binaries/src/ViennaRNA/doc/latex/refman.ind

   1 \begin{theindex}
   2
   3   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h}, \hyperpage{153}
   4   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h}, \hyperpage{155}
   5   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h}, \hyperpage{198}
   6   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/Lfold.h}, \hyperpage{190}
   7   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/MEA.h}, \hyperpage{200}
   8   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS\_\discretionary {-}{}{}dot.h}, \hyperpage{218}
   9   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/RNAstruct.h}, \hyperpage{224}
  10   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}, \hyperpage{156}
  11   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h}, \hyperpage{159}
  12   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\discretionary {-}{}{}epars.h}, \hyperpage{161}
  13   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\discretionary {-}{}{}structures.h}, \hyperpage{162}
  14   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
  15   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/duplex.h}, \hyperpage{167}
  16   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/edit\_\discretionary {-}{}{}cost.h}, \hyperpage{168}
  17   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
  18   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h}, \hyperpage{171}
  19   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h}, \hyperpage{173}
  20   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold\_\discretionary {-}{}{}vars.h}, \hyperpage{180}
  21   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h}, \hyperpage{186}
  22   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/inverse.h}, \hyperpage{189}
  23   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/loop\_\discretionary {-}{}{}energies.h}, \hyperpage{191}
  24   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/mm.h}, \hyperpage{201}
  25   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/naview.h}, \hyperpage{202}
  26   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h}, \hyperpage{203}
  27   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func.h}, \hyperpage{205}
  28   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{208}
  29   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h}, \hyperpage{211}
  30   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{212}
  31   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h}, \hyperpage{216}
  32   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/read\_\discretionary {-}{}{}epars.h}, \hyperpage{223}
  33   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/stringdist.h}, \hyperpage{229}
  34   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/subopt.h}, \hyperpage{231}
  35   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h}, \hyperpage{232}
  36   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/utils.h}, \hyperpage{234}
  37   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}epars.h}, \hyperpage{250}
  38   \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}intloops.h}, \hyperpage{251}
  39
  40   \indexspace
  41
  42   \item {add\_\discretionary {-}{}{}root}
  43     \subitem {RNAstruct.h}, \hyperpage{226}
  44   \item {alifold}
  45     \subitem {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{71}
  46   \item {alifold.h}
  47     \subitem {update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}, \hyperpage{158}
  48   \item {aliLfold}
  49     \subitem {local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}, \hyperpage{81}
  50   \item {alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
  51     \subitem {utils.h}, \hyperpage{246}
  52   \item {alipbacktrack}
  53     \subitem {consensus\_\discretionary {-}{}{}stochbt}, \hyperpage{75}
  54   \item {alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}
  55     \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{74}
  56   \item {alipf\_\discretionary {-}{}{}fold}
  57     \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{73}
  58   \item {alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
  59     \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{73}
  60   \item {aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln}
  61     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
  62   \item {alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}
  63     \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{68}
  64   \item {alpha}
  65     \subitem {pf\_\discretionary {-}{}{}paramT}, \hyperpage{134}
  66   \item {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}
  67     \subitem {fold.h}, \hyperpage{177}
  68   \item {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}
  69     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}
  70
  71   \indexspace
  72
  73   \item {b2C}
  74     \subitem {RNAstruct.h}, \hyperpage{225}
  75   \item {b2HIT}
  76     \subitem {RNAstruct.h}, \hyperpage{225}
  77   \item {b2Shapiro}
  78     \subitem {RNAstruct.h}, \hyperpage{226}
  79   \item {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop}
  80     \subitem {gquad.h}, \hyperpage{187}
  81   \item {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L}
  82     \subitem {gquad.h}, \hyperpage{187}
  83   \item {backtrack\_\discretionary {-}{}{}type}
  84     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{185}
  85   \item {base\_\discretionary {-}{}{}pair}
  86     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
  87   \item {bondT}, \hyperpage{111}
  88   \item {bondTEn}, \hyperpage{112}
  89   \item {BONUS}
  90     \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
  91
  92   \indexspace
  93
  94   \item {Calculate Partition Functions of a Distance Based Partitioning}, \hyperpage{104}
  95   \item {Calculate Secondary Structures of two RNAs upon Dimerization}, \hyperpage{54}
  96   \item {Calculating MFE representatives of a Distance Based Partitioning}, \hyperpage{101}
  97   \item {Calculating Minimum Free Energy (MFE) Structures}, \hyperpage{33}
  98   \item {Calculating Partition Functions and Pair Probabilities}, \hyperpage{37}
  99   \item {centroid}
 100     \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
 101   \item {centroid\_\discretionary {-}{}{}fold}
 102     \subitem {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}, \hyperpage{46}
 103     \subitem {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}, \hyperpage{46}
 104   \item {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, \hyperpage{82}
 105   \item {circalifold}
 106     \subitem {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{71}
 107   \item {circfold}
 108     \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{35}
 109   \item {Classified Dynamic Programming}, \hyperpage{99}
 110   \item {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
 111     \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{59}
 112   \item {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
 113     \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{59}
 114   \item {cofold}
 115     \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{55}
 116   \item {cofold.h}
 117     \subitem {get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}, \hyperpage{160}
 118     \subitem {initialize\_\discretionary {-}{}{}cofold}, \hyperpage{160}
 119   \item {cofoldF}, \hyperpage{113}
 120   \item {Compute the centroid structure}, \hyperpage{46}
 121   \item {Compute the Density of States}, \hyperpage{109}
 122   \item {Compute the structure with maximum expected accuracy (MEA)}, \hyperpage{45}
 123   \item {compute\_\discretionary {-}{}{}probabilities}
 124     \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
 125   \item {ConcEnt}, \hyperpage{114}
 126   \item {consensus\_\discretionary {-}{}{}fold}
 127     \subitem {alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}, \hyperpage{68}
 128     \subitem {cv\_\discretionary {-}{}{}fact}, \hyperpage{70}
 129     \subitem {encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}, \hyperpage{68}
 130     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}, \hyperpage{67}
 131     \subitem {free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}, \hyperpage{69}
 132     \subitem {get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}, \hyperpage{69}
 133     \subitem {get\_\discretionary {-}{}{}mpi}, \hyperpage{67}
 134     \subitem {nc\_\discretionary {-}{}{}fact}, \hyperpage{70}
 135   \item {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}
 136     \subitem {alifold}, \hyperpage{71}
 137     \subitem {circalifold}, \hyperpage{71}
 138   \item {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
 139     \subitem {alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}, \hyperpage{74}
 140     \subitem {alipf\_\discretionary {-}{}{}fold}, \hyperpage{73}
 141     \subitem {alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{73}
 142     \subitem {export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}, \hyperpage{74}
 143   \item {consensus\_\discretionary {-}{}{}stochbt}
 144     \subitem {alipbacktrack}, \hyperpage{75}
 145   \item {constrain}, \hyperpage{115}
 146   \item {constrain\_\discretionary {-}{}{}ptypes}
 147     \subitem {utils.h}, \hyperpage{248}
 148   \item {convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
 149     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
 150   \item {Converting energy parameter files}, \hyperpage{88}
 151   \item {COORDINATE}, \hyperpage{116}
 152   \item {copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
 153     \subitem {utils.h}, \hyperpage{246}
 154   \item {cost\_\discretionary {-}{}{}matrix}
 155     \subitem {dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
 156   \item {cpair}, \hyperpage{117}
 157   \item {cut\_\discretionary {-}{}{}point}
 158     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 159   \item {cv\_\discretionary {-}{}{}fact}
 160     \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{70}
 161
 162   \indexspace
 163
 164   \item {dangles}
 165     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
 166     \subitem {model\_\discretionary {-}{}{}detailsT}, \hyperpage{126}
 167   \item {density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}
 168     \subitem {dos}, \hyperpage{109}
 169   \item {destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}
 170     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
 171   \item {destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}
 172     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
 173   \item {dist\_\discretionary {-}{}{}vars.h}
 174     \subitem {cost\_\discretionary {-}{}{}matrix}, \hyperpage{165}
 175     \subitem {edit\_\discretionary {-}{}{}backtrack}, \hyperpage{165}
 176   \item {Distance based partitioning of the Secondary Structure Space}, \hyperpage{100}
 177   \item {do\_\discretionary {-}{}{}backtrack}
 178     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
 179   \item {dos}
 180     \subitem {density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}, \hyperpage{109}
 181   \item {duplexT}, \hyperpage{118}
 182   \item {dupVar}, \hyperpage{119}
 183
 184   \indexspace
 185
 186   \item {E\_\discretionary {-}{}{}Hairpin}
 187     \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{193}
 188   \item {E\_\discretionary {-}{}{}IntLoop}
 189     \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{192}
 190   \item {E\_\discretionary {-}{}{}Stem}
 191     \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{194}
 192   \item {edit\_\discretionary {-}{}{}backtrack}
 193     \subitem {dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
 194   \item {encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}
 195     \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{68}
 196   \item {Energy evaluation}, \hyperpage{93}
 197   \item {energy\_\discretionary {-}{}{}const.h}
 198     \subitem {BONUS}, \hyperpage{170}
 199     \subitem {FORBIDDEN}, \hyperpage{169}
 200     \subitem {GASCONST}, \hyperpage{169}
 201     \subitem {INF}, \hyperpage{169}
 202     \subitem {K0}, \hyperpage{169}
 203     \subitem {MAXLOOP}, \hyperpage{170}
 204     \subitem {NBPAIRS}, \hyperpage{170}
 205     \subitem {TURN}, \hyperpage{170}
 206   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}
 207     \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{67}
 208   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}
 209     \subitem {fold.h}, \hyperpage{179}
 210   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}
 211     \subitem {eval}, \hyperpage{95}
 212   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}
 213     \subitem {eval}, \hyperpage{94}
 214   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}
 215     \subitem {fold.h}, \hyperpage{175}
 216   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}
 217     \subitem {fold.h}, \hyperpage{176}
 218   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}
 219     \subitem {fold.h}, \hyperpage{177}
 220   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}
 221     \subitem {eval}, \hyperpage{94}
 222   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}
 223     \subitem {fold.h}, \hyperpage{178}
 224   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}
 225     \subitem {eval}, \hyperpage{96}
 226   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}
 227     \subitem {eval}, \hyperpage{94}
 228   \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}
 229     \subitem {eval}, \hyperpage{95}
 230   \item {energy\_\discretionary {-}{}{}parameters}
 231     \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}, \hyperpage{84}
 232     \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}, \hyperpage{84}
 233     \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}, \hyperpage{83}
 234     \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}, \hyperpage{83}
 235     \subitem {scale\_\discretionary {-}{}{}parameters}, \hyperpage{83}
 236   \item {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}
 237     \subitem {convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{91}
 238     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}, \hyperpage{89}
 239     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}, \hyperpage{90}
 240     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}, \hyperpage{90}
 241     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}, \hyperpage{89}
 242     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}, \hyperpage{91}
 243     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}, \hyperpage{89}
 244     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}, \hyperpage{90}
 245     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}, \hyperpage{90}
 246     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}, \hyperpage{90}
 247     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}, \hyperpage{90}
 248     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}, \hyperpage{90}
 249     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}, \hyperpage{90}
 250     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}, \hyperpage{89}
 251     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}, \hyperpage{89}
 252     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}, \hyperpage{89}
 253     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}, \hyperpage{89}
 254     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}, \hyperpage{89}
 255     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}, \hyperpage{89}
 256     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}, \hyperpage{91}
 257     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}, \hyperpage{90}
 258     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}, \hyperpage{89}
 259     \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}, \hyperpage{90}
 260   \item {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}
 261     \subitem {read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{86}
 262     \subitem {write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{86}
 263   \item {energy\_\discretionary {-}{}{}set}
 264     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 265   \item {Enumerating Suboptimal Structures}, \hyperpage{48}
 266   \item {eval}
 267     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}, \hyperpage{95}
 268     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}, \hyperpage{94}
 269     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}, \hyperpage{94}
 270     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}, \hyperpage{96}
 271     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}, \hyperpage{94}
 272     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}, \hyperpage{95}
 273   \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}
 274     \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{195}
 275   \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}
 276     \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{196}
 277   \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}
 278     \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{195}
 279   \item {expand\_\discretionary {-}{}{}Full}
 280     \subitem {RNAstruct.h}, \hyperpage{226}
 281   \item {expand\_\discretionary {-}{}{}Shapiro}
 282     \subitem {RNAstruct.h}, \hyperpage{226}
 283   \item {expHairpinEnergy}
 284     \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
 285   \item {expLoopEnergy}
 286     \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
 287   \item {export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}
 288     \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{74}
 289   \item {export\_\discretionary {-}{}{}bppm}
 290     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}
 291   \item {export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}
 292     \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{60}
 293   \item {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}
 294     \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{56}
 295   \item {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}
 296     \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{56}
 297
 298   \indexspace
 299
 300   \item {FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}
 301     \subitem {utils.h}, \hyperpage{240}
 302   \item {FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}
 303     \subitem {utils.h}, \hyperpage{240}
 304   \item {final\_\discretionary {-}{}{}cost}
 305     \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
 306   \item {find\_\discretionary {-}{}{}saddle}
 307     \subitem {findpath.h}, \hyperpage{171}
 308   \item {findpath.h}
 309     \subitem {find\_\discretionary {-}{}{}saddle}, \hyperpage{171}
 310     \subitem {free\_\discretionary {-}{}{}path}, \hyperpage{172}
 311     \subitem {get\_\discretionary {-}{}{}path}, \hyperpage{172}
 312   \item {fold}
 313     \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{35}
 314   \item {fold.h}
 315     \subitem {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}, \hyperpage{177}
 316     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}, \hyperpage{179}
 317     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}, \hyperpage{175}
 318     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}, \hyperpage{176}
 319     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}, \hyperpage{177}
 320     \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}, \hyperpage{178}
 321     \subitem {HairpinE}, \hyperpage{177}
 322     \subitem {initialize\_\discretionary {-}{}{}fold}, \hyperpage{177}
 323     \subitem {loop\_\discretionary {-}{}{}energy}, \hyperpage{176}
 324     \subitem {LoopEnergy}, \hyperpage{177}
 325     \subitem {parenthesis\_\discretionary {-}{}{}structure}, \hyperpage{175}
 326     \subitem {parenthesis\_\discretionary {-}{}{}zuker}, \hyperpage{175}
 327   \item {fold\_\discretionary {-}{}{}par}
 328     \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{34}
 329   \item {fold\_\discretionary {-}{}{}vars.h}
 330     \subitem {backtrack\_\discretionary {-}{}{}type}, \hyperpage{185}
 331     \subitem {base\_\discretionary {-}{}{}pair}, \hyperpage{184}
 332     \subitem {cut\_\discretionary {-}{}{}point}, \hyperpage{183}
 333     \subitem {dangles}, \hyperpage{182}
 334     \subitem {do\_\discretionary {-}{}{}backtrack}, \hyperpage{184}
 335     \subitem {energy\_\discretionary {-}{}{}set}, \hyperpage{183}
 336     \subitem {iindx}, \hyperpage{184}
 337     \subitem {james\_\discretionary {-}{}{}rule}, \hyperpage{183}
 338     \subitem {logML}, \hyperpage{183}
 339     \subitem {noLonelyPairs}, \hyperpage{182}
 340     \subitem {nonstandards}, \hyperpage{183}
 341     \subitem {oldAliEn}, \hyperpage{183}
 342     \subitem {pf\_\discretionary {-}{}{}scale}, \hyperpage{184}
 343     \subitem {pr}, \hyperpage{184}
 344     \subitem {ribo}, \hyperpage{183}
 345     \subitem {RibosumFile}, \hyperpage{183}
 346     \subitem {set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}, \hyperpage{182}
 347     \subitem {temperature}, \hyperpage{183}
 348     \subitem {tetra\_\discretionary {-}{}{}loop}, \hyperpage{183}
 349   \item {folden}, \hyperpage{120}
 350   \item {FORBIDDEN}
 351     \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
 352   \item {free\_\discretionary {-}{}{}path}
 353     \subitem {findpath.h}, \hyperpage{172}
 354   \item {free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}
 355     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{41}
 356   \item {free\_\discretionary {-}{}{}profile}
 357     \subitem {profiledist.h}, \hyperpage{217}
 358   \item {free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}
 359     \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{69}
 360   \item {free\_\discretionary {-}{}{}tree}
 361     \subitem {treedist.h}, \hyperpage{233}
 362
 363   \indexspace
 364
 365   \item {GASCONST}
 366     \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
 367   \item {get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}
 368     \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{69}
 369   \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}
 370     \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{84}
 371   \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}
 372     \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{84}
 373   \item {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}
 374     \subitem {centroid\_\discretionary {-}{}{}fold}, \hyperpage{46}
 375   \item {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}
 376     \subitem {centroid\_\discretionary {-}{}{}fold}, \hyperpage{46}
 377   \item {get\_\discretionary {-}{}{}concentrations}
 378     \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
 379   \item {get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix}
 380     \subitem {gquad.h}, \hyperpage{186}
 381   \item {get\_\discretionary {-}{}{}iindx}
 382     \subitem {utils.h}, \hyperpage{248}
 383   \item {get\_\discretionary {-}{}{}indx}
 384     \subitem {utils.h}, \hyperpage{248}
 385   \item {get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}
 386     \subitem {utils.h}, \hyperpage{243}
 387   \item {get\_\discretionary {-}{}{}line}
 388     \subitem {utils.h}, \hyperpage{243}
 389   \item {get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}
 390     \subitem {cofold.h}, \hyperpage{160}
 391   \item {get\_\discretionary {-}{}{}mpi}
 392     \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{67}
 393   \item {get\_\discretionary {-}{}{}path}
 394     \subitem {findpath.h}, \hyperpage{172}
 395   \item {get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}
 396     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
 397   \item {get\_\discretionary {-}{}{}plist}
 398     \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{209}
 399   \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}
 400     \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
 401   \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}
 402     \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
 403   \item {get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}
 404     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
 405   \item {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}
 406     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
 407   \item {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}
 408     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
 409   \item {give\_\discretionary {-}{}{}up}
 410     \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
 411   \item {gmlRNA}
 412     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
 413   \item {gquad.h}
 414     \subitem {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop}, \hyperpage{187}
 415     \subitem {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L}, \hyperpage{187}
 416     \subitem {get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix}, \hyperpage{186}
 417     \subitem {parse\_\discretionary {-}{}{}gquad}, \hyperpage{187}
 418
 419   \indexspace
 420
 421   \item {HairpinE}
 422     \subitem {fold.h}, \hyperpage{177}
 423   \item {hamming}
 424     \subitem {utils.h}, \hyperpage{242}
 425   \item {hamming\_\discretionary {-}{}{}bound}
 426     \subitem {utils.h}, \hyperpage{242}
 427
 428   \indexspace
 429
 430   \item {iindx}
 431     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
 432   \item {INF}
 433     \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
 434   \item {init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
 435     \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{209}
 436   \item {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
 437     \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
 438   \item {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}
 439     \subitem {LPfold.h}, \hyperpage{199}
 440   \item {initialize\_\discretionary {-}{}{}cofold}
 441     \subitem {cofold.h}, \hyperpage{160}
 442   \item {initialize\_\discretionary {-}{}{}fold}
 443     \subitem {fold.h}, \hyperpage{177}
 444   \item {int\_\discretionary {-}{}{}urn}
 445     \subitem {utils.h}, \hyperpage{241}
 446   \item {interact}, \hyperpage{121}
 447   \item {intermediate\_\discretionary {-}{}{}t}, \hyperpage{122}
 448   \item {INTERVAL}, \hyperpage{123}
 449   \item {inv\_\discretionary {-}{}{}verbose}
 450     \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
 451   \item {inverse\_\discretionary {-}{}{}fold}
 452     \subitem {final\_\discretionary {-}{}{}cost}, \hyperpage{98}
 453     \subitem {give\_\discretionary {-}{}{}up}, \hyperpage{98}
 454     \subitem {inv\_\discretionary {-}{}{}verbose}, \hyperpage{98}
 455     \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{97}
 456     \subitem {inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{98}
 457     \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{97}
 458   \item {inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
 459     \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
 460
 461   \indexspace
 462
 463   \item {james\_\discretionary {-}{}{}rule}
 464     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 465
 466   \indexspace
 467
 468   \item {K0}
 469     \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
 470   \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}
 471     \subitem {destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}, \hyperpage{102}
 472     \subitem {get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}, \hyperpage{102}
 473     \subitem {TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}, \hyperpage{103}
 474     \subitem {TwoDfoldList}, \hyperpage{102}
 475   \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}
 476     \subitem {destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}, \hyperpage{105}
 477     \subitem {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}, \hyperpage{105}
 478     \subitem {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}, \hyperpage{105}
 479     \subitem {TwoDpfoldList}, \hyperpage{106}
 480   \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}
 481     \subitem {TwoDpfold\_\discretionary {-}{}{}pbacktrack}, \hyperpage{107}
 482     \subitem {TwoDpfold\_\discretionary {-}{}{}pbacktrack5}, \hyperpage{108}
 483
 484   \indexspace
 485
 486   \item {Lfold}
 487     \subitem {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{77}
 488   \item {Lfoldz}
 489     \subitem {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{77}
 490   \item {LIST}, \hyperpage{124}
 491   \item {Local MFE consensus structures for Sequence Alignments}, \hyperpage{81}
 492   \item {Local MFE structure Prediction and Z-\/scores}, \hyperpage{77}
 493   \item {local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}
 494     \subitem {aliLfold}, \hyperpage{81}
 495   \item {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}
 496     \subitem {Lfold}, \hyperpage{77}
 497     \subitem {Lfoldz}, \hyperpage{77}
 498   \item {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
 499     \subitem {pfl\_\discretionary {-}{}{}fold}, \hyperpage{78}
 500     \subitem {putoutpU\_\discretionary {-}{}{}prob}, \hyperpage{79}
 501     \subitem {putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}, \hyperpage{79}
 502     \subitem {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}, \hyperpage{78}
 503   \item {logML}
 504     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 505   \item {loop\_\discretionary {-}{}{}energies.h}
 506     \subitem {E\_\discretionary {-}{}{}Hairpin}, \hyperpage{193}
 507     \subitem {E\_\discretionary {-}{}{}IntLoop}, \hyperpage{192}
 508     \subitem {E\_\discretionary {-}{}{}Stem}, \hyperpage{194}
 509     \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}, \hyperpage{195}
 510     \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}, \hyperpage{196}
 511     \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}, \hyperpage{195}
 512   \item {loop\_\discretionary {-}{}{}energy}
 513     \subitem {fold.h}, \hyperpage{176}
 514   \item {LoopEnergy}
 515     \subitem {fold.h}, \hyperpage{177}
 516   \item {LPfold.h}
 517     \subitem {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}, \hyperpage{199}
 518   \item {LST\_\discretionary {-}{}{}BUCKET}, \hyperpage{125}
 519
 520   \indexspace
 521
 522   \item {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}
 523     \subitem {profiledist.h}, \hyperpage{217}
 524   \item {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}
 525     \subitem {profiledist.h}, \hyperpage{216}
 526   \item {make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt}
 527     \subitem {utils.h}, \hyperpage{246}
 528   \item {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
 529     \subitem {utils.h}, \hyperpage{246}
 530   \item {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}
 531     \subitem {utils.h}, \hyperpage{246}
 532   \item {Make\_\discretionary {-}{}{}swString}
 533     \subitem {stringdist.h}, \hyperpage{229}
 534   \item {make\_\discretionary {-}{}{}tree}
 535     \subitem {treedist.h}, \hyperpage{232}
 536   \item {MAX2}
 537     \subitem {utils.h}, \hyperpage{239}
 538   \item {MAX3}
 539     \subitem {utils.h}, \hyperpage{240}
 540   \item {MAXLOOP}
 541     \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
 542   \item {MEA}
 543     \subitem {MEA.h}, \hyperpage{200}
 544   \item {MEA.h}
 545     \subitem {MEA}, \hyperpage{200}
 546   \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}
 547     \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
 548   \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}
 549     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
 550   \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}
 551     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
 552   \item {MFE Consensus Structures for Sequence Alignment(s)}, \hyperpage{71}
 553   \item {MFE Structures of two hybridized Sequences}, \hyperpage{55}
 554   \item {mfe\_\discretionary {-}{}{}cofold}
 555     \subitem {cofold}, \hyperpage{55}
 556     \subitem {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}, \hyperpage{56}
 557     \subitem {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}, \hyperpage{56}
 558   \item {mfe\_\discretionary {-}{}{}fold}
 559     \subitem {circfold}, \hyperpage{35}
 560     \subitem {fold}, \hyperpage{35}
 561     \subitem {fold\_\discretionary {-}{}{}par}, \hyperpage{34}
 562   \item {MIN2}
 563     \subitem {utils.h}, \hyperpage{239}
 564   \item {MIN3}
 565     \subitem {utils.h}, \hyperpage{239}
 566   \item {model\_\discretionary {-}{}{}detailsT}, \hyperpage{126}
 567     \subitem {dangles}, \hyperpage{126}
 568   \item {move\_\discretionary {-}{}{}t}, \hyperpage{128}
 569
 570   \indexspace
 571
 572   \item {NBPAIRS}
 573     \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
 574   \item {nc\_\discretionary {-}{}{}fact}
 575     \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{70}
 576   \item {noLonelyPairs}
 577     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
 578   \item {nonstandards}
 579     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 580   \item {nrerror}
 581     \subitem {utils.h}, \hyperpage{241}
 582
 583   \indexspace
 584
 585   \item {oldAliEn}
 586     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 587
 588   \indexspace
 589
 590   \item {pack\_\discretionary {-}{}{}structure}
 591     \subitem {utils.h}, \hyperpage{245}
 592   \item {PAIR}, \hyperpage{129}
 593   \item {pair\_\discretionary {-}{}{}info}, \hyperpage{130}
 594   \item {pairpro}, \hyperpage{131}
 595   \item {paramT}, \hyperpage{132}
 596   \item {parenthesis\_\discretionary {-}{}{}structure}
 597     \subitem {fold.h}, \hyperpage{175}
 598   \item {parenthesis\_\discretionary {-}{}{}zuker}
 599     \subitem {fold.h}, \hyperpage{175}
 600   \item {parse\_\discretionary {-}{}{}gquad}
 601     \subitem {gquad.h}, \hyperpage{187}
 602   \item {parse\_\discretionary {-}{}{}structure}
 603     \subitem {RNAstruct.h}, \hyperpage{227}
 604   \item {Parsing and Comparing -\/ Functions to Manipulate Structures}, \hyperpage{110}
 605   \item {part\_\discretionary {-}{}{}func.h}
 606     \subitem {centroid}, \hyperpage{207}
 607     \subitem {expHairpinEnergy}, \hyperpage{207}
 608     \subitem {expLoopEnergy}, \hyperpage{207}
 609     \subitem {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{207}
 610     \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}, \hyperpage{207}
 611   \item {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}
 612     \subitem {get\_\discretionary {-}{}{}plist}, \hyperpage{209}
 613     \subitem {init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{209}
 614   \item {Partition Function and Base Pair Probabilities for Sequence Alignment(s)}, \hyperpage{73}
 615   \item {Partition Function for two hybridized Sequences}, \hyperpage{58}
 616   \item {Partition Function for two hybridized Sequences as a stepwise Process}, \hyperpage{63}
 617   \item {Partition functions for locally stable secondary structures}, \hyperpage{78}
 618   \item {path\_\discretionary {-}{}{}t}, \hyperpage{133}
 619   \item {pbacktrack}
 620     \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{52}
 621   \item {pbacktrack\_\discretionary {-}{}{}circ}
 622     \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{53}
 623   \item {pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}
 624     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{40}
 625   \item {pf\_\discretionary {-}{}{}cofold}
 626     \subitem {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{59}
 627     \subitem {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{59}
 628     \subitem {compute\_\discretionary {-}{}{}probabilities}, \hyperpage{61}
 629     \subitem {export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}, \hyperpage{60}
 630     \subitem {get\_\discretionary {-}{}{}concentrations}, \hyperpage{61}
 631     \subitem {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}, \hyperpage{60}
 632     \subitem {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}, \hyperpage{61}
 633   \item {pf\_\discretionary {-}{}{}fold}
 634     \subitem {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}, \hyperpage{42}
 635     \subitem {export\_\discretionary {-}{}{}bppm}, \hyperpage{42}
 636     \subitem {free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}, \hyperpage{41}
 637     \subitem {get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}, \hyperpage{43}
 638     \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}, \hyperpage{43}
 639     \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}, \hyperpage{43}
 640     \subitem {pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}, \hyperpage{40}
 641     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
 642     \subitem {pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{39}
 643     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
 644     \subitem {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}, \hyperpage{42}
 645   \item {pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
 646     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
 647   \item {pf\_\discretionary {-}{}{}interact}
 648     \subitem {up\_\discretionary {-}{}{}cofold}, \hyperpage{64}
 649   \item {pf\_\discretionary {-}{}{}paramT}, \hyperpage{134}
 650     \subitem {alpha}, \hyperpage{134}
 651   \item {pf\_\discretionary {-}{}{}scale}
 652     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
 653   \item {pf\_\discretionary {-}{}{}unstru}
 654     \subitem {up\_\discretionary {-}{}{}cofold}, \hyperpage{63}
 655   \item {pfl\_\discretionary {-}{}{}fold}
 656     \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{78}
 657   \item {plist}, \hyperpage{136}
 658   \item {plot\_\discretionary {-}{}{}layouts.h}
 659     \subitem {rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}, \hyperpage{215}
 660     \subitem {simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}, \hyperpage{214}
 661     \subitem {simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}, \hyperpage{214}
 662     \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}, \hyperpage{213}
 663     \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}, \hyperpage{213}
 664     \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}, \hyperpage{213}
 665   \item {Postorder\_\discretionary {-}{}{}list}, \hyperpage{137}
 666   \item {pr}
 667     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
 668   \item {Predicting Consensus Structures from Alignment(s)}, \hyperpage{66}
 669   \item {Predicting Locally stable structures of large sequences}, \hyperpage{76}
 670   \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}
 671     \subitem {utils.h}, \hyperpage{247}
 672   \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}
 673     \subitem {utils.h}, \hyperpage{247}
 674   \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}
 675     \subitem {utils.h}, \hyperpage{247}
 676   \item {profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
 677     \subitem {profiledist.h}, \hyperpage{216}
 678   \item {profiledist.h}
 679     \subitem {free\_\discretionary {-}{}{}profile}, \hyperpage{217}
 680     \subitem {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}, \hyperpage{217}
 681     \subitem {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}, \hyperpage{216}
 682     \subitem {profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{216}
 683   \item {PS\_\discretionary {-}{}{}dot.h}
 684     \subitem {aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln}, \hyperpage{221}
 685     \subitem {gmlRNA}, \hyperpage{220}
 686     \subitem {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}, \hyperpage{222}
 687     \subitem {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}, \hyperpage{221}
 688     \subitem {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{219}
 689     \subitem {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}, \hyperpage{219}
 690     \subitem {ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{220}
 691     \subitem {svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{220}
 692     \subitem {xrna\_\discretionary {-}{}{}plot}, \hyperpage{221}
 693   \item {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}
 694     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{222}
 695   \item {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}
 696     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
 697   \item {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
 698     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{219}
 699   \item {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}
 700     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{219}
 701   \item {pu\_\discretionary {-}{}{}contrib}, \hyperpage{138}
 702   \item {pu\_\discretionary {-}{}{}out}, \hyperpage{139}
 703   \item {putoutpU\_\discretionary {-}{}{}prob}
 704     \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{79}
 705   \item {putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}
 706     \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{79}
 707
 708   \indexspace
 709
 710   \item {random\_\discretionary {-}{}{}string}
 711     \subitem {utils.h}, \hyperpage{242}
 712   \item {read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
 713     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}, \hyperpage{86}
 714   \item {read\_\discretionary {-}{}{}record}
 715     \subitem {utils.h}, \hyperpage{244}
 716   \item {Reading/Writing energy parameter sets from/to File}, \hyperpage{86}
 717   \item {ribo}
 718     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 719   \item {RibosumFile}
 720     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 721   \item {RNA Secondary Structure Folding}, \hyperpage{31}
 722   \item {rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}
 723     \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{215}
 724   \item {RNAstruct.h}
 725     \subitem {add\_\discretionary {-}{}{}root}, \hyperpage{226}
 726     \subitem {b2C}, \hyperpage{225}
 727     \subitem {b2HIT}, \hyperpage{225}
 728     \subitem {b2Shapiro}, \hyperpage{226}
 729     \subitem {expand\_\discretionary {-}{}{}Full}, \hyperpage{226}
 730     \subitem {expand\_\discretionary {-}{}{}Shapiro}, \hyperpage{226}
 731     \subitem {parse\_\discretionary {-}{}{}structure}, \hyperpage{227}
 732     \subitem {unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}, \hyperpage{227}
 733     \subitem {unexpand\_\discretionary {-}{}{}Full}, \hyperpage{227}
 734     \subitem {unweight}, \hyperpage{227}
 735
 736   \indexspace
 737
 738   \item {scale\_\discretionary {-}{}{}parameters}
 739     \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
 740   \item {Searching Sequences for Predefined Structures}, \hyperpage{97}
 741   \item {sect}, \hyperpage{140}
 742   \item {set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}
 743     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
 744   \item {simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}
 745     \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{214}
 746   \item {simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}
 747     \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{214}
 748   \item {snoopT}, \hyperpage{141}
 749   \item {SOLUTION}, \hyperpage{142}
 750   \item {space}
 751     \subitem {utils.h}, \hyperpage{240}
 752   \item {ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
 753     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
 754   \item {st\_\discretionary {-}{}{}back}
 755     \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{53}
 756   \item {Stochastic backtracking in the Ensemble}, \hyperpage{52}
 757   \item {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}, \hyperpage{75}
 758   \item {Stochastic Backtracking of Structures from Distance Based Partitioning}, \hyperpage{107}
 759   \item {STR}
 760     \subitem {utils.h}, \hyperpage{240}
 761   \item {str\_\discretionary {-}{}{}DNA2RNA}
 762     \subitem {utils.h}, \hyperpage{247}
 763   \item {str\_\discretionary {-}{}{}uppercase}
 764     \subitem {utils.h}, \hyperpage{247}
 765   \item {string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
 766     \subitem {stringdist.h}, \hyperpage{229}
 767   \item {stringdist.h}
 768     \subitem {Make\_\discretionary {-}{}{}swString}, \hyperpage{229}
 769     \subitem {string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{229}
 770   \item {struct\_\discretionary {-}{}{}en}, \hyperpage{143}
 771   \item {subopt}
 772     \subitem {subopt\_\discretionary {-}{}{}wuchty}, \hyperpage{50}
 773   \item {subopt\_\discretionary {-}{}{}circ}
 774     \subitem {subopt\_\discretionary {-}{}{}wuchty}, \hyperpage{51}
 775   \item {subopt\_\discretionary {-}{}{}stochbt}
 776     \subitem {pbacktrack}, \hyperpage{52}
 777     \subitem {pbacktrack\_\discretionary {-}{}{}circ}, \hyperpage{53}
 778     \subitem {st\_\discretionary {-}{}{}back}, \hyperpage{53}
 779   \item {subopt\_\discretionary {-}{}{}wuchty}
 780     \subitem {subopt}, \hyperpage{50}
 781     \subitem {subopt\_\discretionary {-}{}{}circ}, \hyperpage{51}
 782   \item {subopt\_\discretionary {-}{}{}zuker}
 783     \subitem {zukersubopt}, \hyperpage{49}
 784   \item {Suboptimal structures according to Zuker et al. 1989}, \hyperpage{49}
 785   \item {Suboptimal structures within an energy band arround the MFE}, \hyperpage{50}
 786   \item {svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
 787     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
 788   \item {svm\_\discretionary {-}{}{}model}, \hyperpage{144}
 789   \item {swString}, \hyperpage{145}
 790
 791   \indexspace
 792
 793   \item {temperature}
 794     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 795   \item {tetra\_\discretionary {-}{}{}loop}
 796     \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
 797   \item {time\_\discretionary {-}{}{}stamp}
 798     \subitem {utils.h}, \hyperpage{242}
 799   \item {Tree}, \hyperpage{146}
 800   \item {tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
 801     \subitem {treedist.h}, \hyperpage{232}
 802   \item {treedist.h}
 803     \subitem {free\_\discretionary {-}{}{}tree}, \hyperpage{233}
 804     \subitem {make\_\discretionary {-}{}{}tree}, \hyperpage{232}
 805     \subitem {tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{232}
 806   \item {TURN}
 807     \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
 808   \item {TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}
 809     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{103}
 810   \item {TwoDfold\_\discretionary {-}{}{}solution}, \hyperpage{147}
 811   \item {TwoDfold\_\discretionary {-}{}{}vars}, \hyperpage{148}
 812   \item {TwoDfoldList}
 813     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
 814   \item {TwoDpfold\_\discretionary {-}{}{}pbacktrack}
 815     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}, \hyperpage{107}
 816   \item {TwoDpfold\_\discretionary {-}{}{}pbacktrack5}
 817     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}, \hyperpage{108}
 818   \item {TwoDpfold\_\discretionary {-}{}{}solution}, \hyperpage{150}
 819   \item {TwoDpfold\_\discretionary {-}{}{}vars}, \hyperpage{151}
 820   \item {TwoDpfoldList}
 821     \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{106}
 822
 823   \indexspace
 824
 825   \item {unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}
 826     \subitem {RNAstruct.h}, \hyperpage{227}
 827   \item {unexpand\_\discretionary {-}{}{}Full}
 828     \subitem {RNAstruct.h}, \hyperpage{227}
 829   \item {unpack\_\discretionary {-}{}{}structure}
 830     \subitem {utils.h}, \hyperpage{245}
 831   \item {unweight}
 832     \subitem {RNAstruct.h}, \hyperpage{227}
 833   \item {up\_\discretionary {-}{}{}cofold}
 834     \subitem {pf\_\discretionary {-}{}{}interact}, \hyperpage{64}
 835     \subitem {pf\_\discretionary {-}{}{}unstru}, \hyperpage{63}
 836   \item {update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}
 837     \subitem {alifold.h}, \hyperpage{158}
 838   \item {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}
 839     \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{60}
 840   \item {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}
 841     \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
 842   \item {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}
 843     \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}
 844   \item {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}
 845     \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{78}
 846   \item {urn}
 847     \subitem {utils.h}, \hyperpage{241}
 848   \item {utils.h}
 849     \subitem {alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
 850     \subitem {constrain\_\discretionary {-}{}{}ptypes}, \hyperpage{248}
 851     \subitem {copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
 852     \subitem {FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}, \hyperpage{240}
 853     \subitem {FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}, \hyperpage{240}
 854     \subitem {get\_\discretionary {-}{}{}iindx}, \hyperpage{248}
 855     \subitem {get\_\discretionary {-}{}{}indx}, \hyperpage{248}
 856     \subitem {get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}, \hyperpage{243}
 857     \subitem {get\_\discretionary {-}{}{}line}, \hyperpage{243}
 858     \subitem {hamming}, \hyperpage{242}
 859     \subitem {hamming\_\discretionary {-}{}{}bound}, \hyperpage{242}
 860     \subitem {int\_\discretionary {-}{}{}urn}, \hyperpage{241}
 861     \subitem {make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt}, \hyperpage{246}
 862     \subitem {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
 863     \subitem {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}, \hyperpage{246}
 864     \subitem {MAX2}, \hyperpage{239}
 865     \subitem {MAX3}, \hyperpage{240}
 866     \subitem {MIN2}, \hyperpage{239}
 867     \subitem {MIN3}, \hyperpage{239}
 868     \subitem {nrerror}, \hyperpage{241}
 869     \subitem {pack\_\discretionary {-}{}{}structure}, \hyperpage{245}
 870     \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}, \hyperpage{247}
 871     \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}, \hyperpage{247}
 872     \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}, \hyperpage{247}
 873     \subitem {random\_\discretionary {-}{}{}string}, \hyperpage{242}
 874     \subitem {read\_\discretionary {-}{}{}record}, \hyperpage{244}
 875     \subitem {space}, \hyperpage{240}
 876     \subitem {STR}, \hyperpage{240}
 877     \subitem {str\_\discretionary {-}{}{}DNA2RNA}, \hyperpage{247}
 878     \subitem {str\_\discretionary {-}{}{}uppercase}, \hyperpage{247}
 879     \subitem {time\_\discretionary {-}{}{}stamp}, \hyperpage{242}
 880     \subitem {unpack\_\discretionary {-}{}{}structure}, \hyperpage{245}
 881     \subitem {urn}, \hyperpage{241}
 882     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL}, \hyperpage{239}
 883     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK}, \hyperpage{238}
 884     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}, \hyperpage{238}
 885     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G}, \hyperpage{239}
 886     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE}, \hyperpage{239}
 887     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER}, \hyperpage{239}
 888     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE}, \hyperpage{238}
 889     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK}, \hyperpage{239}
 890     \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X}, \hyperpage{238}
 891     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE}, \hyperpage{238}
 892     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT}, \hyperpage{238}
 893     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}, \hyperpage{237}
 894     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR}, \hyperpage{237}
 895     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}, \hyperpage{237}
 896     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC}, \hyperpage{237}
 897     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST}, \hyperpage{238}
 898     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN}, \hyperpage{238}
 899     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION}, \hyperpage{237}
 900     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES}, \hyperpage{238}
 901     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS}, \hyperpage{238}
 902     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT}, \hyperpage{237}
 903     \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}, \hyperpage{237}
 904     \subitem {VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}, \hyperpage{239}
 905     \subitem {warn\_\discretionary {-}{}{}user}, \hyperpage{241}
 906     \subitem {xrealloc}, \hyperpage{240}
 907     \subitem {XSTR}, \hyperpage{240}
 908     \subitem {xsubi}, \hyperpage{249}
 909
 910   \indexspace
 911
 912   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL}
 913     \subitem {utils.h}, \hyperpage{239}
 914   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK}
 915     \subitem {utils.h}, \hyperpage{238}
 916   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}
 917     \subitem {utils.h}, \hyperpage{238}
 918   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G}
 919     \subitem {utils.h}, \hyperpage{239}
 920   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE}
 921     \subitem {utils.h}, \hyperpage{239}
 922   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER}
 923     \subitem {utils.h}, \hyperpage{239}
 924   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE}
 925     \subitem {utils.h}, \hyperpage{238}
 926   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK}
 927     \subitem {utils.h}, \hyperpage{239}
 928   \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X}
 929     \subitem {utils.h}, \hyperpage{238}
 930   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}
 931     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 932   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}
 933     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 934   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}
 935     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 936   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}
 937     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 938   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}
 939     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
 940   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}
 941     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 942   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}
 943     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 944   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}
 945     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 946   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}
 947     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 948   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}
 949     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 950   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}
 951     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 952   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}
 953     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 954   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}
 955     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 956   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}
 957     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 958   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}
 959     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 960   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}
 961     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 962   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}
 963     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 964   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}
 965     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 966   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}
 967     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
 968   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}
 969     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 970   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}
 971     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
 972   \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}
 973     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
 974   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE}
 975     \subitem {utils.h}, \hyperpage{238}
 976   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT}
 977     \subitem {utils.h}, \hyperpage{238}
 978   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}
 979     \subitem {utils.h}, \hyperpage{237}
 980   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR}
 981     \subitem {utils.h}, \hyperpage{237}
 982   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}
 983     \subitem {utils.h}, \hyperpage{237}
 984   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC}
 985     \subitem {utils.h}, \hyperpage{237}
 986   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST}
 987     \subitem {utils.h}, \hyperpage{238}
 988   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN}
 989     \subitem {utils.h}, \hyperpage{238}
 990   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION}
 991     \subitem {utils.h}, \hyperpage{237}
 992   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES}
 993     \subitem {utils.h}, \hyperpage{238}
 994   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS}
 995     \subitem {utils.h}, \hyperpage{238}
 996   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT}
 997     \subitem {utils.h}, \hyperpage{237}
 998   \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}
 999     \subitem {utils.h}, \hyperpage{237}
1000   \item {VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}
1001     \subitem {utils.h}, \hyperpage{239}
1002   \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}
1003     \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}
1004   \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}
1005     \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}
1006   \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}
1007     \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}
1008
1009   \indexspace
1010
1011   \item {warn\_\discretionary {-}{}{}user}
1012     \subitem {utils.h}, \hyperpage{241}
1013   \item {write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
1014     \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}, \hyperpage{86}
1015
1016   \indexspace
1017
1018   \item {xrealloc}
1019     \subitem {utils.h}, \hyperpage{240}
1020   \item {xrna\_\discretionary {-}{}{}plot}
1021     \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
1022   \item {XSTR}
1023     \subitem {utils.h}, \hyperpage{240}
1024   \item {xsubi}
1025     \subitem {utils.h}, \hyperpage{249}
1026
1027   \indexspace
1028
1029   \item {zukersubopt}
1030     \subitem {subopt\_\discretionary {-}{}{}zuker}, \hyperpage{49}
1031
1032 \end{theindex}