\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}Folding Routines -\/ Functions for Folding RNA Secondary Structures}{3}{chapter.2}
\contentsline {section}{\numberline {2.1}Calculating Minimum Free Energy Structures}{4}{section.2.1}
\contentsline {section}{\numberline {2.2}Calculating Partition Functions and Pair Probabilities}{5}{section.2.2}
\contentsline {section}{\numberline {2.3}Searching for Predefined Structures}{6}{section.2.3}
\contentsline {section}{\numberline {2.4}Enumerating Suboptimal Structures}{6}{section.2.4}
\contentsline {section}{\numberline {2.5}Predicting hybridization structures of two molecules}{7}{section.2.5}
\contentsline {section}{\numberline {2.6}Predicting local structures of large sequences}{9}{section.2.6}
\contentsline {section}{\numberline {2.7}Predicting Consensus Structures from Alignment}{10}{section.2.7}
\contentsline {section}{\numberline {2.8}Global Variables for the Folding Routines}{11}{section.2.8}
\contentsline {section}{\numberline {2.9}Reading Energy Parameters from File}{13}{section.2.9}
\contentsline {chapter}{\numberline {3}Parsing and Comparing -\/ Functions to Manipulate Structures}{15}{chapter.3}
\contentsline {chapter}{\numberline {4}Utilities -\/ Odds and Ends}{21}{chapter.4}
\contentsline {section}{\numberline {4.1}Producing secondary structure graphs}{22}{section.4.1}
\contentsline {section}{\numberline {4.2}Producing (colored) dot plots for base pair probabilities}{23}{section.4.2}
\contentsline {section}{\numberline {4.3}Producing (colored) alignments}{24}{section.4.3}
\contentsline {section}{\numberline {4.4}RNA sequence related utilities}{24}{section.4.4}
\contentsline {section}{\numberline {4.5}RNA secondary structure related utilities}{24}{section.4.5}
\contentsline {section}{\numberline {4.6}Miscellaneous Utilities}{25}{section.4.6}
\contentsline {chapter}{\numberline {5}Example -\/ A Small Example Program}{27}{chapter.5}
\contentsline {chapter}{\numberline {6}References}{31}{chapter.6}
\contentsline {chapter}{\numberline {7}Deprecated List}{35}{chapter.7}
\contentsline {chapter}{\numberline {8}Data Structure Index}{39}{chapter.8}
\contentsline {section}{\numberline {8.1}Data Structures}{39}{section.8.1}
\contentsline {chapter}{\numberline {9}File Index}{41}{chapter.9}
\contentsline {section}{\numberline {9.1}File List}{41}{section.9.1}
\contentsline {chapter}{\numberline {10}Data Structure Documentation}{43}{chapter.10}
\contentsline {section}{\numberline {10.1}bondT Struct Reference}{43}{section.10.1}
\contentsline {subsection}{\numberline {10.1.1}Detailed Description}{43}{subsection.10.1.1}
\contentsline {section}{\numberline {10.2}bondTEn Struct Reference}{44}{section.10.2}
\contentsline {subsection}{\numberline {10.2.1}Detailed Description}{44}{subsection.10.2.1}
\contentsline {section}{\numberline {10.3}cofoldF Struct Reference}{45}{section.10.3}
\contentsline {section}{\numberline {10.4}ConcEnt Struct Reference}{46}{section.10.4}
\contentsline {section}{\numberline {10.5}constrain Struct Reference}{47}{section.10.5}
\contentsline {section}{\numberline {10.6}COORDINATE Struct Reference}{48}{section.10.6}
\contentsline {subsection}{\numberline {10.6.1}Detailed Description}{48}{subsection.10.6.1}
\contentsline {section}{\numberline {10.7}cpair Struct Reference}{49}{section.10.7}
\contentsline {subsection}{\numberline {10.7.1}Detailed Description}{49}{subsection.10.7.1}
\contentsline {section}{\numberline {10.8}duplexT Struct Reference}{50}{section.10.8}
\contentsline {section}{\numberline {10.9}dupVar Struct Reference}{51}{section.10.9}
\contentsline {section}{\numberline {10.10}folden Struct Reference}{52}{section.10.10}
\contentsline {section}{\numberline {10.11}interact Struct Reference}{53}{section.10.11}
\contentsline {section}{\numberline {10.12}intermediate\_\discretionary {-}{}{}t Struct Reference}{54}{section.10.12}
\contentsline {section}{\numberline {10.13}INTERVAL Struct Reference}{55}{section.10.13}
\contentsline {subsection}{\numberline {10.13.1}Detailed Description}{55}{subsection.10.13.1}
\contentsline {section}{\numberline {10.14}LIST Struct Reference}{56}{section.10.14}
\contentsline {section}{\numberline {10.15}LST\_\discretionary {-}{}{}BUCKET Struct Reference}{57}{section.10.15}
\contentsline {section}{\numberline {10.16}model\_\discretionary {-}{}{}detailsT Struct Reference}{58}{section.10.16}
\contentsline {subsection}{\numberline {10.16.1}Detailed Description}{58}{subsection.10.16.1}
\contentsline {section}{\numberline {10.17}move\_\discretionary {-}{}{}t Struct Reference}{59}{section.10.17}
\contentsline {section}{\numberline {10.18}PAIR Struct Reference}{60}{section.10.18}
\contentsline {subsection}{\numberline {10.18.1}Detailed Description}{60}{subsection.10.18.1}
\contentsline {section}{\numberline {10.19}pair\_\discretionary {-}{}{}info Struct Reference}{61}{section.10.19}
\contentsline {subsection}{\numberline {10.19.1}Detailed Description}{61}{subsection.10.19.1}
\contentsline {section}{\numberline {10.20}pairpro Struct Reference}{62}{section.10.20}
\contentsline {section}{\numberline {10.21}paramT Struct Reference}{63}{section.10.21}
\contentsline {subsection}{\numberline {10.21.1}Detailed Description}{63}{subsection.10.21.1}
\contentsline {section}{\numberline {10.22}path\_\discretionary {-}{}{}t Struct Reference}{64}{section.10.22}
\contentsline {section}{\numberline {10.23}pf\_\discretionary {-}{}{}paramT Struct Reference}{65}{section.10.23}
\contentsline {subsection}{\numberline {10.23.1}Detailed Description}{65}{subsection.10.23.1}
\contentsline {section}{\numberline {10.24}plist Struct Reference}{66}{section.10.24}
\contentsline {subsection}{\numberline {10.24.1}Detailed Description}{66}{subsection.10.24.1}
\contentsline {section}{\numberline {10.25}Postorder\_\discretionary {-}{}{}list Struct Reference}{67}{section.10.25}
\contentsline {section}{\numberline {10.26}pu\_\discretionary {-}{}{}contrib Struct Reference}{68}{section.10.26}
\contentsline {section}{\numberline {10.27}pu\_\discretionary {-}{}{}out Struct Reference}{69}{section.10.27}
\contentsline {section}{\numberline {10.28}sect Struct Reference}{70}{section.10.28}
\contentsline {subsection}{\numberline {10.28.1}Detailed Description}{70}{subsection.10.28.1}
\contentsline {section}{\numberline {10.29}snoopT Struct Reference}{71}{section.10.29}
\contentsline {section}{\numberline {10.30}SOLUTION Struct Reference}{72}{section.10.30}
\contentsline {subsection}{\numberline {10.30.1}Detailed Description}{72}{subsection.10.30.1}
\contentsline {section}{\numberline {10.31}svm\_\discretionary {-}{}{}model Struct Reference}{73}{section.10.31}
\contentsline {section}{\numberline {10.32}swString Struct Reference}{74}{section.10.32}
\contentsline {section}{\numberline {10.33}Tree Struct Reference}{75}{section.10.33}
\contentsline {section}{\numberline {10.34}TwoDfold\_\discretionary {-}{}{}solution Struct Reference}{76}{section.10.34}
\contentsline {subsection}{\numberline {10.34.1}Detailed Description}{76}{subsection.10.34.1}
\contentsline {section}{\numberline {10.35}TwoDfold\_\discretionary {-}{}{}vars Struct Reference}{77}{section.10.35}
\contentsline {subsection}{\numberline {10.35.1}Detailed Description}{77}{subsection.10.35.1}
\contentsline {section}{\numberline {10.36}TwoDpfold\_\discretionary {-}{}{}solution Struct Reference}{78}{section.10.36}
\contentsline {subsection}{\numberline {10.36.1}Detailed Description}{78}{subsection.10.36.1}
\contentsline {section}{\numberline {10.37}TwoDpfold\_\discretionary {-}{}{}vars Struct Reference}{79}{section.10.37}
\contentsline {subsection}{\numberline {10.37.1}Detailed Description}{79}{subsection.10.37.1}
\contentsline {chapter}{\numberline {11}File Documentation}{81}{chapter.11}
\contentsline {section}{\numberline {11.1}H/2Dfold.h File Reference}{81}{section.11.1}
\contentsline {subsection}{\numberline {11.1.1}Detailed Description}{81}{subsection.11.1.1}
\contentsline {subsection}{\numberline {11.1.2}Function Documentation}{82}{subsection.11.1.2}
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\contentsline {subsection}{\numberline {11.3.1}Detailed Description}{89}{subsection.11.3.1}
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\contentsline {subsubsection}{\numberline {11.3.2.3}circalifold}{90}{subsubsection.11.3.2.3}
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\contentsline {subsubsection}{\numberline {11.3.2.7}alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}{91}{subsubsection.11.3.2.7}
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\contentsline {subsubsection}{\numberline {11.3.2.9}alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}{92}{subsubsection.11.3.2.9}
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\contentsline {subsubsection}{\numberline {11.3.3.2}nc\_\discretionary {-}{}{}fact}{94}{subsubsection.11.3.3.2}
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\contentsline {subsubsection}{\numberline {11.4.2.2}zukersubopt}{96}{subsubsection.11.4.2.2}
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\contentsline {subsubsection}{\numberline {11.33.3.29}constrain\_\discretionary {-}{}{}ptypes}{196}{subsubsection.11.33.3.29}
\contentsline {subsection}{\numberline {11.33.4}Variable Documentation}{196}{subsection.11.33.4}
\contentsline {subsubsection}{\numberline {11.33.4.1}xsubi}{196}{subsubsection.11.33.4.1}
\contentsline {section}{\numberline {11.34}lib/1.8.4\_\discretionary {-}{}{}epars.h File Reference}{197}{section.11.34}
\contentsline {subsection}{\numberline {11.34.1}Detailed Description}{197}{subsection.11.34.1}
\contentsline {section}{\numberline {11.35}lib/1.8.4\_\discretionary {-}{}{}intloops.h File Reference}{198}{section.11.35}
\contentsline {subsection}{\numberline {11.35.1}Detailed Description}{198}{subsection.11.35.1}
