--- /dev/null
+\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}
+
+ \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 {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}
+ \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}
+ \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}
+
+ \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}
+
+ \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 {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}
+ \item {circalifold}
+ \subitem {M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)},
+ \hyperpage{54}
+ \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}
+ \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}
+
+ \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}
+
+ \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}
+
+ \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 {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}
+
+ \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}
+
+ \indexspace
+
+ \item {Hairpin\discretionary {-}{}{}E}
+ \subitem {fold.\discretionary {-}{}{}h}, \hyperpage{126}
+ \item {hamming}
+ \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
+ \item {hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound}
+ \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{176}
+
+ \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}
+
+ \indexspace
+
+ \item {james\discretionary {-}{}{}\_\discretionary {-}{}{}rule}
+ \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
+ \hyperpage{131}
+
+ \indexspace
+
+ \item {K0}
+ \subitem {energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.\discretionary {-}{}{}h},
+ \hyperpage{120}
+
+ \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}
+ \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}
+
+ \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}
+
+ \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 {nonstandards}
+ \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
+ \hyperpage{131}
+ \item {nrerror}
+ \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{174}
+
+ \indexspace
+
+ \item {old\discretionary {-}{}{}Ali\discretionary {-}{}{}En}
+ \subitem {fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.\discretionary {-}{}{}h},
+ \hyperpage{131}
+
+ \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 {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}
+ \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}
+
+ \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 {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}
+
+ \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 {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}
+ \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}
+
+ \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}
+
+ \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 {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}
+ \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}
+
+ \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}
+
+ \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}
+
+ \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}
+ \item {xsubi}
+ \subitem {utils.\discretionary {-}{}{}h}, \hyperpage{182}
+
+ \indexspace
+
+ \item {zukersubopt}
+ \subitem {Suboptimal structures according to Zuker et al. 1989},
+ \hyperpage{36}
+
+\end{theindex}
git://source.jalview.org / jabaws.git / blobdiff