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

   1 \begin{theindex}
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  22                 \hyperpage{114}
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  30                 \hyperpage{119}
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  32                 \hyperpage{119}
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  36                 \hyperpage{122}
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  38                 \hyperpage{128}
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  40                 \hyperpage{133}
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  42                 \hyperpage{135}
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  44                 \hyperpage{136}
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  46                 \hyperpage{144}
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  60                 \hyperpage{155}
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  62                 \hyperpage{160}
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  64                 \hyperpage{164}
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  66                 \hyperpage{166}
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  70                 \hyperpage{168}
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  72                 \hyperpage{182}
  73   \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.\discretionary {-}{}{}8.\discretionary {-}{}{}4\discretionary {-}{}{}\_\discretionary {-}{}{}intloops.\discretionary {-}{}{}h},
  74                 \hyperpage{182}
  75
  76   \indexspace
  77
  78   \item {add\discretionary {-}{}{}\_\discretionary {-}{}{}root}
  79     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
  80                 \hyperpage{163}
  81   \item {ali\discretionary {-}{}{}Lfold}
  82     \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments},
  83                 \hyperpage{63}
  84   \item {ali\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}color\discretionary {-}{}{}\_\discretionary {-}{}{}aln}
  85     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
  86                 \hyperpage{160}
  87   \item {alifold}
  88     \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)},
  89                 \hyperpage{54}
  90   \item {alifold.\discretionary {-}{}{}h}
  91     \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params},
  92                 \hyperpage{112}
  93   \item {alimake\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}
  94     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
  95   \item {alipbacktrack}
  96     \subitem {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)},
  97                 \hyperpage{58}
  98   \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
  99     \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
 100                 \hyperpage{57}
 101   \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 102     \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
 103                 \hyperpage{56}
 104   \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}
 105     \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
 106                 \hyperpage{56}
 107   \item {alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
 108     \subitem {Predicting Consensus Structures from Alignment(s)},
 109                 \hyperpage{52}
 110   \item {alpha}
 111     \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T},
 112                 \hyperpage{100}
 113   \item {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}db}
 114     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
 115   \item {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr}
 116     \subitem {Calculating Partition Functions and Pair Probabilities},
 117                 \hyperpage{29}
 118
 119   \indexspace
 120
 121   \item {b2\discretionary {-}{}{}C}
 122     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
 123                 \hyperpage{162}
 124   \item {b2\discretionary {-}{}{}H\discretionary {-}{}{}I\discretionary {-}{}{}T}
 125     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
 126                 \hyperpage{162}
 127   \item {b2\discretionary {-}{}{}Shapiro}
 128     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
 129                 \hyperpage{162}
 130   \item {B\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}U\discretionary {-}{}{}S}
 131     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
 132                 \hyperpage{120}
 133   \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}
 134     \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134}
 135   \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L}
 136     \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134}
 137   \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}type}
 138     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 139                 \hyperpage{132}
 140   \item {base\discretionary {-}{}{}\_\discretionary {-}{}{}pair}
 141     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 142                 \hyperpage{132}
 143   \item {bond\discretionary {-}{}{}T}, \hyperpage{91}
 144   \item {bond\discretionary {-}{}{}T\discretionary {-}{}{}En},
 145                 \hyperpage{91}
 146
 147   \indexspace
 148
 149   \item {C\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}D\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}E},
 150                 \hyperpage{92}
 151   \item {Calculate Partition Functions of a Distance Based Partitioning},
 152                 \hyperpage{84}
 153     \subitem {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables},
 154                 \hyperpage{85}
 155     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables},
 156                 \hyperpage{84}
 157     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E},
 158                 \hyperpage{85}
 159     \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List},
 160                 \hyperpage{85}
 161   \item {Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization},
 162                 \hyperpage{41}
 163   \item {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
 164                 \hyperpage{81}
 165     \subitem {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables},
 166                 \hyperpage{82}
 167     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables},
 168                 \hyperpage{81}
 169     \subitem {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5},
 170                 \hyperpage{83}
 171     \subitem {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List},
 172                 \hyperpage{82}
 173   \item {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures},
 174                 \hyperpage{22}
 175     \subitem {circfold}, \hyperpage{24}
 176     \subitem {fold}, \hyperpage{23}
 177     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}par},
 178                 \hyperpage{23}
 179   \item {Calculating Partition Functions and Pair Probabilities},
 180                 \hyperpage{25}
 181     \subitem {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr},
 182                 \hyperpage{29}
 183     \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm},
 184                 \hyperpage{29}
 185     \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
 186                 \hyperpage{29}
 187     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
 188                 \hyperpage{30}
 189     \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance},
 190                 \hyperpage{30}
 191     \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr},
 192                 \hyperpage{31}
 193     \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 194                 \hyperpage{28}
 195     \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 196                 \hyperpage{27}
 197     \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par},
 198                 \hyperpage{26}
 199     \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params},
 200                 \hyperpage{29}
 201   \item {centroid}
 202     \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
 203                 \hyperpage{148}
 204   \item {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
 205                 \hyperpage{64}
 206     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy},
 207                 \hyperpage{66}
 208     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors},
 209                 \hyperpage{65}
 210     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters},
 211                 \hyperpage{65}
 212     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters},
 213                 \hyperpage{65}
 214     \subitem {scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters},
 215                 \hyperpage{65}
 216   \item {circalifold}
 217     \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)},
 218                 \hyperpage{54}
 219   \item {circfold}
 220     \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures},
 221                 \hyperpage{24}
 222   \item {Classified Dynamic Programming}, \hyperpage{79}
 223   \item {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 224     \subitem {Partition Function for two hybridized Sequences},
 225                 \hyperpage{45}
 226   \item {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}
 227     \subitem {Partition Function for two hybridized Sequences},
 228                 \hyperpage{45}
 229   \item {cofold}
 230     \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences},
 231                 \hyperpage{42}
 232   \item {cofold.\discretionary {-}{}{}h}
 233     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes},
 234                 \hyperpage{114}
 235     \subitem {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold},
 236                 \hyperpage{114}
 237   \item {cofold\discretionary {-}{}{}F}, \hyperpage{91}
 238   \item {Compute the centroid structure}, \hyperpage{33}
 239     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl},
 240                 \hyperpage{33}
 241     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr},
 242                 \hyperpage{33}
 243   \item {Compute the Density of States}, \hyperpage{89}
 244     \subitem {density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states},
 245                 \hyperpage{89}
 246   \item {Compute the structure with maximum expected accuracy (\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A)},
 247                 \hyperpage{32}
 248   \item {compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities}
 249     \subitem {Partition Function for two hybridized Sequences},
 250                 \hyperpage{47}
 251   \item {Conc\discretionary {-}{}{}Ent}, \hyperpage{92}
 252   \item {constrain}, \hyperpage{92}
 253   \item {constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes}
 254     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{181}
 255   \item {convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}
 256     \subitem {Converting energy parameter files}, \hyperpage{71}
 257   \item {Converting energy parameter files}, \hyperpage{69}
 258     \subitem {convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file},
 259                 \hyperpage{71}
 260   \item {copy\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}
 261     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
 262   \item {cost\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}
 263     \subitem {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 264                 \hyperpage{118}
 265   \item {cpair}, \hyperpage{93}
 266   \item {cut\discretionary {-}{}{}\_\discretionary {-}{}{}point}
 267     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 268                 \hyperpage{132}
 269   \item {cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact}
 270     \subitem {Predicting Consensus Structures from Alignment(s)},
 271                 \hyperpage{53}
 272
 273   \indexspace
 274
 275   \item {dangles}
 276     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 277                 \hyperpage{130}
 278     \subitem {model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T},
 279                 \hyperpage{96}
 280   \item {density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states}
 281     \subitem {Compute the Density of States}, \hyperpage{89}
 282   \item {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}
 283     \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
 284                 \hyperpage{82}
 285   \item {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}
 286     \subitem {Calculate Partition Functions of a Distance Based Partitioning},
 287                 \hyperpage{85}
 288   \item {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}
 289     \subitem {cost\discretionary {-}{}{}\_\discretionary {-}{}{}matrix},
 290                 \hyperpage{118}
 291     \subitem {edit\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack},
 292                 \hyperpage{118}
 293   \item {Distance based partitioning of the Secondary Structure Space},
 294                 \hyperpage{80}
 295   \item {do\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}
 296     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 297                 \hyperpage{132}
 298   \item {dup\discretionary {-}{}{}Var}, \hyperpage{93}
 299   \item {duplex\discretionary {-}{}{}T}, \hyperpage{93}
 300
 301   \indexspace
 302
 303   \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}
 304     \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
 305                 \hyperpage{138}
 306   \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}
 307     \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
 308                 \hyperpage{137}
 309   \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}
 310     \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
 311                 \hyperpage{138}
 312   \item {edit\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}
 313     \subitem {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 314                 \hyperpage{118}
 315   \item {encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence}
 316     \subitem {Predicting Consensus Structures from Alignment(s)},
 317                 \hyperpage{51}
 318   \item {Energy evaluation}, \hyperpage{73}
 319     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par},
 320                 \hyperpage{75}
 321     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
 322                 \hyperpage{74}
 323     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par},
 324                 \hyperpage{74}
 325     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par},
 326                 \hyperpage{76}
 327     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
 328                 \hyperpage{73}
 329     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt},
 330                 \hyperpage{75}
 331   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}
 332     \subitem {B\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}U\discretionary {-}{}{}S},
 333                 \hyperpage{120}
 334     \subitem {F\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}B\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}N},
 335                 \hyperpage{120}
 336     \subitem {G\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T},
 337                 \hyperpage{120}
 338     \subitem {I\discretionary {-}{}{}N\discretionary {-}{}{}F},
 339                 \hyperpage{120}
 340     \subitem {K0}, \hyperpage{120}
 341     \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}P},
 342                 \hyperpage{120}
 343     \subitem {N\discretionary {-}{}{}B\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}S},
 344                 \hyperpage{120}
 345     \subitem {T\discretionary {-}{}{}U\discretionary {-}{}{}R\discretionary {-}{}{}N},
 346                 \hyperpage{120}
 347   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct}
 348     \subitem {Predicting Consensus Structures from Alignment(s)},
 349                 \hyperpage{51}
 350   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct}
 351     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{127}
 352   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}
 353     \subitem {Energy evaluation}, \hyperpage{75}
 354   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
 355     \subitem {Energy evaluation}, \hyperpage{74}
 356   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move}
 357     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125}
 358   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move\discretionary {-}{}{}\_\discretionary {-}{}{}pt}
 359     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125}
 360   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct}
 361     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
 362   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}
 363     \subitem {Energy evaluation}, \hyperpage{74}
 364   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt}
 365     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{127}
 366   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par}
 367     \subitem {Energy evaluation}, \hyperpage{76}
 368   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
 369     \subitem {Energy evaluation}, \hyperpage{73}
 370   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt}
 371     \subitem {Energy evaluation}, \hyperpage{75}
 372   \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}set}
 373     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 374                 \hyperpage{131}
 375   \item {Enumerating Suboptimal Structures}, \hyperpage{35}
 376   \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}
 377     \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
 378                 \hyperpage{140}
 379   \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}
 380     \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
 381                 \hyperpage{140}
 382   \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}
 383     \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
 384                 \hyperpage{139}
 385   \item {exp\discretionary {-}{}{}Hairpin\discretionary {-}{}{}Energy}
 386     \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
 387                 \hyperpage{148}
 388   \item {exp\discretionary {-}{}{}Loop\discretionary {-}{}{}Energy}
 389     \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
 390                 \hyperpage{148}
 391   \item {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}
 392     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
 393                 \hyperpage{163}
 394   \item {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Shapiro}
 395     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
 396                 \hyperpage{163}
 397   \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}
 398     \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
 399                 \hyperpage{57}
 400   \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}
 401     \subitem {Calculating Partition Functions and Pair Probabilities},
 402                 \hyperpage{29}
 403   \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}
 404     \subitem {Partition Function for two hybridized Sequences},
 405                 \hyperpage{46}
 406   \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
 407     \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences},
 408                 \hyperpage{43}
 409   \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}
 410     \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences},
 411                 \hyperpage{43}
 412
 413   \indexspace
 414
 415   \item {F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H}
 416     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
 417   \item {F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H}
 418     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
 419   \item {F\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}B\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}N}
 420     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
 421                 \hyperpage{120}
 422   \item {final\discretionary {-}{}{}\_\discretionary {-}{}{}cost}
 423     \subitem {Searching Sequences for Predefined Structures},
 424                 \hyperpage{78}
 425   \item {find\discretionary {-}{}{}\_\discretionary {-}{}{}saddle}
 426     \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{121}
 427   \item {findpath.\discretionary {-}{}{}h}
 428     \subitem {find\discretionary {-}{}{}\_\discretionary {-}{}{}saddle},
 429                 \hyperpage{121}
 430     \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}path},
 431                 \hyperpage{122}
 432     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}path},
 433                 \hyperpage{122}
 434   \item {fold}
 435     \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures},
 436                 \hyperpage{23}
 437   \item {fold.\discretionary {-}{}{}h}
 438     \subitem {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}db},
 439                 \hyperpage{126}
 440     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct},
 441                 \hyperpage{127}
 442     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move},
 443                 \hyperpage{125}
 444     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move\discretionary {-}{}{}\_\discretionary {-}{}{}pt},
 445                 \hyperpage{125}
 446     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct},
 447                 \hyperpage{126}
 448     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt},
 449                 \hyperpage{127}
 450     \subitem {Hairpin\discretionary {-}{}{}E}, \hyperpage{126}
 451     \subitem {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 452                 \hyperpage{126}
 453     \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energy},
 454                 \hyperpage{125}
 455     \subitem {Loop\discretionary {-}{}{}Energy}, \hyperpage{126}
 456     \subitem {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
 457                 \hyperpage{124}
 458     \subitem {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}zuker},
 459                 \hyperpage{124}
 460   \item {fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}
 461     \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures},
 462                 \hyperpage{23}
 463   \item {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}
 464     \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}type},
 465                 \hyperpage{132}
 466     \subitem {base\discretionary {-}{}{}\_\discretionary {-}{}{}pair},
 467                 \hyperpage{132}
 468     \subitem {cut\discretionary {-}{}{}\_\discretionary {-}{}{}point},
 469                 \hyperpage{132}
 470     \subitem {dangles}, \hyperpage{130}
 471     \subitem {do\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack},
 472                 \hyperpage{132}
 473     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}set},
 474                 \hyperpage{131}
 475     \subitem {iindx}, \hyperpage{132}
 476     \subitem {james\discretionary {-}{}{}\_\discretionary {-}{}{}rule},
 477                 \hyperpage{131}
 478     \subitem {log\discretionary {-}{}{}M\discretionary {-}{}{}L},
 479                 \hyperpage{131}
 480     \subitem {no\discretionary {-}{}{}Lonely\discretionary {-}{}{}Pairs},
 481                 \hyperpage{130}
 482     \subitem {nonstandards}, \hyperpage{131}
 483     \subitem {old\discretionary {-}{}{}Ali\discretionary {-}{}{}En},
 484                 \hyperpage{131}
 485     \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}scale},
 486                 \hyperpage{132}
 487     \subitem {pr}, \hyperpage{132}
 488     \subitem {ribo}, \hyperpage{131}
 489     \subitem {Ribosum\discretionary {-}{}{}File}, \hyperpage{131}
 490     \subitem {set\discretionary {-}{}{}\_\discretionary {-}{}{}model\discretionary {-}{}{}\_\discretionary {-}{}{}details},
 491                 \hyperpage{130}
 492     \subitem {temperature}, \hyperpage{131}
 493     \subitem {tetra\discretionary {-}{}{}\_\discretionary {-}{}{}loop},
 494                 \hyperpage{131}
 495   \item {folden}, \hyperpage{93}
 496   \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}path}
 497     \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{122}
 498   \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
 499     \subitem {Calculating Partition Functions and Pair Probabilities},
 500                 \hyperpage{29}
 501   \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}profile}
 502     \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156}
 503   \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
 504     \subitem {Predicting Consensus Structures from Alignment(s)},
 505                 \hyperpage{52}
 506   \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}tree}
 507     \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168}
 508
 509   \indexspace
 510
 511   \item {G\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T}
 512     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
 513                 \hyperpage{120}
 514   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}
 515     \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
 516                 \hyperpage{81}
 517   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}
 518     \subitem {Calculate Partition Functions of a Distance Based Partitioning},
 519                 \hyperpage{84}
 520   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E}
 521     \subitem {Calculate Partition Functions of a Distance Based Partitioning},
 522                 \hyperpage{85}
 523   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
 524     \subitem {Predicting Consensus Structures from Alignment(s)},
 525                 \hyperpage{53}
 526   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy}
 527     \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
 528                 \hyperpage{66}
 529   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors}
 530     \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
 531                 \hyperpage{65}
 532   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}
 533     \subitem {Compute the centroid structure}, \hyperpage{33}
 534   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}
 535     \subitem {Compute the centroid structure}, \hyperpage{33}
 536   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations}
 537     \subitem {Partition Function for two hybridized Sequences},
 538                 \hyperpage{47}
 539   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}gquad\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}
 540     \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134}
 541   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}iindx}
 542     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180}
 543   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}indx}
 544     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{181}
 545   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}line}
 546     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
 547   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}line}
 548     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
 549   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes}
 550     \subitem {cofold.\discretionary {-}{}{}h}, \hyperpage{114}
 551   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}
 552     \subitem {Predicting Consensus Structures from Alignment(s)},
 553                 \hyperpage{51}
 554   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}path}
 555     \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{122}
 556   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
 557     \subitem {Calculating Partition Functions and Pair Probabilities},
 558                 \hyperpage{30}
 559   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}plist}
 560     \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h},
 561                 \hyperpage{150}
 562   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}
 563     \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
 564                 \hyperpage{65}
 565   \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}
 566     \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
 567                 \hyperpage{65}
 568   \item {give\discretionary {-}{}{}\_\discretionary {-}{}{}up}
 569     \subitem {Searching Sequences for Predefined Structures},
 570                 \hyperpage{78}
 571   \item {gml\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}
 572     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
 573                 \hyperpage{158}
 574   \item {gquad.\discretionary {-}{}{}h}
 575     \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop},
 576                 \hyperpage{134}
 577     \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L},
 578                 \hyperpage{134}
 579     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}gquad\discretionary {-}{}{}\_\discretionary {-}{}{}matrix},
 580                 \hyperpage{134}
 581     \subitem {parse\discretionary {-}{}{}\_\discretionary {-}{}{}gquad},
 582                 \hyperpage{134}
 583
 584   \indexspace
 585
 586   \item {Hairpin\discretionary {-}{}{}E}
 587     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
 588   \item {hamming}
 589     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
 590   \item {hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound}
 591     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
 592
 593   \indexspace
 594
 595   \item {I\discretionary {-}{}{}N\discretionary {-}{}{}F}
 596     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
 597                 \hyperpage{120}
 598   \item {I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}L},
 599                 \hyperpage{94}
 600   \item {iindx}
 601     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 602                 \hyperpage{132}
 603   \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 604     \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h},
 605                 \hyperpage{150}
 606   \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 607     \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
 608                 \hyperpage{148}
 609   \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}L\discretionary {-}{}{}P}
 610     \subitem {L\discretionary {-}{}{}Pfold.\discretionary {-}{}{}h},
 611                 \hyperpage{142}
 612   \item {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold}
 613     \subitem {cofold.\discretionary {-}{}{}h}, \hyperpage{114}
 614   \item {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 615     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
 616   \item {int\discretionary {-}{}{}\_\discretionary {-}{}{}urn}
 617     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
 618   \item {interact}, \hyperpage{93}
 619   \item {intermediate\discretionary {-}{}{}\_\discretionary {-}{}{}t},
 620                 \hyperpage{94}
 621   \item {inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose}
 622     \subitem {Searching Sequences for Predefined Structures},
 623                 \hyperpage{78}
 624   \item {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 625     \subitem {Searching Sequences for Predefined Structures},
 626                 \hyperpage{77}
 627   \item {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 628     \subitem {Searching Sequences for Predefined Structures},
 629                 \hyperpage{78}
 630
 631   \indexspace
 632
 633   \item {james\discretionary {-}{}{}\_\discretionary {-}{}{}rule}
 634     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 635                 \hyperpage{131}
 636
 637   \indexspace
 638
 639   \item {K0}
 640     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
 641                 \hyperpage{120}
 642
 643   \indexspace
 644
 645   \item {L\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}T},
 646                 \hyperpage{95}
 647   \item {L\discretionary {-}{}{}Pfold.\discretionary {-}{}{}h}
 648     \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}L\discretionary {-}{}{}P},
 649                 \hyperpage{142}
 650   \item {L\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}C\discretionary {-}{}{}K\discretionary {-}{}{}E\discretionary {-}{}{}T},
 651                 \hyperpage{95}
 652   \item {Lfold}
 653     \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores},
 654                 \hyperpage{60}
 655   \item {Lfoldz}
 656     \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores},
 657                 \hyperpage{60}
 658   \item {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments},
 659                 \hyperpage{63}
 660     \subitem {ali\discretionary {-}{}{}Lfold}, \hyperpage{63}
 661   \item {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores},
 662                 \hyperpage{60}
 663     \subitem {Lfold}, \hyperpage{60}
 664     \subitem {Lfoldz}, \hyperpage{60}
 665   \item {log\discretionary {-}{}{}M\discretionary {-}{}{}L}
 666     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 667                 \hyperpage{131}
 668   \item {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}
 669     \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin},
 670                 \hyperpage{138}
 671     \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop},
 672                 \hyperpage{137}
 673     \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem},
 674                 \hyperpage{138}
 675     \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin},
 676                 \hyperpage{140}
 677     \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop},
 678                 \hyperpage{140}
 679     \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem},
 680                 \hyperpage{139}
 681   \item {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energy}
 682     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125}
 683   \item {Loop\discretionary {-}{}{}Energy}
 684     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
 685
 686   \indexspace
 687
 688   \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X2}
 689     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
 690   \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X3}
 691     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
 692   \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}P}
 693     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
 694                 \hyperpage{120}
 695   \item {M\discretionary {-}{}{}E\discretionary {-}{}{}A}
 696     \subitem {M\discretionary {-}{}{}E\discretionary {-}{}{}A.\discretionary {-}{}{}h},
 697                 \hyperpage{143}
 698   \item {M\discretionary {-}{}{}E\discretionary {-}{}{}A.\discretionary {-}{}{}h}
 699     \subitem {M\discretionary {-}{}{}E\discretionary {-}{}{}A},
 700                 \hyperpage{143}
 701   \item {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)},
 702                 \hyperpage{54}
 703     \subitem {alifold}, \hyperpage{54}
 704     \subitem {circalifold}, \hyperpage{54}
 705   \item {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences},
 706                 \hyperpage{42}
 707     \subitem {cofold}, \hyperpage{42}
 708     \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
 709                 \hyperpage{43}
 710     \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq},
 711                 \hyperpage{43}
 712   \item {M\discretionary {-}{}{}I\discretionary {-}{}{}N2}
 713     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
 714   \item {M\discretionary {-}{}{}I\discretionary {-}{}{}N3}
 715     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
 716   \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile}
 717     \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156}
 718   \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}
 719     \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156}
 720   \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}loop\discretionary {-}{}{}\_\discretionary {-}{}{}index\discretionary {-}{}{}\_\discretionary {-}{}{}pt}
 721     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
 722   \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}
 723     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178}
 724   \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table\discretionary {-}{}{}\_\discretionary {-}{}{}snoop}
 725     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
 726   \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}sw\discretionary {-}{}{}String}
 727     \subitem {stringdist.\discretionary {-}{}{}h}, \hyperpage{165}
 728   \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}tree}
 729     \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168}
 730   \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}dist}
 731     \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
 732                 \hyperpage{148}
 733   \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}
 734     \subitem {Calculating Partition Functions and Pair Probabilities},
 735                 \hyperpage{30}
 736   \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}
 737     \subitem {Calculating Partition Functions and Pair Probabilities},
 738                 \hyperpage{31}
 739   \item {model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T},
 740                 \hyperpage{96}
 741     \subitem {dangles}, \hyperpage{96}
 742   \item {move\discretionary {-}{}{}\_\discretionary {-}{}{}t},
 743                 \hyperpage{96}
 744
 745   \indexspace
 746
 747   \item {N\discretionary {-}{}{}B\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}S}
 748     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
 749                 \hyperpage{120}
 750   \item {nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact}
 751     \subitem {Predicting Consensus Structures from Alignment(s)},
 752                 \hyperpage{53}
 753   \item {no\discretionary {-}{}{}Lonely\discretionary {-}{}{}Pairs}
 754     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 755                 \hyperpage{130}
 756   \item {nonstandards}
 757     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 758                 \hyperpage{131}
 759   \item {nrerror}
 760     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
 761
 762   \indexspace
 763
 764   \item {old\discretionary {-}{}{}Ali\discretionary {-}{}{}En}
 765     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 766                 \hyperpage{131}
 767
 768   \indexspace
 769
 770   \item {P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R},
 771                 \hyperpage{97}
 772   \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}
 773     \subitem {ali\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}color\discretionary {-}{}{}\_\discretionary {-}{}{}aln},
 774                 \hyperpage{160}
 775     \subitem {gml\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A},
 776                 \hyperpage{158}
 777     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
 778                 \hyperpage{160}
 779     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}list},
 780                 \hyperpage{159}
 781     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
 782                 \hyperpage{158}
 783     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}a},
 784                 \hyperpage{158}
 785     \subitem {ssv\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
 786                 \hyperpage{159}
 787     \subitem {svg\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
 788                 \hyperpage{159}
 789     \subitem {xrna\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
 790                 \hyperpage{159}
 791   \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
 792     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
 793                 \hyperpage{160}
 794   \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}list}
 795     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
 796                 \hyperpage{159}
 797   \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
 798     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
 799                 \hyperpage{158}
 800   \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}a}
 801     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
 802                 \hyperpage{158}
 803   \item {pack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
 804     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178}
 805   \item {pair\discretionary {-}{}{}\_\discretionary {-}{}{}info},
 806                 \hyperpage{97}
 807   \item {pairpro}, \hyperpage{98}
 808   \item {param\discretionary {-}{}{}T}, \hyperpage{98}
 809   \item {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
 810     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{124}
 811   \item {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}zuker}
 812     \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{124}
 813   \item {parse\discretionary {-}{}{}\_\discretionary {-}{}{}gquad}
 814     \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134}
 815   \item {parse\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
 816     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
 817                 \hyperpage{164}
 818   \item {Parsing and Comparing -\/ Functions to Manipulate Structures},
 819                 \hyperpage{90}
 820   \item {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h}
 821     \subitem {centroid}, \hyperpage{148}
 822     \subitem {exp\discretionary {-}{}{}Hairpin\discretionary {-}{}{}Energy},
 823                 \hyperpage{148}
 824     \subitem {exp\discretionary {-}{}{}Loop\discretionary {-}{}{}Energy},
 825                 \hyperpage{148}
 826     \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 827                 \hyperpage{148}
 828     \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}dist},
 829                 \hyperpage{148}
 830   \item {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h}
 831     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}plist},
 832                 \hyperpage{150}
 833     \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 834                 \hyperpage{150}
 835   \item {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
 836                 \hyperpage{56}
 837     \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 838                 \hyperpage{57}
 839     \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 840                 \hyperpage{56}
 841     \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par},
 842                 \hyperpage{56}
 843     \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm},
 844                 \hyperpage{57}
 845   \item {Partition Function for two hybridized Sequences},
 846                 \hyperpage{44}
 847     \subitem {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 848                 \hyperpage{45}
 849     \subitem {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par},
 850                 \hyperpage{45}
 851     \subitem {compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities},
 852                 \hyperpage{47}
 853     \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm},
 854                 \hyperpage{46}
 855     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations},
 856                 \hyperpage{47}
 857     \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params},
 858                 \hyperpage{46}
 859     \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par},
 860                 \hyperpage{46}
 861   \item {Partition Function for two hybridized Sequences as a stepwise Process},
 862                 \hyperpage{48}
 863     \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact},
 864                 \hyperpage{49}
 865     \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru},
 866                 \hyperpage{48}
 867   \item {Partition functions for locally stable secondary structures},
 868                 \hyperpage{61}
 869     \subitem {pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
 870                 \hyperpage{61}
 871     \subitem {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob},
 872                 \hyperpage{62}
 873     \subitem {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin},
 874                 \hyperpage{62}
 875     \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P},
 876                 \hyperpage{61}
 877   \item {path\discretionary {-}{}{}\_\discretionary {-}{}{}t},
 878                 \hyperpage{99}
 879   \item {pbacktrack}
 880     \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{39}
 881   \item {pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}
 882     \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{40}
 883   \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 884     \subitem {Calculating Partition Functions and Pair Probabilities},
 885                 \hyperpage{28}
 886   \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 887     \subitem {Calculating Partition Functions and Pair Probabilities},
 888                 \hyperpage{27}
 889   \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}
 890     \subitem {Calculating Partition Functions and Pair Probabilities},
 891                 \hyperpage{26}
 892   \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}
 893     \subitem {Partition Function for two hybridized Sequences as a stepwise Process},
 894                 \hyperpage{49}
 895   \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T},
 896                 \hyperpage{99}
 897     \subitem {alpha}, \hyperpage{100}
 898   \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}scale}
 899     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 900                 \hyperpage{132}
 901   \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}
 902     \subitem {Partition Function for two hybridized Sequences as a stepwise Process},
 903                 \hyperpage{48}
 904   \item {pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
 905     \subitem {Partition functions for locally stable secondary structures},
 906                 \hyperpage{61}
 907   \item {plist}, \hyperpage{100}
 908   \item {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h}
 909     \subitem {rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}type},
 910                 \hyperpage{155}
 911     \subitem {simple\discretionary {-}{}{}\_\discretionary {-}{}{}circplot\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates},
 912                 \hyperpage{154}
 913     \subitem {simple\discretionary {-}{}{}\_\discretionary {-}{}{}xy\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates},
 914                 \hyperpage{154}
 915   \item {Postorder\discretionary {-}{}{}\_\discretionary {-}{}{}list},
 916                 \hyperpage{100}
 917   \item {pr}
 918     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
 919                 \hyperpage{132}
 920   \item {Predicting Consensus Structures from Alignment(s)},
 921                 \hyperpage{50}
 922     \subitem {alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
 923                 \hyperpage{52}
 924     \subitem {cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact},
 925                 \hyperpage{53}
 926     \subitem {encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence},
 927                 \hyperpage{51}
 928     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct},
 929                 \hyperpage{51}
 930     \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
 931                 \hyperpage{52}
 932     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
 933                 \hyperpage{53}
 934     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi},
 935                 \hyperpage{51}
 936     \subitem {nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact},
 937                 \hyperpage{53}
 938   \item {Predicting Locally stable structures of large sequences},
 939                 \hyperpage{59}
 940   \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}constraint}
 941     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180}
 942   \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq}
 943     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
 944   \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq\discretionary {-}{}{}\_\discretionary {-}{}{}str}
 945     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
 946   \item {profile\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}
 947     \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156}
 948   \item {profiledist.\discretionary {-}{}{}h}
 949     \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}profile},
 950                 \hyperpage{156}
 951     \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile},
 952                 \hyperpage{156}
 953     \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile\discretionary {-}{}{}\_\discretionary {-}{}{}bppm},
 954                 \hyperpage{156}
 955     \subitem {profile\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance},
 956                 \hyperpage{156}
 957   \item {pu\discretionary {-}{}{}\_\discretionary {-}{}{}contrib},
 958                 \hyperpage{100}
 959   \item {pu\discretionary {-}{}{}\_\discretionary {-}{}{}out},
 960                 \hyperpage{101}
 961   \item {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob}
 962     \subitem {Partition functions for locally stable secondary structures},
 963                 \hyperpage{62}
 964   \item {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin}
 965     \subitem {Partition functions for locally stable secondary structures},
 966                 \hyperpage{62}
 967
 968   \indexspace
 969
 970   \item {R\discretionary {-}{}{}N\discretionary {-}{}{}A Secondary Structure Folding},
 971                 \hyperpage{19}
 972   \item {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}
 973     \subitem {add\discretionary {-}{}{}\_\discretionary {-}{}{}root},
 974                 \hyperpage{163}
 975     \subitem {b2\discretionary {-}{}{}C}, \hyperpage{162}
 976     \subitem {b2\discretionary {-}{}{}H\discretionary {-}{}{}I\discretionary {-}{}{}T},
 977                 \hyperpage{162}
 978     \subitem {b2\discretionary {-}{}{}Shapiro}, \hyperpage{162}
 979     \subitem {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full},
 980                 \hyperpage{163}
 981     \subitem {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Shapiro},
 982                 \hyperpage{163}
 983     \subitem {parse\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
 984                 \hyperpage{164}
 985     \subitem {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full},
 986                 \hyperpage{163}
 987     \subitem {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}aligned\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F},
 988                 \hyperpage{164}
 989     \subitem {unweight}, \hyperpage{163}
 990   \item {random\discretionary {-}{}{}\_\discretionary {-}{}{}string}
 991     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
 992   \item {read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}
 993     \subitem {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File},
 994                 \hyperpage{67}
 995   \item {read\discretionary {-}{}{}\_\discretionary {-}{}{}record}
 996     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{177}
 997   \item {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File},
 998                 \hyperpage{67}
 999     \subitem {read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file},
1000                 \hyperpage{67}
1001     \subitem {write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file},
1002                 \hyperpage{67}
1003   \item {ribo}
1004     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
1005                 \hyperpage{131}
1006   \item {Ribosum\discretionary {-}{}{}File}
1007     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
1008                 \hyperpage{131}
1009   \item {rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}type}
1010     \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h},
1011                 \hyperpage{155}
1012
1013   \indexspace
1014
1015   \item {S\discretionary {-}{}{}O\discretionary {-}{}{}L\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N},
1016                 \hyperpage{102}
1017   \item {S\discretionary {-}{}{}T\discretionary {-}{}{}R}
1018     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
1019   \item {scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}
1020     \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
1021                 \hyperpage{65}
1022   \item {Searching Sequences for Predefined Structures}, \hyperpage{77}
1023     \subitem {final\discretionary {-}{}{}\_\discretionary {-}{}{}cost},
1024                 \hyperpage{78}
1025     \subitem {give\discretionary {-}{}{}\_\discretionary {-}{}{}up},
1026                 \hyperpage{78}
1027     \subitem {inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose},
1028                 \hyperpage{78}
1029     \subitem {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
1030                 \hyperpage{77}
1031     \subitem {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
1032                 \hyperpage{78}
1033   \item {sect}, \hyperpage{101}
1034   \item {set\discretionary {-}{}{}\_\discretionary {-}{}{}model\discretionary {-}{}{}\_\discretionary {-}{}{}details}
1035     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
1036                 \hyperpage{130}
1037   \item {simple\discretionary {-}{}{}\_\discretionary {-}{}{}circplot\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}
1038     \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h},
1039                 \hyperpage{154}
1040   \item {simple\discretionary {-}{}{}\_\discretionary {-}{}{}xy\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}
1041     \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h},
1042                 \hyperpage{154}
1043   \item {snoop\discretionary {-}{}{}T}, \hyperpage{102}
1044   \item {space}
1045     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
1046   \item {ssv\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
1047     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
1048                 \hyperpage{159}
1049   \item {st\discretionary {-}{}{}\_\discretionary {-}{}{}back}
1050     \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{40}
1051   \item {Stochastic backtracking in the Ensemble}, \hyperpage{39}
1052     \subitem {pbacktrack}, \hyperpage{39}
1053     \subitem {pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ},
1054                 \hyperpage{40}
1055     \subitem {st\discretionary {-}{}{}\_\discretionary {-}{}{}back},
1056                 \hyperpage{40}
1057   \item {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)},
1058                 \hyperpage{58}
1059     \subitem {alipbacktrack}, \hyperpage{58}
1060   \item {Stochastic Backtracking of Structures from Distance Based Partitioning},
1061                 \hyperpage{87}
1062     \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack},
1063                 \hyperpage{87}
1064     \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5},
1065                 \hyperpage{88}
1066   \item {str\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}N\discretionary {-}{}{}A2\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}
1067     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180}
1068   \item {str\discretionary {-}{}{}\_\discretionary {-}{}{}uppercase}
1069     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180}
1070   \item {string\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}
1071     \subitem {stringdist.\discretionary {-}{}{}h}, \hyperpage{165}
1072   \item {stringdist.\discretionary {-}{}{}h}
1073     \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}sw\discretionary {-}{}{}String},
1074                 \hyperpage{165}
1075     \subitem {string\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance},
1076                 \hyperpage{165}
1077   \item {struct\discretionary {-}{}{}\_\discretionary {-}{}{}en},
1078                 \hyperpage{102}
1079   \item {subopt}
1080     \subitem {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E},
1081                 \hyperpage{37}
1082   \item {subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}
1083     \subitem {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E},
1084                 \hyperpage{38}
1085   \item {Suboptimal structures according to Zuker et al. 1989},
1086                 \hyperpage{36}
1087     \subitem {zukersubopt}, \hyperpage{36}
1088   \item {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E},
1089                 \hyperpage{37}
1090     \subitem {subopt}, \hyperpage{37}
1091     \subitem {subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ},
1092                 \hyperpage{38}
1093   \item {svg\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
1094     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
1095                 \hyperpage{159}
1096   \item {svm\discretionary {-}{}{}\_\discretionary {-}{}{}model},
1097                 \hyperpage{102}
1098   \item {sw\discretionary {-}{}{}String}, \hyperpage{102}
1099
1100   \indexspace
1101
1102   \item {T\discretionary {-}{}{}U\discretionary {-}{}{}R\discretionary {-}{}{}N}
1103     \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
1104                 \hyperpage{120}
1105   \item {temperature}
1106     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
1107                 \hyperpage{131}
1108   \item {tetra\discretionary {-}{}{}\_\discretionary {-}{}{}loop}
1109     \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
1110                 \hyperpage{131}
1111   \item {time\discretionary {-}{}{}\_\discretionary {-}{}{}stamp}
1112     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
1113   \item {Tree}, \hyperpage{103}
1114   \item {tree\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}
1115     \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168}
1116   \item {treedist.\discretionary {-}{}{}h}
1117     \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}tree},
1118                 \hyperpage{168}
1119     \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}tree},
1120                 \hyperpage{168}
1121     \subitem {tree\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance},
1122                 \hyperpage{168}
1123   \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5}
1124     \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
1125                 \hyperpage{83}
1126   \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution},
1127                 \hyperpage{103}
1128   \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars},
1129                 \hyperpage{104}
1130   \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List}
1131     \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
1132                 \hyperpage{82}
1133   \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack}
1134     \subitem {Stochastic Backtracking of Structures from Distance Based Partitioning},
1135                 \hyperpage{87}
1136   \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5}
1137     \subitem {Stochastic Backtracking of Structures from Distance Based Partitioning},
1138                 \hyperpage{88}
1139   \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution},
1140                 \hyperpage{105}
1141   \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars},
1142                 \hyperpage{106}
1143   \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List}
1144     \subitem {Calculate Partition Functions of a Distance Based Partitioning},
1145                 \hyperpage{85}
1146
1147   \indexspace
1148
1149   \item {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}
1150     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
1151                 \hyperpage{163}
1152   \item {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}aligned\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F}
1153     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
1154                 \hyperpage{164}
1155   \item {unpack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
1156     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178}
1157   \item {unweight}
1158     \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
1159                 \hyperpage{163}
1160   \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params}
1161     \subitem {alifold.\discretionary {-}{}{}h}, \hyperpage{112}
1162   \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}
1163     \subitem {Partition Function for two hybridized Sequences},
1164                 \hyperpage{46}
1165   \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par}
1166     \subitem {Partition Function for two hybridized Sequences},
1167                 \hyperpage{46}
1168   \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}
1169     \subitem {Calculating Partition Functions and Pair Probabilities},
1170                 \hyperpage{29}
1171   \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P}
1172     \subitem {Partition functions for locally stable secondary structures},
1173                 \hyperpage{61}
1174   \item {urn}
1175     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
1176   \item {utils.\discretionary {-}{}{}h}
1177     \subitem {alimake\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table},
1178                 \hyperpage{179}
1179     \subitem {constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes},
1180                 \hyperpage{181}
1181     \subitem {copy\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table},
1182                 \hyperpage{179}
1183     \subitem {F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H},
1184                 \hyperpage{174}
1185     \subitem {F\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}T\discretionary {-}{}{}H},
1186                 \hyperpage{174}
1187     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}iindx},
1188                 \hyperpage{180}
1189     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}indx},
1190                 \hyperpage{181}
1191     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}line},
1192                 \hyperpage{176}
1193     \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}line},
1194                 \hyperpage{176}
1195     \subitem {hamming}, \hyperpage{176}
1196     \subitem {hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound},
1197                 \hyperpage{176}
1198     \subitem {int\discretionary {-}{}{}\_\discretionary {-}{}{}urn},
1199                 \hyperpage{175}
1200     \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X2},
1201                 \hyperpage{173}
1202     \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X3},
1203                 \hyperpage{173}
1204     \subitem {M\discretionary {-}{}{}I\discretionary {-}{}{}N2},
1205                 \hyperpage{173}
1206     \subitem {M\discretionary {-}{}{}I\discretionary {-}{}{}N3},
1207                 \hyperpage{173}
1208     \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}loop\discretionary {-}{}{}\_\discretionary {-}{}{}index\discretionary {-}{}{}\_\discretionary {-}{}{}pt},
1209                 \hyperpage{179}
1210     \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table},
1211                 \hyperpage{178}
1212     \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table\discretionary {-}{}{}\_\discretionary {-}{}{}snoop},
1213                 \hyperpage{179}
1214     \subitem {nrerror}, \hyperpage{174}
1215     \subitem {pack\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
1216                 \hyperpage{178}
1217     \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}constraint},
1218                 \hyperpage{180}
1219     \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq},
1220                 \hyperpage{179}
1221     \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq\discretionary {-}{}{}\_\discretionary {-}{}{}str},
1222                 \hyperpage{179}
1223     \subitem {random\discretionary {-}{}{}\_\discretionary {-}{}{}string},
1224                 \hyperpage{175}
1225     \subitem {read\discretionary {-}{}{}\_\discretionary {-}{}{}record},
1226                 \hyperpage{177}
1227     \subitem {S\discretionary {-}{}{}T\discretionary {-}{}{}R},
1228                 \hyperpage{173}
1229     \subitem {space}, \hyperpage{174}
1230     \subitem {str\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}N\discretionary {-}{}{}A2\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A},
1231                 \hyperpage{180}
1232     \subitem {str\discretionary {-}{}{}\_\discretionary {-}{}{}uppercase},
1233                 \hyperpage{180}
1234     \subitem {time\discretionary {-}{}{}\_\discretionary {-}{}{}stamp},
1235                 \hyperpage{175}
1236     \subitem {unpack\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
1237                 \hyperpage{178}
1238     \subitem {urn}, \hyperpage{175}
1239     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L},
1240                 \hyperpage{173}
1241     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}O\discretionary {-}{}{}T},
1242                 \hyperpage{172}
1243     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G},
1244                 \hyperpage{173}
1245     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}X},
1246                 \hyperpage{172}
1247     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}T},
1248                 \hyperpage{172}
1249     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}R\discretionary {-}{}{}O\discretionary {-}{}{}R},
1250                 \hyperpage{171}
1251     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C},
1252                 \hyperpage{171}
1253     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}R\discretionary {-}{}{}E\discretionary {-}{}{}S\discretionary {-}{}{}T},
1254                 \hyperpage{172}
1255     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}N},
1256                 \hyperpage{172}
1257     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}I\discretionary {-}{}{}T},
1258                 \hyperpage{171}
1259     \subitem {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}E\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}C\discretionary {-}{}{}E},
1260                 \hyperpage{171}
1261     \subitem {warn\discretionary {-}{}{}\_\discretionary {-}{}{}user},
1262                 \hyperpage{175}
1263     \subitem {X\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R},
1264                 \hyperpage{173}
1265     \subitem {xrealloc}, \hyperpage{174}
1266     \subitem {xsubi}, \hyperpage{182}
1267
1268   \indexspace
1269
1270   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L}
1271     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
1272   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}O\discretionary {-}{}{}T}
1273     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
1274   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G}
1275     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
1276   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}I\discretionary {-}{}{}P\discretionary {-}{}{}E}
1277     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
1278   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}X}
1279     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
1280   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}T}
1281     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
1282   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}R\discretionary {-}{}{}O\discretionary {-}{}{}R}
1283     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171}
1284   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C}
1285     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171}
1286   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}R\discretionary {-}{}{}E\discretionary {-}{}{}S\discretionary {-}{}{}T}
1287     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
1288   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}N}
1289     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
1290   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}I\discretionary {-}{}{}T}
1291     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171}
1292   \item {V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}E\discretionary {-}{}{}Q\discretionary {-}{}{}U\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}C\discretionary {-}{}{}E}
1293     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171}
1294
1295   \indexspace
1296
1297   \item {warn\discretionary {-}{}{}\_\discretionary {-}{}{}user}
1298     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
1299   \item {write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}
1300     \subitem {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File},
1301                 \hyperpage{67}
1302
1303   \indexspace
1304
1305   \item {X\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R}
1306     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
1307   \item {xrealloc}
1308     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
1309   \item {xrna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
1310     \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
1311                 \hyperpage{159}
1312   \item {xsubi}
1313     \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{182}
1314
1315   \indexspace
1316
1317   \item {zukersubopt}
1318     \subitem {Suboptimal structures according to Zuker et al. 1989},
1319                 \hyperpage{36}
1320
1321 \end{theindex}