item {plist}, \hyperpage{66}
  \item {plot\_\discretionary {-}{}{}layouts.h}
    \subitem {rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}, \hyperpage{163}
    \subitem {simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}, \hyperpage{162}
    \subitem {simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}, \hyperpage{162}
    \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}, \hyperpage{162}
    \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}, \hyperpage{162}
    \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}, \hyperpage{161}
  \item {Postorder\_\discretionary {-}{}{}list}, \hyperpage{67}
  \item {pr}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{121}
  \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}
    \subitem {utils.h}, \hyperpage{194}
  \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint\_\discretionary {-}{}{}full}
    \subitem {utils.h}, \hyperpage{194}
  \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}
    \subitem {utils.h}, \hyperpage{193}
  \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}
    \subitem {utils.h}, \hyperpage{193}
  \item {profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
    \subitem {profiledist.h}, \hyperpage{164}
  \item {profiledist.h}
    \subitem {free\_\discretionary {-}{}{}profile}, \hyperpage{164}
    \subitem {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}, \hyperpage{165}
    \subitem {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}, \hyperpage{164}
    \subitem {profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{164}
  \item {PS\_\discretionary {-}{}{}dot.h}
    \subitem {gmlRNA}, \hyperpage{167}
    \subitem {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}, \hyperpage{169}
    \subitem {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}, \hyperpage{169}
    \subitem {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{167}
    \subitem {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}, \hyperpage{167}
    \subitem {ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{168}
    \subitem {svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{168}
    \subitem {xrna\_\discretionary {-}{}{}plot}, \hyperpage{168}
  \item {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{169}
  \item {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{169}
  \item {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{167}
  \item {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{167}
  \item {pu\_\discretionary {-}{}{}contrib}, \hyperpage{68}
  \item {pu\_\discretionary {-}{}{}out}, \hyperpage{69}
  \item {putoutpU\_\discretionary {-}{}{}prob}
    \subitem {LPfold.h}, \hyperpage{134}
  \item {putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}
    \subitem {LPfold.h}, \hyperpage{134}

  \indexspace

  \item {random\_\discretionary {-}{}{}string}
    \subitem {utils.h}, \hyperpage{189}
  \item {read\_\discretionary {-}{}{}epars.h}
    \subitem {read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{171}
    \subitem {write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{171}
  \item {read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
    \subitem {read\_\discretionary {-}{}{}epars.h}, \hyperpage{171}
  \item {read\_\discretionary {-}{}{}record}
    \subitem {utils.h}, \hyperpage{190}
  \item {rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{163}
  \item {RNAstruct.h}
    \subitem {add\_\discretionary {-}{}{}root}, \hyperpage{174}
    \subitem {b2C}, \hyperpage{173}
    \subitem {b2HIT}, \hyperpage{173}
    \subitem {b2Shapiro}, \hyperpage{174}
    \subitem {expand\_\discretionary {-}{}{}Full}, \hyperpage{174}
    \subitem {expand\_\discretionary {-}{}{}Shapiro}, \hyperpage{174}
    \subitem {loop\_\discretionary {-}{}{}size}, \hyperpage{176}
    \subitem {parse\_\discretionary {-}{}{}structure}, \hyperpage{175}
    \subitem {unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}, \hyperpage{175}
    \subitem {unexpand\_\discretionary {-}{}{}Full}, \hyperpage{175}
    \subitem {unweight}, \hyperpage{175}

  \indexspace

  \item {scale\_\discretionary {-}{}{}parameters}
    \subitem {params.h}, \hyperpage{139}
  \item {sect}, \hyperpage{70}
  \item {set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{120}
  \item {simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{162}
  \item {simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{162}
  \item {snoopT}, \hyperpage{71}
  \item {SOLUTION}, \hyperpage{72}
  \item {space}
    \subitem {utils.h}, \hyperpage{187}
  \item {ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{168}
  \item {str\_\discretionary {-}{}{}DNA2RNA}
    \subitem {utils.h}, \hyperpage{194}
  \item {str\_\discretionary {-}{}{}uppercase}
    \subitem {utils.h}, \hyperpage{194}
  \item {string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
    \subitem {stringdist.h}, \hyperpage{177}
  \item {stringdist.h}
    \subitem {Make\_\discretionary {-}{}{}swString}, \hyperpage{177}
    \subitem {string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{177}
  \item {subopt}
    \subitem {subopt.h}, \hyperpage{178}
  \item {subopt.h}
    \subitem {subopt}, \hyperpage{178}
    \subitem {subopt\_\discretionary {-}{}{}circ}, \hyperpage{178}
  \item {subopt\_\discretionary {-}{}{}circ}
    \subitem {subopt.h}, \hyperpage{178}
  \item {svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{168}
  \item {svm\_\discretionary {-}{}{}model}, \hyperpage{73}
  \item {swString}, \hyperpage{74}
  \item {symbolset}
    \subitem {inverse.h}, \hyperpage{124}

  \indexspace

  \item {temperature}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{121}
  \item {tetra\_\discretionary {-}{}{}loop}
    \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{120}
  \item {time\_\discretionary {-}{}{}stamp}
    \subitem {utils.h}, \hyperpage{188}
  \item {Tree}, \hyperpage{75}
  \item {tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
    \subitem {treedist.h}, \hyperpage{180}
  \item {treedist.h}
    \subitem {free\_\discretionary {-}{}{}tree}, \hyperpage{181}
    \subitem {make\_\discretionary {-}{}{}tree}, \hyperpage{180}
    \subitem {tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{180}
  \item {TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}
    \subitem {2Dfold.h}, \hyperpage{83}
  \item {TwoDfold\_\discretionary {-}{}{}solution}, \hyperpage{76}
  \item {TwoDfold\_\discretionary {-}{}{}vars}, \hyperpage{77}
  \item {TwoDfoldList}
    \subitem {2Dfold.h}, \hyperpage{82}
  \item {TwoDpfold\_\discretionary {-}{}{}pbacktrack}
    \subitem {2Dpfold.h}, \hyperpage{86}
  \item {TwoDpfold\_\discretionary {-}{}{}pbacktrack5}
    \subitem {2Dpfold.h}, \hyperpage{86}
  \item {TwoDpfold\_\discretionary {-}{}{}solution}, \hyperpage{78}
  \item {TwoDpfold\_\discretionary {-}{}{}vars}, \hyperpage{79}
  \item {TwoDpfoldList}
    \subitem {2Dpfold.h}, \hyperpage{85}

  \indexspace

  \item {unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}
    \subitem {RNAstruct.h}, \hyperpage{175}
  \item {unexpand\_\discretionary {-}{}{}Full}
    \subitem {RNAstruct.h}, \hyperpage{175}
  \item {unpack\_\discretionary {-}{}{}structure}
    \subitem {utils.h}, \hyperpage{192}
  \item {unweight}
    \subitem {RNAstruct.h}, \hyperpage{175}
  \item {update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}
    \subitem {alifold.h}, \hyperpage{89}
  \item {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{154}
  \item {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}
    \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{155}
  \item {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}
    \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{147}
  \item {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}
    \subitem {LPfold.h}, \hyperpage{133}
  \item {urn}
    \subitem {utils.h}, \hyperpage{188}
  \item {utils.h}
    \subitem {alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{193}
    \subitem {bp\_\discretionary {-}{}{}distance}, \hyperpage{193}
    \subitem {constrain\_\discretionary {-}{}{}ptypes}, \hyperpage{195}
    \subitem {copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{192}
    \subitem {FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}, \hyperpage{187}
    \subitem {FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}, \hyperpage{187}
    \subitem {get\_\discretionary {-}{}{}iindx}, \hyperpage{194}
    \subitem {get\_\discretionary {-}{}{}indx}, \hyperpage{195}
    \subitem {get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}, \hyperpage{190}
    \subitem {get\_\discretionary {-}{}{}line}, \hyperpage{189}
    \subitem {hamming}, \hyperpage{189}
    \subitem {hamming\_\discretionary {-}{}{}bound}, \hyperpage{189}
    \subitem {int\_\discretionary {-}{}{}urn}, \hyperpage{188}
    \subitem {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{192}
    \subitem {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}, \hyperpage{193}
    \subitem {nrerror}, \hyperpage{188}
    \subitem {pack\_\discretionary {-}{}{}structure}, \hyperpage{192}
    \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}, \hyperpage{194}
    \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint\_\discretionary {-}{}{}full}, \hyperpage{194}
    \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}, \hyperpage{193}
    \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}, \hyperpage{193}
    \subitem {random\_\discretionary {-}{}{}string}, \hyperpage{189}
    \subitem {read\_\discretionary {-}{}{}record}, \hyperpage{190}
    \subitem {space}, \hyperpage{187}
    \subitem {str\_\discretionary {-}{}{}DNA2RNA}, \hyperpage{194}
    \subitem {str\_\discretionary {-}{}{}uppercase}, \hyperpage{194}
    \subitem {time\_\discretionary {-}{}{}stamp}, \hyperpage{188}
    \subitem {unpack\_\discretionary {-}{}{}structure}, \hyperpage{192}
    \subitem {urn}, \hyperpage{188}
    \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}, \hyperpage{186}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}, \hyperpage{186}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}, \hyperpage{186}
    \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}, \hyperpage{186}
    \subitem {VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}, \hyperpage{187}
    \subitem {warn\_\discretionary {-}{}{}user}, \hyperpage{188}
    \subitem {xrealloc}, \hyperpage{187}
    \subitem {xsubi}, \hyperpage{196}

  \indexspace

  \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}
    \subitem {utils.h}, \hyperpage{186}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}
    \subitem {utils.h}, \hyperpage{186}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}
    \subitem {utils.h}, \hyperpage{186}
  \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}
    \subitem {utils.h}, \hyperpage{186}
  \item {VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}
    \subitem {utils.h}, \hyperpage{187}
  \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{162}
  \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{162}
  \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}
    \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{161}

  \indexspace

  \item {warn\_\discretionary {-}{}{}user}
    \subitem {utils.h}, \hyperpage{188}
  \item {write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
    \subitem {read\_\discretionary {-}{}{}epars.h}, \hyperpage{171}

  \indexspace

  \item {xrealloc}
    \subitem {utils.h}, \hyperpage{187}
  \item {xrna\_\discretionary {-}{}{}plot}
    \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{168}
  \item {xsubi}
    \subitem {utils.h}, \hyperpage{196}

  \indexspace

  \item {zukersubopt}
    \subitem {cofold.h}, \hyperpage{96}

\end{theindex}
