\contentsline {chapter}{\numberline {1}ViennaRNA Package core -\/ RNAlib}{1}{chapter.1}
\contentsline {section}{\numberline {1.1}Introduction}{1}{section.1.1}
\contentsline {chapter}{\numberline {2}Parsing and Comparing -\/ Functions to Manipulate Structures}{3}{chapter.2}
\contentsline {chapter}{\numberline {3}Utilities -\/ Odds and Ends}{9}{chapter.3}
\contentsline {section}{\numberline {3.1}Producing secondary structure graphs}{10}{section.3.1}
\contentsline {section}{\numberline {3.2}Producing (colored) dot plots for base pair probabilities}{11}{section.3.2}
\contentsline {section}{\numberline {3.3}Producing (colored) alignments}{12}{section.3.3}
\contentsline {section}{\numberline {3.4}RNA sequence related utilities}{12}{section.3.4}
\contentsline {section}{\numberline {3.5}RNA secondary structure related utilities}{12}{section.3.5}
\contentsline {section}{\numberline {3.6}Miscellaneous Utilities}{13}{section.3.6}
\contentsline {chapter}{\numberline {4}Example -\/ A Small Example Program}{15}{chapter.4}
\contentsline {chapter}{\numberline {5}Deprecated List}{19}{chapter.5}
\contentsline {chapter}{\numberline {6}Module Index}{23}{chapter.6}
\contentsline {section}{\numberline {6.1}Modules}{23}{section.6.1}
\contentsline {chapter}{\numberline {7}Data Structure Index}{25}{chapter.7}
\contentsline {section}{\numberline {7.1}Data Structures}{25}{section.7.1}
\contentsline {chapter}{\numberline {8}File Index}{27}{chapter.8}
\contentsline {section}{\numberline {8.1}File List}{27}{section.8.1}
\contentsline {chapter}{\numberline {9}Module Documentation}{31}{chapter.9}
\contentsline {section}{\numberline {9.1}RNA Secondary Structure Folding}{31}{section.9.1}
\contentsline {subsection}{\numberline {9.1.1}Detailed Description}{32}{subsection.9.1.1}
\contentsline {section}{\numberline {9.2}Calculating Minimum Free Energy (MFE) Structures}{33}{section.9.2}
\contentsline {subsection}{\numberline {9.2.1}Detailed Description}{34}{subsection.9.2.1}
\contentsline {subsection}{\numberline {9.2.2}Function Documentation}{34}{subsection.9.2.2}
\contentsline {subsubsection}{\numberline {9.2.2.1}fold\_\discretionary {-}{}{}par}{34}{subsubsection.9.2.2.1}
\contentsline {subsubsection}{\numberline {9.2.2.2}fold}{35}{subsubsection.9.2.2.2}
\contentsline {subsubsection}{\numberline {9.2.2.3}circfold}{36}{subsubsection.9.2.2.3}
\contentsline {section}{\numberline {9.3}Calculating Partition Functions and Pair Probabilities}{37}{section.9.3}
\contentsline {subsection}{\numberline {9.3.1}Detailed Description}{38}{subsection.9.3.1}
\contentsline {subsection}{\numberline {9.3.2}Function Documentation}{39}{subsection.9.3.2}
\contentsline {subsubsection}{\numberline {9.3.2.1}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}{39}{subsubsection.9.3.2.1}
\contentsline {subsubsection}{\numberline {9.3.2.2}pf\_\discretionary {-}{}{}fold}{40}{subsubsection.9.3.2.2}
\contentsline {subsubsection}{\numberline {9.3.2.3}pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}{41}{subsubsection.9.3.2.3}
\contentsline {subsubsection}{\numberline {9.3.2.4}free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}{41}{subsubsection.9.3.2.4}
\contentsline {subsubsection}{\numberline {9.3.2.5}update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}{42}{subsubsection.9.3.2.5}
\contentsline {subsubsection}{\numberline {9.3.2.6}export\_\discretionary {-}{}{}bppm}{42}{subsubsection.9.3.2.6}
\contentsline {subsubsection}{\numberline {9.3.2.7}assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}{42}{subsubsection.9.3.2.7}
\contentsline {subsubsection}{\numberline {9.3.2.8}get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}{43}{subsubsection.9.3.2.8}
\contentsline {subsubsection}{\numberline {9.3.2.9}mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}{43}{subsubsection.9.3.2.9}
\contentsline {subsubsection}{\numberline {9.3.2.10}mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}{44}{subsubsection.9.3.2.10}
\contentsline {section}{\numberline {9.4}Compute the structure with maximum expected accuracy (MEA)}{45}{section.9.4}
\contentsline {section}{\numberline {9.5}Compute the centroid structure}{46}{section.9.5}
\contentsline {subsection}{\numberline {9.5.1}Function Documentation}{46}{subsection.9.5.1}
\contentsline {subsubsection}{\numberline {9.5.1.1}get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}{46}{subsubsection.9.5.1.1}
\contentsline {subsubsection}{\numberline {9.5.1.2}get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}{46}{subsubsection.9.5.1.2}
\contentsline {section}{\numberline {9.6}Enumerating Suboptimal Structures}{48}{section.9.6}
\contentsline {section}{\numberline {9.7}Suboptimal structures according to Zuker et al. 1989}{49}{section.9.7}
\contentsline {subsection}{\numberline {9.7.1}Function Documentation}{49}{subsection.9.7.1}
\contentsline {subsubsection}{\numberline {9.7.1.1}zukersubopt}{49}{subsubsection.9.7.1.1}
\contentsline {section}{\numberline {9.8}Suboptimal structures within an energy band arround the MFE}{50}{section.9.8}
\contentsline {subsection}{\numberline {9.8.1}Function Documentation}{50}{subsection.9.8.1}
\contentsline {subsubsection}{\numberline {9.8.1.1}subopt}{50}{subsubsection.9.8.1.1}
\contentsline {subsubsection}{\numberline {9.8.1.2}subopt\_\discretionary {-}{}{}circ}{51}{subsubsection.9.8.1.2}
\contentsline {section}{\numberline {9.9}Stochastic backtracking in the Ensemble}{52}{section.9.9}
\contentsline {subsection}{\numberline {9.9.1}Function Documentation}{52}{subsection.9.9.1}
\contentsline {subsubsection}{\numberline {9.9.1.1}pbacktrack}{52}{subsubsection.9.9.1.1}
\contentsline {subsubsection}{\numberline {9.9.1.2}pbacktrack\_\discretionary {-}{}{}circ}{53}{subsubsection.9.9.1.2}
\contentsline {subsection}{\numberline {9.9.2}Variable Documentation}{53}{subsection.9.9.2}
\contentsline {subsubsection}{\numberline {9.9.2.1}st\_\discretionary {-}{}{}back}{53}{subsubsection.9.9.2.1}
\contentsline {section}{\numberline {9.10}Calculate Secondary Structures of two RNAs upon Dimerization}{54}{section.9.10}
\contentsline {subsection}{\numberline {9.10.1}Detailed Description}{54}{subsection.9.10.1}
\contentsline {section}{\numberline {9.11}MFE Structures of two hybridized Sequences}{55}{section.9.11}
\contentsline {subsection}{\numberline {9.11.1}Function Documentation}{55}{subsection.9.11.1}
\contentsline {subsubsection}{\numberline {9.11.1.1}cofold}{55}{subsubsection.9.11.1.1}
\contentsline {subsubsection}{\numberline {9.11.1.2}export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}{56}{subsubsection.9.11.1.2}
\contentsline {subsubsection}{\numberline {9.11.1.3}export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}{56}{subsubsection.9.11.1.3}
\contentsline {section}{\numberline {9.12}Partition Function for two hybridized Sequences}{58}{section.9.12}
\contentsline {subsection}{\numberline {9.12.1}Detailed Description}{59}{subsection.9.12.1}
\contentsline {subsection}{\numberline {9.12.2}Function Documentation}{59}{subsection.9.12.2}
\contentsline {subsubsection}{\numberline {9.12.2.1}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}{59}{subsubsection.9.12.2.1}
\contentsline {subsubsection}{\numberline {9.12.2.2}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}{60}{subsubsection.9.12.2.2}
\contentsline {subsubsection}{\numberline {9.12.2.3}export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}{60}{subsubsection.9.12.2.3}
\contentsline {subsubsection}{\numberline {9.12.2.4}update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}{60}{subsubsection.9.12.2.4}
\contentsline {subsubsection}{\numberline {9.12.2.5}update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}{61}{subsubsection.9.12.2.5}
\contentsline {subsubsection}{\numberline {9.12.2.6}compute\_\discretionary {-}{}{}probabilities}{61}{subsubsection.9.12.2.6}
\contentsline {subsubsection}{\numberline {9.12.2.7}get\_\discretionary {-}{}{}concentrations}{62}{subsubsection.9.12.2.7}
\contentsline {section}{\numberline {9.13}Partition Function for two hybridized Sequences as a stepwise Process}{63}{section.9.13}
\contentsline {subsection}{\numberline {9.13.1}Detailed Description}{63}{subsection.9.13.1}
\contentsline {subsection}{\numberline {9.13.2}Function Documentation}{63}{subsection.9.13.2}
\contentsline {subsubsection}{\numberline {9.13.2.1}pf\_\discretionary {-}{}{}unstru}{63}{subsubsection.9.13.2.1}
\contentsline {subsubsection}{\numberline {9.13.2.2}pf\_\discretionary {-}{}{}interact}{64}{subsubsection.9.13.2.2}
\contentsline {section}{\numberline {9.14}Predicting Consensus Structures from Alignment(s)}{66}{section.9.14}
\contentsline {subsection}{\numberline {9.14.1}Detailed Description}{67}{subsection.9.14.1}
\contentsline {subsection}{\numberline {9.14.2}Function Documentation}{67}{subsection.9.14.2}
\contentsline {subsubsection}{\numberline {9.14.2.1}get\_\discretionary {-}{}{}mpi}{67}{subsubsection.9.14.2.1}
\contentsline {subsubsection}{\numberline {9.14.2.2}energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}{68}{subsubsection.9.14.2.2}
\contentsline {subsubsection}{\numberline {9.14.2.3}encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}{68}{subsubsection.9.14.2.3}
\contentsline {subsubsection}{\numberline {9.14.2.4}alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}{68}{subsubsection.9.14.2.4}
\contentsline {subsubsection}{\numberline {9.14.2.5}free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}{69}{subsubsection.9.14.2.5}
\contentsline {subsubsection}{\numberline {9.14.2.6}get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}{69}{subsubsection.9.14.2.6}
\contentsline {subsection}{\numberline {9.14.3}Variable Documentation}{70}{subsection.9.14.3}
\contentsline {subsubsection}{\numberline {9.14.3.1}cv\_\discretionary {-}{}{}fact}{70}{subsubsection.9.14.3.1}
\contentsline {subsubsection}{\numberline {9.14.3.2}nc\_\discretionary {-}{}{}fact}{70}{subsubsection.9.14.3.2}
\contentsline {section}{\numberline {9.15}MFE Consensus Structures for Sequence Alignment(s)}{71}{section.9.15}
\contentsline {subsection}{\numberline {9.15.1}Function Documentation}{71}{subsection.9.15.1}
\contentsline {subsubsection}{\numberline {9.15.1.1}alifold}{71}{subsubsection.9.15.1.1}
\contentsline {subsubsection}{\numberline {9.15.1.2}circalifold}{71}{subsubsection.9.15.1.2}
\contentsline {section}{\numberline {9.16}Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{73}{section.9.16}
\contentsline {subsection}{\numberline {9.16.1}Function Documentation}{73}{subsection.9.16.1}
\contentsline {subsubsection}{\numberline {9.16.1.1}alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}{73}{subsubsection.9.16.1.1}
\contentsline {subsubsection}{\numberline {9.16.1.2}alipf\_\discretionary {-}{}{}fold}{74}{subsubsection.9.16.1.2}
\contentsline {subsubsection}{\numberline {9.16.1.3}alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}{74}{subsubsection.9.16.1.3}
\contentsline {subsubsection}{\numberline {9.16.1.4}export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}{74}{subsubsection.9.16.1.4}
\contentsline {section}{\numberline {9.17}Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{75}{section.9.17}
\contentsline {subsection}{\numberline {9.17.1}Function Documentation}{75}{subsection.9.17.1}
\contentsline {subsubsection}{\numberline {9.17.1.1}alipbacktrack}{75}{subsubsection.9.17.1.1}
\contentsline {section}{\numberline {9.18}Predicting Locally stable structures of large sequences}{76}{section.9.18}
\contentsline {subsection}{\numberline {9.18.1}Detailed Description}{76}{subsection.9.18.1}
\contentsline {section}{\numberline {9.19}Local MFE structure Prediction and Z-\/scores}{77}{section.9.19}
\contentsline {subsection}{\numberline {9.19.1}Function Documentation}{77}{subsection.9.19.1}
\contentsline {subsubsection}{\numberline {9.19.1.1}Lfold}{77}{subsubsection.9.19.1.1}
\contentsline {subsubsection}{\numberline {9.19.1.2}Lfoldz}{77}{subsubsection.9.19.1.2}
\contentsline {section}{\numberline {9.20}Partition functions for locally stable secondary structures}{78}{section.9.20}
\contentsline {subsection}{\numberline {9.20.1}Function Documentation}{78}{subsection.9.20.1}
\contentsline {subsubsection}{\numberline {9.20.1.1}update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}{78}{subsubsection.9.20.1.1}
\contentsline {subsubsection}{\numberline {9.20.1.2}pfl\_\discretionary {-}{}{}fold}{78}{subsubsection.9.20.1.2}
\contentsline {subsubsection}{\numberline {9.20.1.3}putoutpU\_\discretionary {-}{}{}prob}{79}{subsubsection.9.20.1.3}
\contentsline {subsubsection}{\numberline {9.20.1.4}putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}{80}{subsubsection.9.20.1.4}
\contentsline {section}{\numberline {9.21}Local MFE consensus structures for Sequence Alignments}{81}{section.9.21}
\contentsline {subsection}{\numberline {9.21.1}Function Documentation}{81}{subsection.9.21.1}
\contentsline {subsubsection}{\numberline {9.21.1.1}aliLfold}{81}{subsubsection.9.21.1.1}
\contentsline {section}{\numberline {9.22}Change and Precalculate Energy Parameter Sets and Boltzmann Factors}{82}{section.9.22}
\contentsline {subsection}{\numberline {9.22.1}Detailed Description}{83}{subsection.9.22.1}
\contentsline {subsection}{\numberline {9.22.2}Function Documentation}{83}{subsection.9.22.2}
\contentsline {subsubsection}{\numberline {9.22.2.1}scale\_\discretionary {-}{}{}parameters}{83}{subsubsection.9.22.2.1}
\contentsline {subsubsection}{\numberline {9.22.2.2}get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}{83}{subsubsection.9.22.2.2}
\contentsline {subsubsection}{\numberline {9.22.2.3}get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}{84}{subsubsection.9.22.2.3}
\contentsline {subsubsection}{\numberline {9.22.2.4}get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}{84}{subsubsection.9.22.2.4}
\contentsline {subsubsection}{\numberline {9.22.2.5}get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}{84}{subsubsection.9.22.2.5}
\contentsline {section}{\numberline {9.23}Reading/Writing energy parameter sets from/to File}{86}{section.9.23}
\contentsline {subsection}{\numberline {9.23.1}Detailed Description}{86}{subsection.9.23.1}
\contentsline {subsection}{\numberline {9.23.2}Function Documentation}{86}{subsection.9.23.2}
\contentsline {subsubsection}{\numberline {9.23.2.1}read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}{86}{subsubsection.9.23.2.1}
\contentsline {subsubsection}{\numberline {9.23.2.2}write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}{87}{subsubsection.9.23.2.2}
\contentsline {section}{\numberline {9.24}Converting energy parameter files}{88}{section.9.24}
\contentsline {subsection}{\numberline {9.24.1}Detailed Description}{89}{subsection.9.24.1}
\contentsline {subsection}{\numberline {9.24.2}Define Documentation}{89}{subsection.9.24.2}
\contentsline {subsubsection}{\numberline {9.24.2.1}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}{89}{subsubsection.9.24.2.1}
\contentsline {subsubsection}{\numberline {9.24.2.2}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}{89}{subsubsection.9.24.2.2}
\contentsline {subsubsection}{\numberline {9.24.2.3}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}{89}{subsubsection.9.24.2.3}
\contentsline {subsubsection}{\numberline {9.24.2.4}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}{89}{subsubsection.9.24.2.4}
\contentsline {subsubsection}{\numberline {9.24.2.5}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}{89}{subsubsection.9.24.2.5}
\contentsline {subsubsection}{\numberline {9.24.2.6}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}{89}{subsubsection.9.24.2.6}
\contentsline {subsubsection}{\numberline {9.24.2.7}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}{89}{subsubsection.9.24.2.7}
\contentsline {subsubsection}{\numberline {9.24.2.8}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}{89}{subsubsection.9.24.2.8}
\contentsline {subsubsection}{\numberline {9.24.2.9}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}{89}{subsubsection.9.24.2.9}
\contentsline {subsubsection}{\numberline {9.24.2.10}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}{90}{subsubsection.9.24.2.10}
\contentsline {subsubsection}{\numberline {9.24.2.11}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}{90}{subsubsection.9.24.2.11}
\contentsline {subsubsection}{\numberline {9.24.2.12}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}{90}{subsubsection.9.24.2.12}
\contentsline {subsubsection}{\numberline {9.24.2.13}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}{90}{subsubsection.9.24.2.13}
\contentsline {subsubsection}{\numberline {9.24.2.14}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}{90}{subsubsection.9.24.2.14}
\contentsline {subsubsection}{\numberline {9.24.2.15}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}{90}{subsubsection.9.24.2.15}
\contentsline {subsubsection}{\numberline {9.24.2.16}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}{90}{subsubsection.9.24.2.16}
\contentsline {subsubsection}{\numberline {9.24.2.17}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}{90}{subsubsection.9.24.2.17}
\contentsline {subsubsection}{\numberline {9.24.2.18}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}{90}{subsubsection.9.24.2.18}
\contentsline {subsubsection}{\numberline {9.24.2.19}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}{90}{subsubsection.9.24.2.19}
\contentsline {subsubsection}{\numberline {9.24.2.20}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}{91}{subsubsection.9.24.2.20}
\contentsline {subsubsection}{\numberline {9.24.2.21}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}{91}{subsubsection.9.24.2.21}
\contentsline {subsubsection}{\numberline {9.24.2.22}VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}{91}{subsubsection.9.24.2.22}
\contentsline {subsection}{\numberline {9.24.3}Function Documentation}{91}{subsection.9.24.3}
\contentsline {subsubsection}{\numberline {9.24.3.1}convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}{91}{subsubsection.9.24.3.1}
\contentsline {section}{\numberline {9.25}Energy evaluation}{93}{section.9.25}
\contentsline {subsection}{\numberline {9.25.1}Detailed Description}{93}{subsection.9.25.1}
\contentsline {subsection}{\numberline {9.25.2}Function Documentation}{94}{subsection.9.25.2}
\contentsline {subsubsection}{\numberline {9.25.2.1}energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}{94}{subsubsection.9.25.2.1}
\contentsline {subsubsection}{\numberline {9.25.2.2}energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}{94}{subsubsection.9.25.2.2}
\contentsline {subsubsection}{\numberline {9.25.2.3}energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}{95}{subsubsection.9.25.2.3}
\contentsline {subsubsection}{\numberline {9.25.2.4}energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}{95}{subsubsection.9.25.2.4}
\contentsline {subsubsection}{\numberline {9.25.2.5}energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}{96}{subsubsection.9.25.2.5}
\contentsline {subsubsection}{\numberline {9.25.2.6}energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}{96}{subsubsection.9.25.2.6}
\contentsline {section}{\numberline {9.26}Searching Sequences for Predefined Structures}{97}{section.9.26}
\contentsline {subsection}{\numberline {9.26.1}Detailed Description}{97}{subsection.9.26.1}
\contentsline {subsection}{\numberline {9.26.2}Function Documentation}{97}{subsection.9.26.2}
\contentsline {subsubsection}{\numberline {9.26.2.1}inverse\_\discretionary {-}{}{}fold}{97}{subsubsection.9.26.2.1}
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