\begin{theindex}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dfold.\discretionary {-}{}{}h},
- \hyperpage{109}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dpfold.\discretionary {-}{}{}h},
- \hyperpage{110}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}L\discretionary {-}{}{}Pfold.\discretionary {-}{}{}h},
- \hyperpage{141}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}Lfold.\discretionary {-}{}{}h},
- \hyperpage{135}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A.\discretionary {-}{}{}h},
- \hyperpage{142}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{157}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{161}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/alifold.\discretionary {-}{}{}h},
- \hyperpage{111}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/cofold.\discretionary {-}{}{}h},
- \hyperpage{113}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/convert\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h},
- \hyperpage{114}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/data\discretionary {-}{}{}\_\discretionary {-}{}{}structures.\discretionary {-}{}{}h},
- \hyperpage{115}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{117}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/duplex.\discretionary {-}{}{}h},
- \hyperpage{118}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/edit\discretionary {-}{}{}\_\discretionary {-}{}{}cost.\discretionary {-}{}{}h},
- \hyperpage{119}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{119}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/findpath.\discretionary {-}{}{}h},
- \hyperpage{120}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/fold.\discretionary {-}{}{}h},
- \hyperpage{122}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{128}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/gquad.\discretionary {-}{}{}h},
- \hyperpage{133}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/inverse.\discretionary {-}{}{}h},
- \hyperpage{135}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
- \hyperpage{136}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/mm.\discretionary {-}{}{}h},
- \hyperpage{144}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/naview.\discretionary {-}{}{}h},
- \hyperpage{144}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/params.\discretionary {-}{}{}h},
- \hyperpage{145}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
- \hyperpage{146}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h},
- \hyperpage{148}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}up.\discretionary {-}{}{}h},
- \hyperpage{150}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h},
- \hyperpage{152}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/profiledist.\discretionary {-}{}{}h},
- \hyperpage{155}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/read\discretionary {-}{}{}\_\discretionary {-}{}{}epars.\discretionary {-}{}{}h},
- \hyperpage{160}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/stringdist.\discretionary {-}{}{}h},
- \hyperpage{164}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/subopt.\discretionary {-}{}{}h},
- \hyperpage{166}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/treedist.\discretionary {-}{}{}h},
- \hyperpage{167}
- \item {/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.\discretionary {-}{}{}projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/utils.\discretionary {-}{}{}h},
- \hyperpage{168}
- \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 {-}{}{}epars.\discretionary {-}{}{}h},
- \hyperpage{182}
- \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},
- \hyperpage{182}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h}, \hyperpage{153}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h}, \hyperpage{155}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h}, \hyperpage{198}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/Lfold.h}, \hyperpage{190}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/MEA.h}, \hyperpage{200}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS\_\discretionary {-}{}{}dot.h}, \hyperpage{218}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/RNAstruct.h}, \hyperpage{224}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}, \hyperpage{156}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h}, \hyperpage{159}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\discretionary {-}{}{}epars.h}, \hyperpage{161}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\discretionary {-}{}{}structures.h}, \hyperpage{162}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/duplex.h}, \hyperpage{167}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/edit\_\discretionary {-}{}{}cost.h}, \hyperpage{168}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h}, \hyperpage{171}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h}, \hyperpage{173}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold\_\discretionary {-}{}{}vars.h}, \hyperpage{180}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h}, \hyperpage{186}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/inverse.h}, \hyperpage{189}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/loop\_\discretionary {-}{}{}energies.h}, \hyperpage{191}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/mm.h}, \hyperpage{201}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/naview.h}, \hyperpage{202}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h}, \hyperpage{203}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func.h}, \hyperpage{205}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{208}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h}, \hyperpage{211}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{212}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h}, \hyperpage{216}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/read\_\discretionary {-}{}{}epars.h}, \hyperpage{223}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/stringdist.h}, \hyperpage{229}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/subopt.h}, \hyperpage{231}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h}, \hyperpage{232}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/utils.h}, \hyperpage{234}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}epars.h}, \hyperpage{250}
+ \item {/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}intloops.h}, \hyperpage{251}
\indexspace
- \item {add\discretionary {-}{}{}\_\discretionary {-}{}{}root}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{163}
- \item {ali\discretionary {-}{}{}Lfold}
- \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments},
- \hyperpage{63}
- \item {ali\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}color\discretionary {-}{}{}\_\discretionary {-}{}{}aln}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{160}
+ \item {add\_\discretionary {-}{}{}root}
+ \subitem {RNAstruct.h}, \hyperpage{226}
\item {alifold}
- \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)},
- \hyperpage{54}
- \item {alifold.\discretionary {-}{}{}h}
- \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params},
- \hyperpage{112}
- \item {alimake\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
+ \subitem {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{71}
+ \item {alifold.h}
+ \subitem {update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}, \hyperpage{158}
+ \item {aliLfold}
+ \subitem {local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}, \hyperpage{81}
+ \item {alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
+ \subitem {utils.h}, \hyperpage{246}
\item {alipbacktrack}
- \subitem {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)},
- \hyperpage{58}
- \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
- \hyperpage{57}
- \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
- \hyperpage{56}
- \item {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}
- \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
- \hyperpage{56}
- \item {alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
- \subitem {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{52}
+ \subitem {consensus\_\discretionary {-}{}{}stochbt}, \hyperpage{75}
+ \item {alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}
+ \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{74}
+ \item {alipf\_\discretionary {-}{}{}fold}
+ \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{73}
+ \item {alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
+ \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{73}
+ \item {aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
+ \item {alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}
+ \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{68}
\item {alpha}
- \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T},
- \hyperpage{100}
- \item {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}db}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
- \item {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{29}
+ \subitem {pf\_\discretionary {-}{}{}paramT}, \hyperpage{134}
+ \item {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}
+ \subitem {fold.h}, \hyperpage{177}
+ \item {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}
\indexspace
- \item {b2\discretionary {-}{}{}C}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{162}
- \item {b2\discretionary {-}{}{}H\discretionary {-}{}{}I\discretionary {-}{}{}T}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{162}
- \item {b2\discretionary {-}{}{}Shapiro}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{162}
- \item {B\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}U\discretionary {-}{}{}S}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{120}
- \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}
- \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134}
- \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L}
- \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134}
- \item {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}type}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{132}
- \item {base\discretionary {-}{}{}\_\discretionary {-}{}{}pair}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{132}
- \item {bond\discretionary {-}{}{}T}, \hyperpage{91}
- \item {bond\discretionary {-}{}{}T\discretionary {-}{}{}En},
- \hyperpage{91}
+ \item {b2C}
+ \subitem {RNAstruct.h}, \hyperpage{225}
+ \item {b2HIT}
+ \subitem {RNAstruct.h}, \hyperpage{225}
+ \item {b2Shapiro}
+ \subitem {RNAstruct.h}, \hyperpage{226}
+ \item {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop}
+ \subitem {gquad.h}, \hyperpage{187}
+ \item {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L}
+ \subitem {gquad.h}, \hyperpage{187}
+ \item {backtrack\_\discretionary {-}{}{}type}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{185}
+ \item {base\_\discretionary {-}{}{}pair}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
+ \item {bondT}, \hyperpage{111}
+ \item {bondTEn}, \hyperpage{112}
+ \item {BONUS}
+ \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
\indexspace
- \item {C\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}D\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}E},
- \hyperpage{92}
- \item {Calculate Partition Functions of a Distance Based Partitioning},
- \hyperpage{84}
- \subitem {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables},
- \hyperpage{85}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables},
- \hyperpage{84}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E},
- \hyperpage{85}
- \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List},
- \hyperpage{85}
- \item {Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization},
- \hyperpage{41}
- \item {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
- \hyperpage{81}
- \subitem {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables},
- \hyperpage{82}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables},
- \hyperpage{81}
- \subitem {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5},
- \hyperpage{83}
- \subitem {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List},
- \hyperpage{82}
- \item {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures},
- \hyperpage{22}
- \subitem {circfold}, \hyperpage{24}
- \subitem {fold}, \hyperpage{23}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}par},
- \hyperpage{23}
- \item {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{25}
- \subitem {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr},
- \hyperpage{29}
- \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm},
- \hyperpage{29}
- \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
- \hyperpage{29}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
- \hyperpage{30}
- \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance},
- \hyperpage{30}
- \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr},
- \hyperpage{31}
- \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{28}
- \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{27}
- \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par},
- \hyperpage{26}
- \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params},
- \hyperpage{29}
+ \item {Calculate Partition Functions of a Distance Based Partitioning}, \hyperpage{104}
+ \item {Calculate Secondary Structures of two RNAs upon Dimerization}, \hyperpage{54}
+ \item {Calculating MFE representatives of a Distance Based Partitioning}, \hyperpage{101}
+ \item {Calculating Minimum Free Energy (MFE) Structures}, \hyperpage{33}
+ \item {Calculating Partition Functions and Pair Probabilities}, \hyperpage{37}
\item {centroid}
- \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
- \hyperpage{148}
- \item {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
- \hyperpage{64}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy},
- \hyperpage{66}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors},
- \hyperpage{65}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters},
- \hyperpage{65}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters},
- \hyperpage{65}
- \subitem {scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters},
- \hyperpage{65}
+ \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
+ \item {centroid\_\discretionary {-}{}{}fold}
+ \subitem {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}, \hyperpage{46}
+ \subitem {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}, \hyperpage{46}
+ \item {Change and Precalculate Energy Parameter Sets and Boltzmann Factors}, \hyperpage{82}
\item {circalifold}
- \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)},
- \hyperpage{54}
+ \subitem {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{71}
\item {circfold}
- \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures},
- \hyperpage{24}
- \item {Classified Dynamic Programming}, \hyperpage{79}
- \item {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {Partition Function for two hybridized Sequences},
- \hyperpage{45}
- \item {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}
- \subitem {Partition Function for two hybridized Sequences},
- \hyperpage{45}
+ \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{35}
+ \item {Classified Dynamic Programming}, \hyperpage{99}
+ \item {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
+ \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{59}
+ \item {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
+ \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{59}
\item {cofold}
- \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences},
- \hyperpage{42}
- \item {cofold.\discretionary {-}{}{}h}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes},
- \hyperpage{114}
- \subitem {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold},
- \hyperpage{114}
- \item {cofold\discretionary {-}{}{}F}, \hyperpage{91}
- \item {Compute the centroid structure}, \hyperpage{33}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl},
- \hyperpage{33}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr},
- \hyperpage{33}
- \item {Compute the Density of States}, \hyperpage{89}
- \subitem {density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states},
- \hyperpage{89}
- \item {Compute the structure with maximum expected accuracy (\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A)},
- \hyperpage{32}
- \item {compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities}
- \subitem {Partition Function for two hybridized Sequences},
- \hyperpage{47}
- \item {Conc\discretionary {-}{}{}Ent}, \hyperpage{92}
- \item {constrain}, \hyperpage{92}
- \item {constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{181}
- \item {convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}
- \subitem {Converting energy parameter files}, \hyperpage{71}
- \item {Converting energy parameter files}, \hyperpage{69}
- \subitem {convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file},
- \hyperpage{71}
- \item {copy\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
- \item {cost\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}
- \subitem {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{118}
- \item {cpair}, \hyperpage{93}
- \item {cut\discretionary {-}{}{}\_\discretionary {-}{}{}point}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{132}
- \item {cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact}
- \subitem {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{53}
+ \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{55}
+ \item {cofold.h}
+ \subitem {get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}, \hyperpage{160}
+ \subitem {initialize\_\discretionary {-}{}{}cofold}, \hyperpage{160}
+ \item {cofoldF}, \hyperpage{113}
+ \item {Compute the centroid structure}, \hyperpage{46}
+ \item {Compute the Density of States}, \hyperpage{109}
+ \item {Compute the structure with maximum expected accuracy (MEA)}, \hyperpage{45}
+ \item {compute\_\discretionary {-}{}{}probabilities}
+ \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
+ \item {ConcEnt}, \hyperpage{114}
+ \item {consensus\_\discretionary {-}{}{}fold}
+ \subitem {alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}, \hyperpage{68}
+ \subitem {cv\_\discretionary {-}{}{}fact}, \hyperpage{70}
+ \subitem {encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}, \hyperpage{68}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}, \hyperpage{67}
+ \subitem {free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}, \hyperpage{69}
+ \subitem {get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}, \hyperpage{69}
+ \subitem {get\_\discretionary {-}{}{}mpi}, \hyperpage{67}
+ \subitem {nc\_\discretionary {-}{}{}fact}, \hyperpage{70}
+ \item {consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}
+ \subitem {alifold}, \hyperpage{71}
+ \subitem {circalifold}, \hyperpage{71}
+ \item {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
+ \subitem {alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}, \hyperpage{74}
+ \subitem {alipf\_\discretionary {-}{}{}fold}, \hyperpage{73}
+ \subitem {alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{73}
+ \subitem {export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}, \hyperpage{74}
+ \item {consensus\_\discretionary {-}{}{}stochbt}
+ \subitem {alipbacktrack}, \hyperpage{75}
+ \item {constrain}, \hyperpage{115}
+ \item {constrain\_\discretionary {-}{}{}ptypes}
+ \subitem {utils.h}, \hyperpage{248}
+ \item {convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
+ \item {Converting energy parameter files}, \hyperpage{88}
+ \item {COORDINATE}, \hyperpage{116}
+ \item {copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
+ \subitem {utils.h}, \hyperpage{246}
+ \item {cost\_\discretionary {-}{}{}matrix}
+ \subitem {dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
+ \item {cpair}, \hyperpage{117}
+ \item {cut\_\discretionary {-}{}{}point}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
+ \item {cv\_\discretionary {-}{}{}fact}
+ \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{70}
\indexspace
\item {dangles}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{130}
- \subitem {model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T},
- \hyperpage{96}
- \item {density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states}
- \subitem {Compute the Density of States}, \hyperpage{89}
- \item {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}
- \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
- \hyperpage{82}
- \item {destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}
- \subitem {Calculate Partition Functions of a Distance Based Partitioning},
- \hyperpage{85}
- \item {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}
- \subitem {cost\discretionary {-}{}{}\_\discretionary {-}{}{}matrix},
- \hyperpage{118}
- \subitem {edit\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack},
- \hyperpage{118}
- \item {Distance based partitioning of the Secondary Structure Space},
- \hyperpage{80}
- \item {do\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{132}
- \item {dup\discretionary {-}{}{}Var}, \hyperpage{93}
- \item {duplex\discretionary {-}{}{}T}, \hyperpage{93}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
+ \subitem {model\_\discretionary {-}{}{}detailsT}, \hyperpage{126}
+ \item {density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}
+ \subitem {dos}, \hyperpage{109}
+ \item {destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
+ \item {destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
+ \item {dist\_\discretionary {-}{}{}vars.h}
+ \subitem {cost\_\discretionary {-}{}{}matrix}, \hyperpage{165}
+ \subitem {edit\_\discretionary {-}{}{}backtrack}, \hyperpage{165}
+ \item {Distance based partitioning of the Secondary Structure Space}, \hyperpage{100}
+ \item {do\_\discretionary {-}{}{}backtrack}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
+ \item {dos}
+ \subitem {density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}, \hyperpage{109}
+ \item {duplexT}, \hyperpage{118}
+ \item {dupVar}, \hyperpage{119}
\indexspace
- \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}
- \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
- \hyperpage{138}
- \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}
- \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
- \hyperpage{137}
- \item {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}
- \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
- \hyperpage{138}
- \item {edit\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}
- \subitem {dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{118}
- \item {encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence}
- \subitem {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{51}
- \item {Energy evaluation}, \hyperpage{73}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par},
- \hyperpage{75}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
- \hyperpage{74}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par},
- \hyperpage{74}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par},
- \hyperpage{76}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
- \hyperpage{73}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt},
- \hyperpage{75}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h}
- \subitem {B\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}U\discretionary {-}{}{}S},
- \hyperpage{120}
- \subitem {F\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}B\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}N},
- \hyperpage{120}
- \subitem {G\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T},
- \hyperpage{120}
- \subitem {I\discretionary {-}{}{}N\discretionary {-}{}{}F},
- \hyperpage{120}
- \subitem {K0}, \hyperpage{120}
- \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}P},
- \hyperpage{120}
- \subitem {N\discretionary {-}{}{}B\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}S},
- \hyperpage{120}
- \subitem {T\discretionary {-}{}{}U\discretionary {-}{}{}R\discretionary {-}{}{}N},
- \hyperpage{120}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct}
- \subitem {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{51}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{127}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}
- \subitem {Energy evaluation}, \hyperpage{75}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
- \subitem {Energy evaluation}, \hyperpage{74}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move\discretionary {-}{}{}\_\discretionary {-}{}{}pt}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}
- \subitem {Energy evaluation}, \hyperpage{74}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{127}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par}
- \subitem {Energy evaluation}, \hyperpage{76}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
- \subitem {Energy evaluation}, \hyperpage{73}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt}
- \subitem {Energy evaluation}, \hyperpage{75}
- \item {energy\discretionary {-}{}{}\_\discretionary {-}{}{}set}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
- \item {Enumerating Suboptimal Structures}, \hyperpage{35}
- \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}
- \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
- \hyperpage{140}
- \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}
- \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
- \hyperpage{140}
- \item {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}
- \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h},
- \hyperpage{139}
- \item {exp\discretionary {-}{}{}Hairpin\discretionary {-}{}{}Energy}
- \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
- \hyperpage{148}
- \item {exp\discretionary {-}{}{}Loop\discretionary {-}{}{}Energy}
- \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
- \hyperpage{148}
- \item {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{163}
- \item {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Shapiro}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{163}
- \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}
- \subitem {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
- \hyperpage{57}
- \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{29}
- \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}
- \subitem {Partition Function for two hybridized Sequences},
- \hyperpage{46}
- \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
- \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences},
- \hyperpage{43}
- \item {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}
- \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences},
- \hyperpage{43}
+ \item {E\_\discretionary {-}{}{}Hairpin}
+ \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{193}
+ \item {E\_\discretionary {-}{}{}IntLoop}
+ \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{192}
+ \item {E\_\discretionary {-}{}{}Stem}
+ \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{194}
+ \item {edit\_\discretionary {-}{}{}backtrack}
+ \subitem {dist\_\discretionary {-}{}{}vars.h}, \hyperpage{165}
+ \item {encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}
+ \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{68}
+ \item {Energy evaluation}, \hyperpage{93}
+ \item {energy\_\discretionary {-}{}{}const.h}
+ \subitem {BONUS}, \hyperpage{170}
+ \subitem {FORBIDDEN}, \hyperpage{169}
+ \subitem {GASCONST}, \hyperpage{169}
+ \subitem {INF}, \hyperpage{169}
+ \subitem {K0}, \hyperpage{169}
+ \subitem {MAXLOOP}, \hyperpage{170}
+ \subitem {NBPAIRS}, \hyperpage{170}
+ \subitem {TURN}, \hyperpage{170}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}
+ \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{67}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}
+ \subitem {fold.h}, \hyperpage{179}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}
+ \subitem {eval}, \hyperpage{95}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}
+ \subitem {eval}, \hyperpage{94}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}
+ \subitem {fold.h}, \hyperpage{175}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}
+ \subitem {fold.h}, \hyperpage{176}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}
+ \subitem {fold.h}, \hyperpage{177}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}
+ \subitem {eval}, \hyperpage{94}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}
+ \subitem {fold.h}, \hyperpage{178}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}
+ \subitem {eval}, \hyperpage{96}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}
+ \subitem {eval}, \hyperpage{94}
+ \item {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}
+ \subitem {eval}, \hyperpage{95}
+ \item {energy\_\discretionary {-}{}{}parameters}
+ \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}, \hyperpage{84}
+ \subitem {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}, \hyperpage{84}
+ \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}, \hyperpage{83}
+ \subitem {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}, \hyperpage{83}
+ \subitem {scale\_\discretionary {-}{}{}parameters}, \hyperpage{83}
+ \item {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}
+ \subitem {convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{91}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}, \hyperpage{91}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}, \hyperpage{91}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}, \hyperpage{90}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}, \hyperpage{89}
+ \subitem {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}, \hyperpage{90}
+ \item {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}
+ \subitem {read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{86}
+ \subitem {write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}, \hyperpage{86}
+ \item {energy\_\discretionary {-}{}{}set}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
+ \item {Enumerating Suboptimal Structures}, \hyperpage{48}
+ \item {eval}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}, \hyperpage{95}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}, \hyperpage{94}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}, \hyperpage{94}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}, \hyperpage{96}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}, \hyperpage{94}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}, \hyperpage{95}
+ \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}
+ \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{195}
+ \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}
+ \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{196}
+ \item {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}
+ \subitem {loop\_\discretionary {-}{}{}energies.h}, \hyperpage{195}
+ \item {expand\_\discretionary {-}{}{}Full}
+ \subitem {RNAstruct.h}, \hyperpage{226}
+ \item {expand\_\discretionary {-}{}{}Shapiro}
+ \subitem {RNAstruct.h}, \hyperpage{226}
+ \item {expHairpinEnergy}
+ \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
+ \item {expLoopEnergy}
+ \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
+ \item {export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}
+ \subitem {consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{74}
+ \item {export\_\discretionary {-}{}{}bppm}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}
+ \item {export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}
+ \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{60}
+ \item {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}
+ \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{56}
+ \item {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}
+ \subitem {mfe\_\discretionary {-}{}{}cofold}, \hyperpage{56}
\indexspace
- \item {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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
- \item {F\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}B\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}N}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{120}
- \item {final\discretionary {-}{}{}\_\discretionary {-}{}{}cost}
- \subitem {Searching Sequences for Predefined Structures},
- \hyperpage{78}
- \item {find\discretionary {-}{}{}\_\discretionary {-}{}{}saddle}
- \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{121}
- \item {findpath.\discretionary {-}{}{}h}
- \subitem {find\discretionary {-}{}{}\_\discretionary {-}{}{}saddle},
- \hyperpage{121}
- \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}path},
- \hyperpage{122}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}path},
- \hyperpage{122}
+ \item {FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}
+ \subitem {utils.h}, \hyperpage{240}
+ \item {FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}
+ \subitem {utils.h}, \hyperpage{240}
+ \item {final\_\discretionary {-}{}{}cost}
+ \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
+ \item {find\_\discretionary {-}{}{}saddle}
+ \subitem {findpath.h}, \hyperpage{171}
+ \item {findpath.h}
+ \subitem {find\_\discretionary {-}{}{}saddle}, \hyperpage{171}
+ \subitem {free\_\discretionary {-}{}{}path}, \hyperpage{172}
+ \subitem {get\_\discretionary {-}{}{}path}, \hyperpage{172}
\item {fold}
- \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures},
- \hyperpage{23}
- \item {fold.\discretionary {-}{}{}h}
- \subitem {assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}db},
- \hyperpage{126}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct},
- \hyperpage{127}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move},
- \hyperpage{125}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move\discretionary {-}{}{}\_\discretionary {-}{}{}pt},
- \hyperpage{125}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct},
- \hyperpage{126}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt},
- \hyperpage{127}
- \subitem {Hairpin\discretionary {-}{}{}E}, \hyperpage{126}
- \subitem {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{126}
- \subitem {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energy},
- \hyperpage{125}
- \subitem {Loop\discretionary {-}{}{}Energy}, \hyperpage{126}
- \subitem {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
- \hyperpage{124}
- \subitem {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}zuker},
- \hyperpage{124}
- \item {fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}
- \subitem {Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures},
- \hyperpage{23}
- \item {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h}
- \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}type},
- \hyperpage{132}
- \subitem {base\discretionary {-}{}{}\_\discretionary {-}{}{}pair},
- \hyperpage{132}
- \subitem {cut\discretionary {-}{}{}\_\discretionary {-}{}{}point},
- \hyperpage{132}
- \subitem {dangles}, \hyperpage{130}
- \subitem {do\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack},
- \hyperpage{132}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}set},
- \hyperpage{131}
- \subitem {iindx}, \hyperpage{132}
- \subitem {james\discretionary {-}{}{}\_\discretionary {-}{}{}rule},
- \hyperpage{131}
- \subitem {log\discretionary {-}{}{}M\discretionary {-}{}{}L},
- \hyperpage{131}
- \subitem {no\discretionary {-}{}{}Lonely\discretionary {-}{}{}Pairs},
- \hyperpage{130}
- \subitem {nonstandards}, \hyperpage{131}
- \subitem {old\discretionary {-}{}{}Ali\discretionary {-}{}{}En},
- \hyperpage{131}
- \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}scale},
- \hyperpage{132}
- \subitem {pr}, \hyperpage{132}
- \subitem {ribo}, \hyperpage{131}
- \subitem {Ribosum\discretionary {-}{}{}File}, \hyperpage{131}
- \subitem {set\discretionary {-}{}{}\_\discretionary {-}{}{}model\discretionary {-}{}{}\_\discretionary {-}{}{}details},
- \hyperpage{130}
- \subitem {temperature}, \hyperpage{131}
- \subitem {tetra\discretionary {-}{}{}\_\discretionary {-}{}{}loop},
- \hyperpage{131}
- \item {folden}, \hyperpage{93}
- \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}path}
- \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{122}
- \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{29}
- \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}profile}
- \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156}
- \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
- \subitem {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{52}
- \item {free\discretionary {-}{}{}\_\discretionary {-}{}{}tree}
- \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168}
+ \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{35}
+ \item {fold.h}
+ \subitem {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}, \hyperpage{177}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}, \hyperpage{179}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}, \hyperpage{175}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}, \hyperpage{176}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}, \hyperpage{177}
+ \subitem {energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}, \hyperpage{178}
+ \subitem {HairpinE}, \hyperpage{177}
+ \subitem {initialize\_\discretionary {-}{}{}fold}, \hyperpage{177}
+ \subitem {loop\_\discretionary {-}{}{}energy}, \hyperpage{176}
+ \subitem {LoopEnergy}, \hyperpage{177}
+ \subitem {parenthesis\_\discretionary {-}{}{}structure}, \hyperpage{175}
+ \subitem {parenthesis\_\discretionary {-}{}{}zuker}, \hyperpage{175}
+ \item {fold\_\discretionary {-}{}{}par}
+ \subitem {mfe\_\discretionary {-}{}{}fold}, \hyperpage{34}
+ \item {fold\_\discretionary {-}{}{}vars.h}
+ \subitem {backtrack\_\discretionary {-}{}{}type}, \hyperpage{185}
+ \subitem {base\_\discretionary {-}{}{}pair}, \hyperpage{184}
+ \subitem {cut\_\discretionary {-}{}{}point}, \hyperpage{183}
+ \subitem {dangles}, \hyperpage{182}
+ \subitem {do\_\discretionary {-}{}{}backtrack}, \hyperpage{184}
+ \subitem {energy\_\discretionary {-}{}{}set}, \hyperpage{183}
+ \subitem {iindx}, \hyperpage{184}
+ \subitem {james\_\discretionary {-}{}{}rule}, \hyperpage{183}
+ \subitem {logML}, \hyperpage{183}
+ \subitem {noLonelyPairs}, \hyperpage{182}
+ \subitem {nonstandards}, \hyperpage{183}
+ \subitem {oldAliEn}, \hyperpage{183}
+ \subitem {pf\_\discretionary {-}{}{}scale}, \hyperpage{184}
+ \subitem {pr}, \hyperpage{184}
+ \subitem {ribo}, \hyperpage{183}
+ \subitem {RibosumFile}, \hyperpage{183}
+ \subitem {set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}, \hyperpage{182}
+ \subitem {temperature}, \hyperpage{183}
+ \subitem {tetra\_\discretionary {-}{}{}loop}, \hyperpage{183}
+ \item {folden}, \hyperpage{120}
+ \item {FORBIDDEN}
+ \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
+ \item {free\_\discretionary {-}{}{}path}
+ \subitem {findpath.h}, \hyperpage{172}
+ \item {free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{41}
+ \item {free\_\discretionary {-}{}{}profile}
+ \subitem {profiledist.h}, \hyperpage{217}
+ \item {free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}
+ \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{69}
+ \item {free\_\discretionary {-}{}{}tree}
+ \subitem {treedist.h}, \hyperpage{233}
\indexspace
- \item {G\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{120}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}
- \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
- \hyperpage{81}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}
- \subitem {Calculate Partition Functions of a Distance Based Partitioning},
- \hyperpage{84}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E}
- \subitem {Calculate Partition Functions of a Distance Based Partitioning},
- \hyperpage{85}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
- \subitem {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{53}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy}
- \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
- \hyperpage{66}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors}
- \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
- \hyperpage{65}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}
- \subitem {Compute the centroid structure}, \hyperpage{33}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}
- \subitem {Compute the centroid structure}, \hyperpage{33}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations}
- \subitem {Partition Function for two hybridized Sequences},
- \hyperpage{47}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}gquad\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}
- \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}iindx}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}indx}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{181}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}line}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}line}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes}
- \subitem {cofold.\discretionary {-}{}{}h}, \hyperpage{114}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}
- \subitem {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{51}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}path}
- \subitem {findpath.\discretionary {-}{}{}h}, \hyperpage{122}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{30}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}plist}
- \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h},
- \hyperpage{150}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}
- \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
- \hyperpage{65}
- \item {get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}
- \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
- \hyperpage{65}
- \item {give\discretionary {-}{}{}\_\discretionary {-}{}{}up}
- \subitem {Searching Sequences for Predefined Structures},
- \hyperpage{78}
- \item {gml\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{158}
- \item {gquad.\discretionary {-}{}{}h}
- \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop},
- \hyperpage{134}
- \subitem {backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L},
- \hyperpage{134}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}gquad\discretionary {-}{}{}\_\discretionary {-}{}{}matrix},
- \hyperpage{134}
- \subitem {parse\discretionary {-}{}{}\_\discretionary {-}{}{}gquad},
- \hyperpage{134}
+ \item {GASCONST}
+ \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
+ \item {get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}
+ \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{69}
+ \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}
+ \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{84}
+ \item {get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}
+ \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{84}
+ \item {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}
+ \subitem {centroid\_\discretionary {-}{}{}fold}, \hyperpage{46}
+ \item {get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}
+ \subitem {centroid\_\discretionary {-}{}{}fold}, \hyperpage{46}
+ \item {get\_\discretionary {-}{}{}concentrations}
+ \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
+ \item {get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix}
+ \subitem {gquad.h}, \hyperpage{186}
+ \item {get\_\discretionary {-}{}{}iindx}
+ \subitem {utils.h}, \hyperpage{248}
+ \item {get\_\discretionary {-}{}{}indx}
+ \subitem {utils.h}, \hyperpage{248}
+ \item {get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}
+ \subitem {utils.h}, \hyperpage{243}
+ \item {get\_\discretionary {-}{}{}line}
+ \subitem {utils.h}, \hyperpage{243}
+ \item {get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}
+ \subitem {cofold.h}, \hyperpage{160}
+ \item {get\_\discretionary {-}{}{}mpi}
+ \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{67}
+ \item {get\_\discretionary {-}{}{}path}
+ \subitem {findpath.h}, \hyperpage{172}
+ \item {get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
+ \item {get\_\discretionary {-}{}{}plist}
+ \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{209}
+ \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}
+ \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
+ \item {get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}
+ \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
+ \item {get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
+ \item {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
+ \item {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{105}
+ \item {give\_\discretionary {-}{}{}up}
+ \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
+ \item {gmlRNA}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
+ \item {gquad.h}
+ \subitem {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop}, \hyperpage{187}
+ \subitem {backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L}, \hyperpage{187}
+ \subitem {get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix}, \hyperpage{186}
+ \subitem {parse\_\discretionary {-}{}{}gquad}, \hyperpage{187}
\indexspace
- \item {Hairpin\discretionary {-}{}{}E}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
+ \item {HairpinE}
+ \subitem {fold.h}, \hyperpage{177}
\item {hamming}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
- \item {hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
+ \subitem {utils.h}, \hyperpage{242}
+ \item {hamming\_\discretionary {-}{}{}bound}
+ \subitem {utils.h}, \hyperpage{242}
\indexspace
- \item {I\discretionary {-}{}{}N\discretionary {-}{}{}F}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{120}
- \item {I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}L},
- \hyperpage{94}
\item {iindx}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{132}
- \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h},
- \hyperpage{150}
- \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
- \hyperpage{148}
- \item {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}L\discretionary {-}{}{}P}
- \subitem {L\discretionary {-}{}{}Pfold.\discretionary {-}{}{}h},
- \hyperpage{142}
- \item {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold}
- \subitem {cofold.\discretionary {-}{}{}h}, \hyperpage{114}
- \item {initialize\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
- \item {int\discretionary {-}{}{}\_\discretionary {-}{}{}urn}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
- \item {interact}, \hyperpage{93}
- \item {intermediate\discretionary {-}{}{}\_\discretionary {-}{}{}t},
- \hyperpage{94}
- \item {inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose}
- \subitem {Searching Sequences for Predefined Structures},
- \hyperpage{78}
- \item {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {Searching Sequences for Predefined Structures},
- \hyperpage{77}
- \item {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {Searching Sequences for Predefined Structures},
- \hyperpage{78}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
+ \item {INF}
+ \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
+ \item {init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
+ \subitem {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}, \hyperpage{209}
+ \item {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
+ \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
+ \item {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}
+ \subitem {LPfold.h}, \hyperpage{199}
+ \item {initialize\_\discretionary {-}{}{}cofold}
+ \subitem {cofold.h}, \hyperpage{160}
+ \item {initialize\_\discretionary {-}{}{}fold}
+ \subitem {fold.h}, \hyperpage{177}
+ \item {int\_\discretionary {-}{}{}urn}
+ \subitem {utils.h}, \hyperpage{241}
+ \item {interact}, \hyperpage{121}
+ \item {intermediate\_\discretionary {-}{}{}t}, \hyperpage{122}
+ \item {INTERVAL}, \hyperpage{123}
+ \item {inv\_\discretionary {-}{}{}verbose}
+ \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
+ \item {inverse\_\discretionary {-}{}{}fold}
+ \subitem {final\_\discretionary {-}{}{}cost}, \hyperpage{98}
+ \subitem {give\_\discretionary {-}{}{}up}, \hyperpage{98}
+ \subitem {inv\_\discretionary {-}{}{}verbose}, \hyperpage{98}
+ \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{97}
+ \subitem {inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{98}
+ \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{97}
+ \item {inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
+ \subitem {inverse\_\discretionary {-}{}{}fold}, \hyperpage{98}
\indexspace
- \item {james\discretionary {-}{}{}\_\discretionary {-}{}{}rule}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
+ \item {james\_\discretionary {-}{}{}rule}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
\indexspace
\item {K0}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{120}
+ \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{169}
+ \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}
+ \subitem {destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}, \hyperpage{102}
+ \subitem {get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}, \hyperpage{102}
+ \subitem {TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}, \hyperpage{103}
+ \subitem {TwoDfoldList}, \hyperpage{102}
+ \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}
+ \subitem {destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}, \hyperpage{105}
+ \subitem {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}, \hyperpage{105}
+ \subitem {get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}, \hyperpage{105}
+ \subitem {TwoDpfoldList}, \hyperpage{106}
+ \item {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}
+ \subitem {TwoDpfold\_\discretionary {-}{}{}pbacktrack}, \hyperpage{107}
+ \subitem {TwoDpfold\_\discretionary {-}{}{}pbacktrack5}, \hyperpage{108}
\indexspace
- \item {L\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}T},
- \hyperpage{95}
- \item {L\discretionary {-}{}{}Pfold.\discretionary {-}{}{}h}
- \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}L\discretionary {-}{}{}P},
- \hyperpage{142}
- \item {L\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}C\discretionary {-}{}{}K\discretionary {-}{}{}E\discretionary {-}{}{}T},
- \hyperpage{95}
\item {Lfold}
- \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores},
- \hyperpage{60}
+ \subitem {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{77}
\item {Lfoldz}
- \subitem {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores},
- \hyperpage{60}
- \item {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments},
- \hyperpage{63}
- \subitem {ali\discretionary {-}{}{}Lfold}, \hyperpage{63}
- \item {Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores},
- \hyperpage{60}
- \subitem {Lfold}, \hyperpage{60}
- \subitem {Lfoldz}, \hyperpage{60}
- \item {log\discretionary {-}{}{}M\discretionary {-}{}{}L}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
- \item {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.\discretionary {-}{}{}h}
- \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin},
- \hyperpage{138}
- \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop},
- \hyperpage{137}
- \subitem {E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem},
- \hyperpage{138}
- \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin},
- \hyperpage{140}
- \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop},
- \hyperpage{140}
- \subitem {exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem},
- \hyperpage{139}
- \item {loop\discretionary {-}{}{}\_\discretionary {-}{}{}energy}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{125}
- \item {Loop\discretionary {-}{}{}Energy}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
+ \subitem {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}, \hyperpage{77}
+ \item {LIST}, \hyperpage{124}
+ \item {Local MFE consensus structures for Sequence Alignments}, \hyperpage{81}
+ \item {Local MFE structure Prediction and Z-\/scores}, \hyperpage{77}
+ \item {local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}
+ \subitem {aliLfold}, \hyperpage{81}
+ \item {local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}
+ \subitem {Lfold}, \hyperpage{77}
+ \subitem {Lfoldz}, \hyperpage{77}
+ \item {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}
+ \subitem {pfl\_\discretionary {-}{}{}fold}, \hyperpage{78}
+ \subitem {putoutpU\_\discretionary {-}{}{}prob}, \hyperpage{79}
+ \subitem {putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}, \hyperpage{79}
+ \subitem {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}, \hyperpage{78}
+ \item {logML}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
+ \item {loop\_\discretionary {-}{}{}energies.h}
+ \subitem {E\_\discretionary {-}{}{}Hairpin}, \hyperpage{193}
+ \subitem {E\_\discretionary {-}{}{}IntLoop}, \hyperpage{192}
+ \subitem {E\_\discretionary {-}{}{}Stem}, \hyperpage{194}
+ \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}, \hyperpage{195}
+ \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}, \hyperpage{196}
+ \subitem {exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}, \hyperpage{195}
+ \item {loop\_\discretionary {-}{}{}energy}
+ \subitem {fold.h}, \hyperpage{176}
+ \item {LoopEnergy}
+ \subitem {fold.h}, \hyperpage{177}
+ \item {LPfold.h}
+ \subitem {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}, \hyperpage{199}
+ \item {LST\_\discretionary {-}{}{}BUCKET}, \hyperpage{125}
\indexspace
- \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X2}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
- \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X3}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
- \item {M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}P}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{120}
- \item {M\discretionary {-}{}{}E\discretionary {-}{}{}A}
- \subitem {M\discretionary {-}{}{}E\discretionary {-}{}{}A.\discretionary {-}{}{}h},
- \hyperpage{143}
- \item {M\discretionary {-}{}{}E\discretionary {-}{}{}A.\discretionary {-}{}{}h}
- \subitem {M\discretionary {-}{}{}E\discretionary {-}{}{}A},
- \hyperpage{143}
- \item {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)},
- \hyperpage{54}
- \subitem {alifold}, \hyperpage{54}
- \subitem {circalifold}, \hyperpage{54}
- \item {M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences},
- \hyperpage{42}
- \subitem {cofold}, \hyperpage{42}
- \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
- \hyperpage{43}
- \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq},
- \hyperpage{43}
- \item {M\discretionary {-}{}{}I\discretionary {-}{}{}N2}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
- \item {M\discretionary {-}{}{}I\discretionary {-}{}{}N3}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
- \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile}
- \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156}
- \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}
- \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156}
- \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}loop\discretionary {-}{}{}\_\discretionary {-}{}{}index\discretionary {-}{}{}\_\discretionary {-}{}{}pt}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
- \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178}
- \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table\discretionary {-}{}{}\_\discretionary {-}{}{}snoop}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
- \item {Make\discretionary {-}{}{}\_\discretionary {-}{}{}sw\discretionary {-}{}{}String}
- \subitem {stringdist.\discretionary {-}{}{}h}, \hyperpage{165}
- \item {make\discretionary {-}{}{}\_\discretionary {-}{}{}tree}
- \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168}
- \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}dist}
- \subitem {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h},
- \hyperpage{148}
- \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{30}
- \item {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{31}
- \item {model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T},
- \hyperpage{96}
- \subitem {dangles}, \hyperpage{96}
- \item {move\discretionary {-}{}{}\_\discretionary {-}{}{}t},
- \hyperpage{96}
+ \item {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}
+ \subitem {profiledist.h}, \hyperpage{217}
+ \item {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}
+ \subitem {profiledist.h}, \hyperpage{216}
+ \item {make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt}
+ \subitem {utils.h}, \hyperpage{246}
+ \item {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}
+ \subitem {utils.h}, \hyperpage{246}
+ \item {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}
+ \subitem {utils.h}, \hyperpage{246}
+ \item {Make\_\discretionary {-}{}{}swString}
+ \subitem {stringdist.h}, \hyperpage{229}
+ \item {make\_\discretionary {-}{}{}tree}
+ \subitem {treedist.h}, \hyperpage{232}
+ \item {MAX2}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {MAX3}
+ \subitem {utils.h}, \hyperpage{240}
+ \item {MAXLOOP}
+ \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
+ \item {MEA}
+ \subitem {MEA.h}, \hyperpage{200}
+ \item {MEA.h}
+ \subitem {MEA}, \hyperpage{200}
+ \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}
+ \subitem {part\_\discretionary {-}{}{}func.h}, \hyperpage{207}
+ \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
+ \item {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{43}
+ \item {MFE Consensus Structures for Sequence Alignment(s)}, \hyperpage{71}
+ \item {MFE Structures of two hybridized Sequences}, \hyperpage{55}
+ \item {mfe\_\discretionary {-}{}{}cofold}
+ \subitem {cofold}, \hyperpage{55}
+ \subitem {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}, \hyperpage{56}
+ \subitem {export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}, \hyperpage{56}
+ \item {mfe\_\discretionary {-}{}{}fold}
+ \subitem {circfold}, \hyperpage{35}
+ \subitem {fold}, \hyperpage{35}
+ \subitem {fold\_\discretionary {-}{}{}par}, \hyperpage{34}
+ \item {MIN2}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {MIN3}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {model\_\discretionary {-}{}{}detailsT}, \hyperpage{126}
+ \subitem {dangles}, \hyperpage{126}
+ \item {move\_\discretionary {-}{}{}t}, \hyperpage{128}
\indexspace
- \item {N\discretionary {-}{}{}B\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}S}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{120}
- \item {nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact}
- \subitem {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{53}
- \item {no\discretionary {-}{}{}Lonely\discretionary {-}{}{}Pairs}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{130}
+ \item {NBPAIRS}
+ \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
+ \item {nc\_\discretionary {-}{}{}fact}
+ \subitem {consensus\_\discretionary {-}{}{}fold}, \hyperpage{70}
+ \item {noLonelyPairs}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
\item {nonstandards}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
\item {nrerror}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
+ \subitem {utils.h}, \hyperpage{241}
\indexspace
- \item {old\discretionary {-}{}{}Ali\discretionary {-}{}{}En}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
+ \item {oldAliEn}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
\indexspace
- \item {P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R},
- \hyperpage{97}
- \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h}
- \subitem {ali\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}color\discretionary {-}{}{}\_\discretionary {-}{}{}aln},
- \hyperpage{160}
- \subitem {gml\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A},
- \hyperpage{158}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
- \hyperpage{160}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}list},
- \hyperpage{159}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
- \hyperpage{158}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}a},
- \hyperpage{158}
- \subitem {ssv\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
- \hyperpage{159}
- \subitem {svg\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
- \hyperpage{159}
- \subitem {xrna\discretionary {-}{}{}\_\discretionary {-}{}{}plot},
- \hyperpage{159}
- \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{160}
- \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}list}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{159}
- \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{158}
- \item {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}a}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{158}
- \item {pack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178}
- \item {pair\discretionary {-}{}{}\_\discretionary {-}{}{}info},
- \hyperpage{97}
- \item {pairpro}, \hyperpage{98}
- \item {param\discretionary {-}{}{}T}, \hyperpage{98}
- \item {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{124}
- \item {parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}zuker}
- \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{124}
- \item {parse\discretionary {-}{}{}\_\discretionary {-}{}{}gquad}
- \subitem {gquad.\discretionary {-}{}{}h}, \hyperpage{134}
- \item {parse\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{164}
- \item {Parsing and Comparing -\/ Functions to Manipulate Structures},
- \hyperpage{90}
- \item {part\discretionary {-}{}{}\_\discretionary {-}{}{}func.\discretionary {-}{}{}h}
- \subitem {centroid}, \hyperpage{148}
- \subitem {exp\discretionary {-}{}{}Hairpin\discretionary {-}{}{}Energy},
- \hyperpage{148}
- \subitem {exp\discretionary {-}{}{}Loop\discretionary {-}{}{}Energy},
- \hyperpage{148}
- \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{148}
- \subitem {mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}dist},
- \hyperpage{148}
- \item {part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.\discretionary {-}{}{}h}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}plist},
- \hyperpage{150}
- \subitem {init\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{150}
- \item {Partition Function and Base Pair Probabilities for Sequence Alignment(s)},
- \hyperpage{56}
- \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{57}
- \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{56}
- \subitem {alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par},
- \hyperpage{56}
- \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm},
- \hyperpage{57}
- \item {Partition Function for two hybridized Sequences},
- \hyperpage{44}
- \subitem {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{45}
- \subitem {co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par},
- \hyperpage{45}
- \subitem {compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities},
- \hyperpage{47}
- \subitem {export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm},
- \hyperpage{46}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations},
- \hyperpage{47}
- \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params},
- \hyperpage{46}
- \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par},
- \hyperpage{46}
- \item {Partition Function for two hybridized Sequences as a stepwise Process},
- \hyperpage{48}
- \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact},
- \hyperpage{49}
- \subitem {pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru},
- \hyperpage{48}
- \item {Partition functions for locally stable secondary structures},
- \hyperpage{61}
- \subitem {pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{61}
- \subitem {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob},
- \hyperpage{62}
- \subitem {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin},
- \hyperpage{62}
- \subitem {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P},
- \hyperpage{61}
- \item {path\discretionary {-}{}{}\_\discretionary {-}{}{}t},
- \hyperpage{99}
+ \item {pack\_\discretionary {-}{}{}structure}
+ \subitem {utils.h}, \hyperpage{245}
+ \item {PAIR}, \hyperpage{129}
+ \item {pair\_\discretionary {-}{}{}info}, \hyperpage{130}
+ \item {pairpro}, \hyperpage{131}
+ \item {paramT}, \hyperpage{132}
+ \item {parenthesis\_\discretionary {-}{}{}structure}
+ \subitem {fold.h}, \hyperpage{175}
+ \item {parenthesis\_\discretionary {-}{}{}zuker}
+ \subitem {fold.h}, \hyperpage{175}
+ \item {parse\_\discretionary {-}{}{}gquad}
+ \subitem {gquad.h}, \hyperpage{187}
+ \item {parse\_\discretionary {-}{}{}structure}
+ \subitem {RNAstruct.h}, \hyperpage{227}
+ \item {Parsing and Comparing -\/ Functions to Manipulate Structures}, \hyperpage{110}
+ \item {part\_\discretionary {-}{}{}func.h}
+ \subitem {centroid}, \hyperpage{207}
+ \subitem {expHairpinEnergy}, \hyperpage{207}
+ \subitem {expLoopEnergy}, \hyperpage{207}
+ \subitem {init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{207}
+ \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}, \hyperpage{207}
+ \item {part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}
+ \subitem {get\_\discretionary {-}{}{}plist}, \hyperpage{209}
+ \subitem {init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{209}
+ \item {Partition Function and Base Pair Probabilities for Sequence Alignment(s)}, \hyperpage{73}
+ \item {Partition Function for two hybridized Sequences}, \hyperpage{58}
+ \item {Partition Function for two hybridized Sequences as a stepwise Process}, \hyperpage{63}
+ \item {Partition functions for locally stable secondary structures}, \hyperpage{78}
+ \item {path\_\discretionary {-}{}{}t}, \hyperpage{133}
\item {pbacktrack}
- \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{39}
- \item {pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}
- \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{40}
- \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{28}
- \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{27}
- \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{26}
- \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}
- \subitem {Partition Function for two hybridized Sequences as a stepwise Process},
- \hyperpage{49}
- \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T},
- \hyperpage{99}
- \subitem {alpha}, \hyperpage{100}
- \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}scale}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{132}
- \item {pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}
- \subitem {Partition Function for two hybridized Sequences as a stepwise Process},
- \hyperpage{48}
- \item {pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold}
- \subitem {Partition functions for locally stable secondary structures},
- \hyperpage{61}
- \item {plist}, \hyperpage{100}
- \item {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h}
- \subitem {rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}type},
- \hyperpage{155}
- \subitem {simple\discretionary {-}{}{}\_\discretionary {-}{}{}circplot\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates},
- \hyperpage{154}
- \subitem {simple\discretionary {-}{}{}\_\discretionary {-}{}{}xy\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates},
- \hyperpage{154}
- \item {Postorder\discretionary {-}{}{}\_\discretionary {-}{}{}list},
- \hyperpage{100}
+ \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{52}
+ \item {pbacktrack\_\discretionary {-}{}{}circ}
+ \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{53}
+ \item {pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{40}
+ \item {pf\_\discretionary {-}{}{}cofold}
+ \subitem {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{59}
+ \subitem {co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{59}
+ \subitem {compute\_\discretionary {-}{}{}probabilities}, \hyperpage{61}
+ \subitem {export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}, \hyperpage{60}
+ \subitem {get\_\discretionary {-}{}{}concentrations}, \hyperpage{61}
+ \subitem {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}, \hyperpage{60}
+ \subitem {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}, \hyperpage{61}
+ \item {pf\_\discretionary {-}{}{}fold}
+ \subitem {assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}, \hyperpage{42}
+ \subitem {export\_\discretionary {-}{}{}bppm}, \hyperpage{42}
+ \subitem {free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}, \hyperpage{41}
+ \subitem {get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}, \hyperpage{43}
+ \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}, \hyperpage{43}
+ \subitem {mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}, \hyperpage{43}
+ \subitem {pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}, \hyperpage{40}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
+ \subitem {pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}, \hyperpage{39}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
+ \subitem {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}, \hyperpage{42}
+ \item {pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{39}
+ \item {pf\_\discretionary {-}{}{}interact}
+ \subitem {up\_\discretionary {-}{}{}cofold}, \hyperpage{64}
+ \item {pf\_\discretionary {-}{}{}paramT}, \hyperpage{134}
+ \subitem {alpha}, \hyperpage{134}
+ \item {pf\_\discretionary {-}{}{}scale}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
+ \item {pf\_\discretionary {-}{}{}unstru}
+ \subitem {up\_\discretionary {-}{}{}cofold}, \hyperpage{63}
+ \item {pfl\_\discretionary {-}{}{}fold}
+ \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{78}
+ \item {plist}, \hyperpage{136}
+ \item {plot\_\discretionary {-}{}{}layouts.h}
+ \subitem {rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}, \hyperpage{215}
+ \subitem {simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}, \hyperpage{214}
+ \subitem {simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}, \hyperpage{214}
+ \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}, \hyperpage{213}
+ \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}, \hyperpage{213}
+ \subitem {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}, \hyperpage{213}
+ \item {Postorder\_\discretionary {-}{}{}list}, \hyperpage{137}
\item {pr}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{132}
- \item {Predicting Consensus Structures from Alignment(s)},
- \hyperpage{50}
- \subitem {alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
- \hyperpage{52}
- \subitem {cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact},
- \hyperpage{53}
- \subitem {encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence},
- \hyperpage{51}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct},
- \hyperpage{51}
- \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
- \hyperpage{52}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays},
- \hyperpage{53}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi},
- \hyperpage{51}
- \subitem {nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact},
- \hyperpage{53}
- \item {Predicting Locally stable structures of large sequences},
- \hyperpage{59}
- \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}constraint}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180}
- \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
- \item {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq\discretionary {-}{}{}\_\discretionary {-}{}{}str}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{179}
- \item {profile\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}
- \subitem {profiledist.\discretionary {-}{}{}h}, \hyperpage{156}
- \item {profiledist.\discretionary {-}{}{}h}
- \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}profile},
- \hyperpage{156}
- \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile},
- \hyperpage{156}
- \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile\discretionary {-}{}{}\_\discretionary {-}{}{}bppm},
- \hyperpage{156}
- \subitem {profile\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance},
- \hyperpage{156}
- \item {pu\discretionary {-}{}{}\_\discretionary {-}{}{}contrib},
- \hyperpage{100}
- \item {pu\discretionary {-}{}{}\_\discretionary {-}{}{}out},
- \hyperpage{101}
- \item {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob}
- \subitem {Partition functions for locally stable secondary structures},
- \hyperpage{62}
- \item {putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin}
- \subitem {Partition functions for locally stable secondary structures},
- \hyperpage{62}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{184}
+ \item {Predicting Consensus Structures from Alignment(s)}, \hyperpage{66}
+ \item {Predicting Locally stable structures of large sequences}, \hyperpage{76}
+ \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}
+ \subitem {utils.h}, \hyperpage{247}
+ \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}
+ \subitem {utils.h}, \hyperpage{247}
+ \item {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}
+ \subitem {utils.h}, \hyperpage{247}
+ \item {profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
+ \subitem {profiledist.h}, \hyperpage{216}
+ \item {profiledist.h}
+ \subitem {free\_\discretionary {-}{}{}profile}, \hyperpage{217}
+ \subitem {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}, \hyperpage{217}
+ \subitem {Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}, \hyperpage{216}
+ \subitem {profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{216}
+ \item {PS\_\discretionary {-}{}{}dot.h}
+ \subitem {aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln}, \hyperpage{221}
+ \subitem {gmlRNA}, \hyperpage{220}
+ \subitem {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}, \hyperpage{222}
+ \subitem {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}, \hyperpage{221}
+ \subitem {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{219}
+ \subitem {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}, \hyperpage{219}
+ \subitem {ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{220}
+ \subitem {svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}, \hyperpage{220}
+ \subitem {xrna\_\discretionary {-}{}{}plot}, \hyperpage{221}
+ \item {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{222}
+ \item {PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
+ \item {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{219}
+ \item {PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{219}
+ \item {pu\_\discretionary {-}{}{}contrib}, \hyperpage{138}
+ \item {pu\_\discretionary {-}{}{}out}, \hyperpage{139}
+ \item {putoutpU\_\discretionary {-}{}{}prob}
+ \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{79}
+ \item {putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}
+ \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{79}
\indexspace
- \item {R\discretionary {-}{}{}N\discretionary {-}{}{}A Secondary Structure Folding},
- \hyperpage{19}
- \item {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h}
- \subitem {add\discretionary {-}{}{}\_\discretionary {-}{}{}root},
- \hyperpage{163}
- \subitem {b2\discretionary {-}{}{}C}, \hyperpage{162}
- \subitem {b2\discretionary {-}{}{}H\discretionary {-}{}{}I\discretionary {-}{}{}T},
- \hyperpage{162}
- \subitem {b2\discretionary {-}{}{}Shapiro}, \hyperpage{162}
- \subitem {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full},
- \hyperpage{163}
- \subitem {expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Shapiro},
- \hyperpage{163}
- \subitem {parse\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
- \hyperpage{164}
- \subitem {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full},
- \hyperpage{163}
- \subitem {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}aligned\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F},
- \hyperpage{164}
- \subitem {unweight}, \hyperpage{163}
- \item {random\discretionary {-}{}{}\_\discretionary {-}{}{}string}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
- \item {read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}
- \subitem {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File},
- \hyperpage{67}
- \item {read\discretionary {-}{}{}\_\discretionary {-}{}{}record}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{177}
- \item {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File},
- \hyperpage{67}
- \subitem {read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file},
- \hyperpage{67}
- \subitem {write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file},
- \hyperpage{67}
+ \item {random\_\discretionary {-}{}{}string}
+ \subitem {utils.h}, \hyperpage{242}
+ \item {read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}, \hyperpage{86}
+ \item {read\_\discretionary {-}{}{}record}
+ \subitem {utils.h}, \hyperpage{244}
+ \item {Reading/Writing energy parameter sets from/to File}, \hyperpage{86}
\item {ribo}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
- \item {Ribosum\discretionary {-}{}{}File}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
- \item {rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}type}
- \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h},
- \hyperpage{155}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
+ \item {RibosumFile}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
+ \item {RNA Secondary Structure Folding}, \hyperpage{31}
+ \item {rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}
+ \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{215}
+ \item {RNAstruct.h}
+ \subitem {add\_\discretionary {-}{}{}root}, \hyperpage{226}
+ \subitem {b2C}, \hyperpage{225}
+ \subitem {b2HIT}, \hyperpage{225}
+ \subitem {b2Shapiro}, \hyperpage{226}
+ \subitem {expand\_\discretionary {-}{}{}Full}, \hyperpage{226}
+ \subitem {expand\_\discretionary {-}{}{}Shapiro}, \hyperpage{226}
+ \subitem {parse\_\discretionary {-}{}{}structure}, \hyperpage{227}
+ \subitem {unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}, \hyperpage{227}
+ \subitem {unexpand\_\discretionary {-}{}{}Full}, \hyperpage{227}
+ \subitem {unweight}, \hyperpage{227}
\indexspace
- \item {S\discretionary {-}{}{}O\discretionary {-}{}{}L\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N},
- \hyperpage{102}
- \item {S\discretionary {-}{}{}T\discretionary {-}{}{}R}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
- \item {scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}
- \subitem {Change and Precalculate Energy Parameter Sets and Boltzmann Factors},
- \hyperpage{65}
- \item {Searching Sequences for Predefined Structures}, \hyperpage{77}
- \subitem {final\discretionary {-}{}{}\_\discretionary {-}{}{}cost},
- \hyperpage{78}
- \subitem {give\discretionary {-}{}{}\_\discretionary {-}{}{}up},
- \hyperpage{78}
- \subitem {inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose},
- \hyperpage{78}
- \subitem {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{77}
- \subitem {inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold},
- \hyperpage{78}
- \item {sect}, \hyperpage{101}
- \item {set\discretionary {-}{}{}\_\discretionary {-}{}{}model\discretionary {-}{}{}\_\discretionary {-}{}{}details}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{130}
- \item {simple\discretionary {-}{}{}\_\discretionary {-}{}{}circplot\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}
- \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h},
- \hyperpage{154}
- \item {simple\discretionary {-}{}{}\_\discretionary {-}{}{}xy\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}
- \subitem {plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.\discretionary {-}{}{}h},
- \hyperpage{154}
- \item {snoop\discretionary {-}{}{}T}, \hyperpage{102}
+ \item {scale\_\discretionary {-}{}{}parameters}
+ \subitem {energy\_\discretionary {-}{}{}parameters}, \hyperpage{83}
+ \item {Searching Sequences for Predefined Structures}, \hyperpage{97}
+ \item {sect}, \hyperpage{140}
+ \item {set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{182}
+ \item {simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}
+ \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{214}
+ \item {simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}
+ \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{214}
+ \item {snoopT}, \hyperpage{141}
+ \item {SOLUTION}, \hyperpage{142}
\item {space}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
- \item {ssv\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{159}
- \item {st\discretionary {-}{}{}\_\discretionary {-}{}{}back}
- \subitem {Stochastic backtracking in the Ensemble}, \hyperpage{40}
- \item {Stochastic backtracking in the Ensemble}, \hyperpage{39}
- \subitem {pbacktrack}, \hyperpage{39}
- \subitem {pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ},
- \hyperpage{40}
- \subitem {st\discretionary {-}{}{}\_\discretionary {-}{}{}back},
- \hyperpage{40}
- \item {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)},
- \hyperpage{58}
- \subitem {alipbacktrack}, \hyperpage{58}
- \item {Stochastic Backtracking of Structures from Distance Based Partitioning},
- \hyperpage{87}
- \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack},
- \hyperpage{87}
- \subitem {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5},
- \hyperpage{88}
- \item {str\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}N\discretionary {-}{}{}A2\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180}
- \item {str\discretionary {-}{}{}\_\discretionary {-}{}{}uppercase}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{180}
- \item {string\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}
- \subitem {stringdist.\discretionary {-}{}{}h}, \hyperpage{165}
- \item {stringdist.\discretionary {-}{}{}h}
- \subitem {Make\discretionary {-}{}{}\_\discretionary {-}{}{}sw\discretionary {-}{}{}String},
- \hyperpage{165}
- \subitem {string\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance},
- \hyperpage{165}
- \item {struct\discretionary {-}{}{}\_\discretionary {-}{}{}en},
- \hyperpage{102}
+ \subitem {utils.h}, \hyperpage{240}
+ \item {ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
+ \item {st\_\discretionary {-}{}{}back}
+ \subitem {subopt\_\discretionary {-}{}{}stochbt}, \hyperpage{53}
+ \item {Stochastic backtracking in the Ensemble}, \hyperpage{52}
+ \item {Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}, \hyperpage{75}
+ \item {Stochastic Backtracking of Structures from Distance Based Partitioning}, \hyperpage{107}
+ \item {STR}
+ \subitem {utils.h}, \hyperpage{240}
+ \item {str\_\discretionary {-}{}{}DNA2RNA}
+ \subitem {utils.h}, \hyperpage{247}
+ \item {str\_\discretionary {-}{}{}uppercase}
+ \subitem {utils.h}, \hyperpage{247}
+ \item {string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
+ \subitem {stringdist.h}, \hyperpage{229}
+ \item {stringdist.h}
+ \subitem {Make\_\discretionary {-}{}{}swString}, \hyperpage{229}
+ \subitem {string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{229}
+ \item {struct\_\discretionary {-}{}{}en}, \hyperpage{143}
\item {subopt}
- \subitem {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E},
- \hyperpage{37}
- \item {subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}
- \subitem {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E},
- \hyperpage{38}
- \item {Suboptimal structures according to Zuker et al. 1989},
- \hyperpage{36}
- \subitem {zukersubopt}, \hyperpage{36}
- \item {Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E},
- \hyperpage{37}
- \subitem {subopt}, \hyperpage{37}
- \subitem {subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ},
- \hyperpage{38}
- \item {svg\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{159}
- \item {svm\discretionary {-}{}{}\_\discretionary {-}{}{}model},
- \hyperpage{102}
- \item {sw\discretionary {-}{}{}String}, \hyperpage{102}
+ \subitem {subopt\_\discretionary {-}{}{}wuchty}, \hyperpage{50}
+ \item {subopt\_\discretionary {-}{}{}circ}
+ \subitem {subopt\_\discretionary {-}{}{}wuchty}, \hyperpage{51}
+ \item {subopt\_\discretionary {-}{}{}stochbt}
+ \subitem {pbacktrack}, \hyperpage{52}
+ \subitem {pbacktrack\_\discretionary {-}{}{}circ}, \hyperpage{53}
+ \subitem {st\_\discretionary {-}{}{}back}, \hyperpage{53}
+ \item {subopt\_\discretionary {-}{}{}wuchty}
+ \subitem {subopt}, \hyperpage{50}
+ \subitem {subopt\_\discretionary {-}{}{}circ}, \hyperpage{51}
+ \item {subopt\_\discretionary {-}{}{}zuker}
+ \subitem {zukersubopt}, \hyperpage{49}
+ \item {Suboptimal structures according to Zuker et al. 1989}, \hyperpage{49}
+ \item {Suboptimal structures within an energy band arround the MFE}, \hyperpage{50}
+ \item {svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{220}
+ \item {svm\_\discretionary {-}{}{}model}, \hyperpage{144}
+ \item {swString}, \hyperpage{145}
\indexspace
- \item {T\discretionary {-}{}{}U\discretionary {-}{}{}R\discretionary {-}{}{}N}
- \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
- \hyperpage{120}
\item {temperature}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
- \item {tetra\discretionary {-}{}{}\_\discretionary {-}{}{}loop}
- \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
- \hyperpage{131}
- \item {time\discretionary {-}{}{}\_\discretionary {-}{}{}stamp}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
- \item {Tree}, \hyperpage{103}
- \item {tree\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}
- \subitem {treedist.\discretionary {-}{}{}h}, \hyperpage{168}
- \item {treedist.\discretionary {-}{}{}h}
- \subitem {free\discretionary {-}{}{}\_\discretionary {-}{}{}tree},
- \hyperpage{168}
- \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}tree},
- \hyperpage{168}
- \subitem {tree\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance},
- \hyperpage{168}
- \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5}
- \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
- \hyperpage{83}
- \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution},
- \hyperpage{103}
- \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars},
- \hyperpage{104}
- \item {Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List}
- \subitem {Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning},
- \hyperpage{82}
- \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack}
- \subitem {Stochastic Backtracking of Structures from Distance Based Partitioning},
- \hyperpage{87}
- \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5}
- \subitem {Stochastic Backtracking of Structures from Distance Based Partitioning},
- \hyperpage{88}
- \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution},
- \hyperpage{105}
- \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars},
- \hyperpage{106}
- \item {Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List}
- \subitem {Calculate Partition Functions of a Distance Based Partitioning},
- \hyperpage{85}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
+ \item {tetra\_\discretionary {-}{}{}loop}
+ \subitem {fold\_\discretionary {-}{}{}vars.h}, \hyperpage{183}
+ \item {time\_\discretionary {-}{}{}stamp}
+ \subitem {utils.h}, \hyperpage{242}
+ \item {Tree}, \hyperpage{146}
+ \item {tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}
+ \subitem {treedist.h}, \hyperpage{232}
+ \item {treedist.h}
+ \subitem {free\_\discretionary {-}{}{}tree}, \hyperpage{233}
+ \subitem {make\_\discretionary {-}{}{}tree}, \hyperpage{232}
+ \subitem {tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}, \hyperpage{232}
+ \item {TURN}
+ \subitem {energy\_\discretionary {-}{}{}const.h}, \hyperpage{170}
+ \item {TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{103}
+ \item {TwoDfold\_\discretionary {-}{}{}solution}, \hyperpage{147}
+ \item {TwoDfold\_\discretionary {-}{}{}vars}, \hyperpage{148}
+ \item {TwoDfoldList}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}, \hyperpage{102}
+ \item {TwoDpfold\_\discretionary {-}{}{}pbacktrack}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}, \hyperpage{107}
+ \item {TwoDpfold\_\discretionary {-}{}{}pbacktrack5}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}, \hyperpage{108}
+ \item {TwoDpfold\_\discretionary {-}{}{}solution}, \hyperpage{150}
+ \item {TwoDpfold\_\discretionary {-}{}{}vars}, \hyperpage{151}
+ \item {TwoDpfoldList}
+ \subitem {kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}, \hyperpage{106}
\indexspace
- \item {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{163}
- \item {unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}aligned\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{164}
- \item {unpack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{178}
+ \item {unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}
+ \subitem {RNAstruct.h}, \hyperpage{227}
+ \item {unexpand\_\discretionary {-}{}{}Full}
+ \subitem {RNAstruct.h}, \hyperpage{227}
+ \item {unpack\_\discretionary {-}{}{}structure}
+ \subitem {utils.h}, \hyperpage{245}
\item {unweight}
- \subitem {R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.\discretionary {-}{}{}h},
- \hyperpage{163}
- \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params}
- \subitem {alifold.\discretionary {-}{}{}h}, \hyperpage{112}
- \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}
- \subitem {Partition Function for two hybridized Sequences},
- \hyperpage{46}
- \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par}
- \subitem {Partition Function for two hybridized Sequences},
- \hyperpage{46}
- \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}
- \subitem {Calculating Partition Functions and Pair Probabilities},
- \hyperpage{29}
- \item {update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P}
- \subitem {Partition functions for locally stable secondary structures},
- \hyperpage{61}
+ \subitem {RNAstruct.h}, \hyperpage{227}
+ \item {up\_\discretionary {-}{}{}cofold}
+ \subitem {pf\_\discretionary {-}{}{}interact}, \hyperpage{64}
+ \subitem {pf\_\discretionary {-}{}{}unstru}, \hyperpage{63}
+ \item {update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}
+ \subitem {alifold.h}, \hyperpage{158}
+ \item {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}
+ \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{60}
+ \item {update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}
+ \subitem {pf\_\discretionary {-}{}{}cofold}, \hyperpage{61}
+ \item {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}
+ \subitem {pf\_\discretionary {-}{}{}fold}, \hyperpage{42}
+ \item {update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}
+ \subitem {local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}, \hyperpage{78}
\item {urn}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
- \item {utils.\discretionary {-}{}{}h}
- \subitem {alimake\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table},
- \hyperpage{179}
- \subitem {constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes},
- \hyperpage{181}
- \subitem {copy\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table},
- \hyperpage{179}
- \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},
- \hyperpage{174}
- \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},
- \hyperpage{174}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}iindx},
- \hyperpage{180}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}indx},
- \hyperpage{181}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}line},
- \hyperpage{176}
- \subitem {get\discretionary {-}{}{}\_\discretionary {-}{}{}line},
- \hyperpage{176}
- \subitem {hamming}, \hyperpage{176}
- \subitem {hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound},
- \hyperpage{176}
- \subitem {int\discretionary {-}{}{}\_\discretionary {-}{}{}urn},
- \hyperpage{175}
- \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X2},
- \hyperpage{173}
- \subitem {M\discretionary {-}{}{}A\discretionary {-}{}{}X3},
- \hyperpage{173}
- \subitem {M\discretionary {-}{}{}I\discretionary {-}{}{}N2},
- \hyperpage{173}
- \subitem {M\discretionary {-}{}{}I\discretionary {-}{}{}N3},
- \hyperpage{173}
- \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}loop\discretionary {-}{}{}\_\discretionary {-}{}{}index\discretionary {-}{}{}\_\discretionary {-}{}{}pt},
- \hyperpage{179}
- \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table},
- \hyperpage{178}
- \subitem {make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table\discretionary {-}{}{}\_\discretionary {-}{}{}snoop},
- \hyperpage{179}
- \subitem {nrerror}, \hyperpage{174}
- \subitem {pack\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
- \hyperpage{178}
- \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}constraint},
- \hyperpage{180}
- \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq},
- \hyperpage{179}
- \subitem {print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq\discretionary {-}{}{}\_\discretionary {-}{}{}str},
- \hyperpage{179}
- \subitem {random\discretionary {-}{}{}\_\discretionary {-}{}{}string},
- \hyperpage{175}
- \subitem {read\discretionary {-}{}{}\_\discretionary {-}{}{}record},
- \hyperpage{177}
- \subitem {S\discretionary {-}{}{}T\discretionary {-}{}{}R},
- \hyperpage{173}
- \subitem {space}, \hyperpage{174}
- \subitem {str\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}N\discretionary {-}{}{}A2\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A},
- \hyperpage{180}
- \subitem {str\discretionary {-}{}{}\_\discretionary {-}{}{}uppercase},
- \hyperpage{180}
- \subitem {time\discretionary {-}{}{}\_\discretionary {-}{}{}stamp},
- \hyperpage{175}
- \subitem {unpack\discretionary {-}{}{}\_\discretionary {-}{}{}structure},
- \hyperpage{178}
- \subitem {urn}, \hyperpage{175}
- \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},
- \hyperpage{173}
- \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},
- \hyperpage{172}
- \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},
- \hyperpage{173}
- \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},
- \hyperpage{172}
- \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},
- \hyperpage{172}
- \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},
- \hyperpage{171}
- \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},
- \hyperpage{171}
- \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},
- \hyperpage{172}
- \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},
- \hyperpage{172}
- \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},
- \hyperpage{171}
- \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},
- \hyperpage{171}
- \subitem {warn\discretionary {-}{}{}\_\discretionary {-}{}{}user},
- \hyperpage{175}
- \subitem {X\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R},
- \hyperpage{173}
- \subitem {xrealloc}, \hyperpage{174}
- \subitem {xsubi}, \hyperpage{182}
+ \subitem {utils.h}, \hyperpage{241}
+ \item {utils.h}
+ \subitem {alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
+ \subitem {constrain\_\discretionary {-}{}{}ptypes}, \hyperpage{248}
+ \subitem {copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
+ \subitem {FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}, \hyperpage{240}
+ \subitem {FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}, \hyperpage{240}
+ \subitem {get\_\discretionary {-}{}{}iindx}, \hyperpage{248}
+ \subitem {get\_\discretionary {-}{}{}indx}, \hyperpage{248}
+ \subitem {get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}, \hyperpage{243}
+ \subitem {get\_\discretionary {-}{}{}line}, \hyperpage{243}
+ \subitem {hamming}, \hyperpage{242}
+ \subitem {hamming\_\discretionary {-}{}{}bound}, \hyperpage{242}
+ \subitem {int\_\discretionary {-}{}{}urn}, \hyperpage{241}
+ \subitem {make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt}, \hyperpage{246}
+ \subitem {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}, \hyperpage{246}
+ \subitem {make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}, \hyperpage{246}
+ \subitem {MAX2}, \hyperpage{239}
+ \subitem {MAX3}, \hyperpage{240}
+ \subitem {MIN2}, \hyperpage{239}
+ \subitem {MIN3}, \hyperpage{239}
+ \subitem {nrerror}, \hyperpage{241}
+ \subitem {pack\_\discretionary {-}{}{}structure}, \hyperpage{245}
+ \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}, \hyperpage{247}
+ \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}, \hyperpage{247}
+ \subitem {print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}, \hyperpage{247}
+ \subitem {random\_\discretionary {-}{}{}string}, \hyperpage{242}
+ \subitem {read\_\discretionary {-}{}{}record}, \hyperpage{244}
+ \subitem {space}, \hyperpage{240}
+ \subitem {STR}, \hyperpage{240}
+ \subitem {str\_\discretionary {-}{}{}DNA2RNA}, \hyperpage{247}
+ \subitem {str\_\discretionary {-}{}{}uppercase}, \hyperpage{247}
+ \subitem {time\_\discretionary {-}{}{}stamp}, \hyperpage{242}
+ \subitem {unpack\_\discretionary {-}{}{}structure}, \hyperpage{245}
+ \subitem {urn}, \hyperpage{241}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL}, \hyperpage{239}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G}, \hyperpage{239}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE}, \hyperpage{239}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER}, \hyperpage{239}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK}, \hyperpage{239}
+ \subitem {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}, \hyperpage{237}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR}, \hyperpage{237}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}, \hyperpage{237}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC}, \hyperpage{237}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION}, \hyperpage{237}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS}, \hyperpage{238}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT}, \hyperpage{237}
+ \subitem {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}, \hyperpage{237}
+ \subitem {VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}, \hyperpage{239}
+ \subitem {warn\_\discretionary {-}{}{}user}, \hyperpage{241}
+ \subitem {xrealloc}, \hyperpage{240}
+ \subitem {XSTR}, \hyperpage{240}
+ \subitem {xsubi}, \hyperpage{249}
\indexspace
- \item {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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{172}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171}
- \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}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{171}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{91}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{89}
+ \item {VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}, \hyperpage{90}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}
+ \subitem {utils.h}, \hyperpage{237}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR}
+ \subitem {utils.h}, \hyperpage{237}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}
+ \subitem {utils.h}, \hyperpage{237}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC}
+ \subitem {utils.h}, \hyperpage{237}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION}
+ \subitem {utils.h}, \hyperpage{237}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS}
+ \subitem {utils.h}, \hyperpage{238}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT}
+ \subitem {utils.h}, \hyperpage{237}
+ \item {VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}
+ \subitem {utils.h}, \hyperpage{237}
+ \item {VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}
+ \subitem {utils.h}, \hyperpage{239}
+ \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}
+ \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}
+ \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}
+ \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}
+ \item {VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}
+ \subitem {plot\_\discretionary {-}{}{}layouts.h}, \hyperpage{213}
\indexspace
- \item {warn\discretionary {-}{}{}\_\discretionary {-}{}{}user}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{175}
- \item {write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}
- \subitem {Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File},
- \hyperpage{67}
+ \item {warn\_\discretionary {-}{}{}user}
+ \subitem {utils.h}, \hyperpage{241}
+ \item {write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}
+ \subitem {energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}, \hyperpage{86}
\indexspace
- \item {X\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{173}
\item {xrealloc}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
- \item {xrna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}
- \subitem {P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.\discretionary {-}{}{}h},
- \hyperpage{159}
+ \subitem {utils.h}, \hyperpage{240}
+ \item {xrna\_\discretionary {-}{}{}plot}
+ \subitem {PS\_\discretionary {-}{}{}dot.h}, \hyperpage{221}
+ \item {XSTR}
+ \subitem {utils.h}, \hyperpage{240}
\item {xsubi}
- \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{182}
+ \subitem {utils.h}, \hyperpage{249}
\indexspace
\item {zukersubopt}
- \subitem {Suboptimal structures according to Zuker et al. 1989},
- \hyperpage{36}
+ \subitem {subopt\_\discretionary {-}{}{}zuker}, \hyperpage{49}
\end{theindex}
git://source.jalview.org / jabaws.git / blobdiff