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\contentsline {chapter}{\numberline {1}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A Package core -\/ R\discretionary {-}{}{}N\discretionary {-}{}{}Alib}{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}{5}{chapter.3}
\contentsline {section}{\numberline {3.1}Producing secondary structure graphs}{5}{section.3.1}
\contentsline {chapter}{\numberline {4}Example -\/ A Small Example Program}{7}{chapter.4}
\contentsline {chapter}{\numberline {5}Deprecated List}{9}{chapter.5}
\contentsline {chapter}{\numberline {6}Module Index}{11}{chapter.6}
\contentsline {section}{\numberline {6.1}Modules}{11}{section.6.1}
\contentsline {chapter}{\numberline {7}Data Structure Index}{13}{chapter.7}
\contentsline {section}{\numberline {7.1}Data Structures}{13}{section.7.1}
\contentsline {chapter}{\numberline {8}File Index}{15}{chapter.8}
\contentsline {section}{\numberline {8.1}File List}{15}{section.8.1}
\contentsline {chapter}{\numberline {9}Module Documentation}{19}{chapter.9}
\contentsline {section}{\numberline {9.1}R\discretionary {-}{}{}N\discretionary {-}{}{}A Secondary Structure Folding}{19}{section.9.1}
\contentsline {subsection}{\numberline {9.1.1}Detailed Description}{21}{subsection.9.1.1}
\contentsline {section}{\numberline {9.2}Calculating Minimum Free Energy (M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}{22}{section.9.2}
\contentsline {subsection}{\numberline {9.2.1}Detailed Description}{22}{subsection.9.2.1}
\contentsline {subsection}{\numberline {9.2.2}Function Documentation}{23}{subsection.9.2.2}
\contentsline {subsubsection}{\numberline {9.2.2.1}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}{23}{subsubsection.9.2.2.1}
\contentsline {subsubsection}{\numberline {9.2.2.2}fold}{24}{subsubsection.9.2.2.2}
\contentsline {subsubsection}{\numberline {9.2.2.3}circfold}{24}{subsubsection.9.2.2.3}
\contentsline {section}{\numberline {9.3}Calculating Partition Functions and Pair Probabilities}{25}{section.9.3}
\contentsline {subsection}{\numberline {9.3.1}Detailed Description}{26}{subsection.9.3.1}
\contentsline {subsection}{\numberline {9.3.2}Function Documentation}{26}{subsection.9.3.2}
\contentsline {subsubsection}{\numberline {9.3.2.1}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}{26}{subsubsection.9.3.2.1}
\contentsline {subsubsection}{\numberline {9.3.2.2}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{27}{subsubsection.9.3.2.2}
\contentsline {subsubsection}{\numberline {9.3.2.3}pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{28}{subsubsection.9.3.2.3}
\contentsline {subsubsection}{\numberline {9.3.2.4}free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{29}{subsubsection.9.3.2.4}
\contentsline {subsubsection}{\numberline {9.3.2.5}update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}{29}{subsubsection.9.3.2.5}
\contentsline {subsubsection}{\numberline {9.3.2.6}export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}{29}{subsubsection.9.3.2.6}
\contentsline {subsubsection}{\numberline {9.3.2.7}assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr}{30}{subsubsection.9.3.2.7}
\contentsline {subsubsection}{\numberline {9.3.2.8}get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{30}{subsubsection.9.3.2.8}
\contentsline {subsubsection}{\numberline {9.3.2.9}mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}{30}{subsubsection.9.3.2.9}
\contentsline {subsubsection}{\numberline {9.3.2.10}mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}{31}{subsubsection.9.3.2.10}
\contentsline {section}{\numberline {9.4}Compute the structure with maximum expected accuracy (M\discretionary {-}{}{}E\discretionary {-}{}{}A)}{32}{section.9.4}
\contentsline {section}{\numberline {9.5}Compute the centroid structure}{33}{section.9.5}
\contentsline {subsection}{\numberline {9.5.1}Detailed Description}{33}{subsection.9.5.1}
\contentsline {subsection}{\numberline {9.5.2}Function Documentation}{33}{subsection.9.5.2}
\contentsline {subsubsection}{\numberline {9.5.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}{33}{subsubsection.9.5.2.1}
\contentsline {subsubsection}{\numberline {9.5.2.2}get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}{33}{subsubsection.9.5.2.2}
\contentsline {section}{\numberline {9.6}Enumerating Suboptimal Structures}{35}{section.9.6}
\contentsline {subsection}{\numberline {9.6.1}Detailed Description}{35}{subsection.9.6.1}
\contentsline {section}{\numberline {9.7}Suboptimal structures according to Zuker et al. 1989}{36}{section.9.7}
\contentsline {subsection}{\numberline {9.7.1}Detailed Description}{36}{subsection.9.7.1}
\contentsline {subsection}{\numberline {9.7.2}Function Documentation}{36}{subsection.9.7.2}
\contentsline {subsubsection}{\numberline {9.7.2.1}zukersubopt}{36}{subsubsection.9.7.2.1}
\contentsline {section}{\numberline {9.8}Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}{37}{section.9.8}
\contentsline {subsection}{\numberline {9.8.1}Detailed Description}{37}{subsection.9.8.1}
\contentsline {subsection}{\numberline {9.8.2}Function Documentation}{37}{subsection.9.8.2}
\contentsline {subsubsection}{\numberline {9.8.2.1}subopt}{37}{subsubsection.9.8.2.1}
\contentsline {subsubsection}{\numberline {9.8.2.2}subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}{38}{subsubsection.9.8.2.2}
\contentsline {section}{\numberline {9.9}Stochastic backtracking in the Ensemble}{39}{section.9.9}
\contentsline {subsection}{\numberline {9.9.1}Detailed Description}{39}{subsection.9.9.1}
\contentsline {subsection}{\numberline {9.9.2}Function Documentation}{39}{subsection.9.9.2}
\contentsline {subsubsection}{\numberline {9.9.2.1}pbacktrack}{39}{subsubsection.9.9.2.1}
\contentsline {subsubsection}{\numberline {9.9.2.2}pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}{40}{subsubsection.9.9.2.2}
\contentsline {subsection}{\numberline {9.9.3}Variable Documentation}{40}{subsection.9.9.3}
\contentsline {subsubsection}{\numberline {9.9.3.1}st\discretionary {-}{}{}\_\discretionary {-}{}{}back}{40}{subsubsection.9.9.3.1}
\contentsline {section}{\numberline {9.10}Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization}{41}{section.9.10}
\contentsline {subsection}{\numberline {9.10.1}Detailed Description}{41}{subsection.9.10.1}
\contentsline {section}{\numberline {9.11}M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}{42}{section.9.11}
\contentsline {subsection}{\numberline {9.11.1}Detailed Description}{42}{subsection.9.11.1}
\contentsline {subsection}{\numberline {9.11.2}Function Documentation}{42}{subsection.9.11.2}
\contentsline {subsubsection}{\numberline {9.11.2.1}cofold}{42}{subsubsection.9.11.2.1}
\contentsline {subsubsection}{\numberline {9.11.2.2}export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}{43}{subsubsection.9.11.2.2}
\contentsline {subsubsection}{\numberline {9.11.2.3}export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{43}{subsubsection.9.11.2.3}
\contentsline {section}{\numberline {9.12}Partition Function for two hybridized Sequences}{44}{section.9.12}
\contentsline {subsection}{\numberline {9.12.1}Detailed Description}{45}{subsection.9.12.1}
\contentsline {subsection}{\numberline {9.12.2}Function Documentation}{45}{subsection.9.12.2}
\contentsline {subsubsection}{\numberline {9.12.2.1}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{45}{subsubsection.9.12.2.1}
\contentsline {subsubsection}{\numberline {9.12.2.2}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}{45}{subsubsection.9.12.2.2}
\contentsline {subsubsection}{\numberline {9.12.2.3}export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}{46}{subsubsection.9.12.2.3}
\contentsline {subsubsection}{\numberline {9.12.2.4}update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}{46}{subsubsection.9.12.2.4}
\contentsline {subsubsection}{\numberline {9.12.2.5}update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par}{46}{subsubsection.9.12.2.5}
\contentsline {subsubsection}{\numberline {9.12.2.6}compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities}{47}{subsubsection.9.12.2.6}
\contentsline {subsubsection}{\numberline {9.12.2.7}get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations}{47}{subsubsection.9.12.2.7}
\contentsline {section}{\numberline {9.13}Partition Function for two hybridized Sequences as a stepwise Process}{48}{section.9.13}
\contentsline {subsection}{\numberline {9.13.1}Detailed Description}{48}{subsection.9.13.1}
\contentsline {subsection}{\numberline {9.13.2}Function Documentation}{48}{subsection.9.13.2}
\contentsline {subsubsection}{\numberline {9.13.2.1}pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}{48}{subsubsection.9.13.2.1}
\contentsline {subsubsection}{\numberline {9.13.2.2}pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}{49}{subsubsection.9.13.2.2}
\contentsline {section}{\numberline {9.14}Predicting Consensus Structures from Alignment(s)}{50}{section.9.14}
\contentsline {subsection}{\numberline {9.14.1}Detailed Description}{51}{subsection.9.14.1}
\contentsline {subsection}{\numberline {9.14.2}Function Documentation}{51}{subsection.9.14.2}
\contentsline {subsubsection}{\numberline {9.14.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}{51}{subsubsection.9.14.2.1}
\contentsline {subsubsection}{\numberline {9.14.2.2}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct}{51}{subsubsection.9.14.2.2}
\contentsline {subsubsection}{\numberline {9.14.2.3}encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence}{52}{subsubsection.9.14.2.3}
\contentsline {subsubsection}{\numberline {9.14.2.4}alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{52}{subsubsection.9.14.2.4}
\contentsline {subsubsection}{\numberline {9.14.2.5}free\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{52}{subsubsection.9.14.2.5}
\contentsline {subsubsection}{\numberline {9.14.2.6}get\discretionary {-}{}{}\_\discretionary {-}{}{}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}{53}{subsubsection.9.14.2.6}
\contentsline {subsection}{\numberline {9.14.3}Variable Documentation}{53}{subsection.9.14.3}
\contentsline {subsubsection}{\numberline {9.14.3.1}cv\discretionary {-}{}{}\_\discretionary {-}{}{}fact}{53}{subsubsection.9.14.3.1}
\contentsline {subsubsection}{\numberline {9.14.3.2}nc\discretionary {-}{}{}\_\discretionary {-}{}{}fact}{53}{subsubsection.9.14.3.2}
\contentsline {section}{\numberline {9.15}M\discretionary {-}{}{}F\discretionary {-}{}{}E Consensus Structures for Sequence Alignment(s)}{54}{section.9.15}
\contentsline {subsection}{\numberline {9.15.1}Detailed Description}{54}{subsection.9.15.1}
\contentsline {subsection}{\numberline {9.15.2}Function Documentation}{54}{subsection.9.15.2}
\contentsline {subsubsection}{\numberline {9.15.2.1}alifold}{54}{subsubsection.9.15.2.1}
\contentsline {subsubsection}{\numberline {9.15.2.2}circalifold}{54}{subsubsection.9.15.2.2}
\contentsline {section}{\numberline {9.16}Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{56}{section.9.16}
\contentsline {subsection}{\numberline {9.16.1}Detailed Description}{56}{subsection.9.16.1}
\contentsline {subsection}{\numberline {9.16.2}Function Documentation}{56}{subsection.9.16.2}
\contentsline {subsubsection}{\numberline {9.16.2.1}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}{56}{subsubsection.9.16.2.1}
\contentsline {subsubsection}{\numberline {9.16.2.2}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{56}{subsubsection.9.16.2.2}
\contentsline {subsubsection}{\numberline {9.16.2.3}alipf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{57}{subsubsection.9.16.2.3}
\contentsline {subsubsection}{\numberline {9.16.2.4}export\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}{57}{subsubsection.9.16.2.4}
\contentsline {section}{\numberline {9.17}Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{58}{section.9.17}
\contentsline {subsection}{\numberline {9.17.1}Detailed Description}{58}{subsection.9.17.1}
\contentsline {subsection}{\numberline {9.17.2}Function Documentation}{58}{subsection.9.17.2}
\contentsline {subsubsection}{\numberline {9.17.2.1}alipbacktrack}{58}{subsubsection.9.17.2.1}
\contentsline {section}{\numberline {9.18}Predicting Locally stable structures of large sequences}{59}{section.9.18}
\contentsline {subsection}{\numberline {9.18.1}Detailed Description}{59}{subsection.9.18.1}
\contentsline {section}{\numberline {9.19}Local M\discretionary {-}{}{}F\discretionary {-}{}{}E structure Prediction and Z-\/scores}{60}{section.9.19}
\contentsline {subsection}{\numberline {9.19.1}Detailed Description}{60}{subsection.9.19.1}
\contentsline {subsection}{\numberline {9.19.2}Function Documentation}{60}{subsection.9.19.2}
\contentsline {subsubsection}{\numberline {9.19.2.1}Lfold}{60}{subsubsection.9.19.2.1}
\contentsline {subsubsection}{\numberline {9.19.2.2}Lfoldz}{60}{subsubsection.9.19.2.2}
\contentsline {section}{\numberline {9.20}Partition functions for locally stable secondary structures}{61}{section.9.20}
\contentsline {subsection}{\numberline {9.20.1}Detailed Description}{61}{subsection.9.20.1}
\contentsline {subsection}{\numberline {9.20.2}Function Documentation}{61}{subsection.9.20.2}
\contentsline {subsubsection}{\numberline {9.20.2.1}update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}L\discretionary {-}{}{}P}{61}{subsubsection.9.20.2.1}
\contentsline {subsubsection}{\numberline {9.20.2.2}pfl\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{61}{subsubsection.9.20.2.2}
\contentsline {subsubsection}{\numberline {9.20.2.3}putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob}{62}{subsubsection.9.20.2.3}
\contentsline {subsubsection}{\numberline {9.20.2.4}putoutp\discretionary {-}{}{}U\discretionary {-}{}{}\_\discretionary {-}{}{}prob\discretionary {-}{}{}\_\discretionary {-}{}{}bin}{62}{subsubsection.9.20.2.4}
\contentsline {section}{\numberline {9.21}Local M\discretionary {-}{}{}F\discretionary {-}{}{}E consensus structures for Sequence Alignments}{63}{section.9.21}
\contentsline {subsection}{\numberline {9.21.1}Detailed Description}{63}{subsection.9.21.1}
\contentsline {subsection}{\numberline {9.21.2}Function Documentation}{63}{subsection.9.21.2}
\contentsline {subsubsection}{\numberline {9.21.2.1}ali\discretionary {-}{}{}Lfold}{63}{subsubsection.9.21.2.1}
\contentsline {section}{\numberline {9.22}Change and Precalculate Energy Parameter Sets and Boltzmann Factors}{64}{section.9.22}
\contentsline {subsection}{\numberline {9.22.1}Detailed Description}{64}{subsection.9.22.1}
\contentsline {subsection}{\numberline {9.22.2}Function Documentation}{65}{subsection.9.22.2}
\contentsline {subsubsection}{\numberline {9.22.2.1}scale\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}{65}{subsubsection.9.22.2.1}
\contentsline {subsubsection}{\numberline {9.22.2.2}get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}{65}{subsubsection.9.22.2.2}
\contentsline {subsubsection}{\numberline {9.22.2.3}get\discretionary {-}{}{}\_\discretionary {-}{}{}scaled\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}parameters}{65}{subsubsection.9.22.2.3}
\contentsline {subsubsection}{\numberline {9.22.2.4}get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factors}{65}{subsubsection.9.22.2.4}
\contentsline {subsubsection}{\numberline {9.22.2.5}get\discretionary {-}{}{}\_\discretionary {-}{}{}boltzmann\discretionary {-}{}{}\_\discretionary {-}{}{}factor\discretionary {-}{}{}\_\discretionary {-}{}{}copy}{66}{subsubsection.9.22.2.5}
\contentsline {section}{\numberline {9.23}Reading/\discretionary {-}{}{}Writing energy parameter sets from/to File}{67}{section.9.23}
\contentsline {subsection}{\numberline {9.23.1}Detailed Description}{67}{subsection.9.23.1}
\contentsline {subsection}{\numberline {9.23.2}Function Documentation}{67}{subsection.9.23.2}
\contentsline {subsubsection}{\numberline {9.23.2.1}read\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}{67}{subsubsection.9.23.2.1}
\contentsline {subsubsection}{\numberline {9.23.2.2}write\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}{67}{subsubsection.9.23.2.2}
\contentsline {section}{\numberline {9.24}Converting energy parameter files}{69}{section.9.24}
\contentsline {subsection}{\numberline {9.24.1}Detailed Description}{69}{subsection.9.24.1}
\contentsline {subsection}{\numberline {9.24.2}Macro Definition Documentation}{70}{subsection.9.24.2}
\contentsline {subsubsection}{\numberline {9.24.2.1}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}L}{70}{subsubsection.9.24.2.1}
\contentsline {subsubsection}{\numberline {9.24.2.2}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}{70}{subsubsection.9.24.2.2}
\contentsline {subsubsection}{\numberline {9.24.2.3}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K}{70}{subsubsection.9.24.2.3}
\contentsline {subsubsection}{\numberline {9.24.2.4}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}{70}{subsubsection.9.24.2.4}
\contentsline {subsubsection}{\numberline {9.24.2.5}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T}{70}{subsubsection.9.24.2.5}
\contentsline {subsubsection}{\numberline {9.24.2.6}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}1\discretionary {-}{}{}N}{70}{subsubsection.9.24.2.6}
\contentsline {subsubsection}{\numberline {9.24.2.7}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}23}{70}{subsubsection.9.24.2.7}
\contentsline {subsubsection}{\numberline {9.24.2.8}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I}{70}{subsubsection.9.24.2.8}
\contentsline {subsubsection}{\numberline {9.24.2.9}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}X\discretionary {-}{}{}T}{70}{subsubsection.9.24.2.9}
\contentsline {subsubsection}{\numberline {9.24.2.10}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E5}{70}{subsubsection.9.24.2.10}
\contentsline {subsubsection}{\numberline {9.24.2.11}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}L\discretionary {-}{}{}E3}{70}{subsubsection.9.24.2.11}
\contentsline {subsubsection}{\numberline {9.24.2.12}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}11}{70}{subsubsection.9.24.2.12}
\contentsline {subsubsection}{\numberline {9.24.2.13}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}21}{71}{subsubsection.9.24.2.13}
\contentsline {subsubsection}{\numberline {9.24.2.14}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}22}{71}{subsubsection.9.24.2.14}
\contentsline {subsubsection}{\numberline {9.24.2.15}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}G\discretionary {-}{}{}E}{71}{subsubsection.9.24.2.15}
\contentsline {subsubsection}{\numberline {9.24.2.16}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T}{71}{subsubsection.9.24.2.16}
\contentsline {subsubsection}{\numberline {9.24.2.17}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}L}{71}{subsubsection.9.24.2.17}
\contentsline {subsubsection}{\numberline {9.24.2.18}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}C}{71}{subsubsection.9.24.2.18}
\contentsline {subsubsection}{\numberline {9.24.2.19}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}C\discretionary {-}{}{}I\discretionary {-}{}{}A\discretionary {-}{}{}L\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}P}{71}{subsubsection.9.24.2.19}
\contentsline {subsubsection}{\numberline {9.24.2.20}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}L\discretionary {-}{}{}A}{71}{subsubsection.9.24.2.20}
\contentsline {subsubsection}{\numberline {9.24.2.21}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}I\discretionary {-}{}{}O}{71}{subsubsection.9.24.2.21}
\contentsline {subsubsection}{\numberline {9.24.2.22}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}V\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}U\discretionary {-}{}{}M\discretionary {-}{}{}P}{71}{subsubsection.9.24.2.22}
\contentsline {subsection}{\numberline {9.24.3}Function Documentation}{71}{subsection.9.24.3}
\contentsline {subsubsection}{\numberline {9.24.3.1}convert\discretionary {-}{}{}\_\discretionary {-}{}{}parameter\discretionary {-}{}{}\_\discretionary {-}{}{}file}{71}{subsubsection.9.24.3.1}
\contentsline {section}{\numberline {9.25}Energy evaluation}{73}{section.9.25}
\contentsline {subsection}{\numberline {9.25.1}Detailed Description}{73}{subsection.9.25.1}
\contentsline {subsection}{\numberline {9.25.2}Function Documentation}{73}{subsection.9.25.2}
\contentsline {subsubsection}{\numberline {9.25.2.1}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{73}{subsubsection.9.25.2.1}
\contentsline {subsubsection}{\numberline {9.25.2.2}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}{74}{subsubsection.9.25.2.2}
\contentsline {subsubsection}{\numberline {9.25.2.3}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{74}{subsubsection.9.25.2.3}
\contentsline {subsubsection}{\numberline {9.25.2.4}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}par}{75}{subsubsection.9.25.2.4}
\contentsline {subsubsection}{\numberline {9.25.2.5}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}structure\discretionary {-}{}{}\_\discretionary {-}{}{}pt}{75}{subsubsection.9.25.2.5}
\contentsline {subsubsection}{\numberline {9.25.2.6}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt\discretionary {-}{}{}\_\discretionary {-}{}{}par}{76}{subsubsection.9.25.2.6}
\contentsline {section}{\numberline {9.26}Searching Sequences for Predefined Structures}{77}{section.9.26}
\contentsline {subsection}{\numberline {9.26.1}Detailed Description}{77}{subsection.9.26.1}
\contentsline {subsection}{\numberline {9.26.2}Function Documentation}{77}{subsection.9.26.2}
\contentsline {subsubsection}{\numberline {9.26.2.1}inverse\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{77}{subsubsection.9.26.2.1}
\contentsline {subsubsection}{\numberline {9.26.2.2}inverse\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{78}{subsubsection.9.26.2.2}
\contentsline {subsection}{\numberline {9.26.3}Variable Documentation}{78}{subsection.9.26.3}
\contentsline {subsubsection}{\numberline {9.26.3.1}final\discretionary {-}{}{}\_\discretionary {-}{}{}cost}{78}{subsubsection.9.26.3.1}
\contentsline {subsubsection}{\numberline {9.26.3.2}give\discretionary {-}{}{}\_\discretionary {-}{}{}up}{78}{subsubsection.9.26.3.2}
\contentsline {subsubsection}{\numberline {9.26.3.3}inv\discretionary {-}{}{}\_\discretionary {-}{}{}verbose}{78}{subsubsection.9.26.3.3}
\contentsline {section}{\numberline {9.27}Classified Dynamic Programming}{79}{section.9.27}
\contentsline {subsection}{\numberline {9.27.1}Detailed Description}{79}{subsection.9.27.1}
\contentsline {section}{\numberline {9.28}Distance based partitioning of the Secondary Structure Space}{80}{section.9.28}
\contentsline {subsection}{\numberline {9.28.1}Detailed Description}{80}{subsection.9.28.1}
\contentsline {section}{\numberline {9.29}Calculating M\discretionary {-}{}{}F\discretionary {-}{}{}E representatives of a Distance Based Partitioning}{81}{section.9.29}
\contentsline {subsection}{\numberline {9.29.1}Detailed Description}{81}{subsection.9.29.1}
\contentsline {subsection}{\numberline {9.29.2}Function Documentation}{81}{subsection.9.29.2}
\contentsline {subsubsection}{\numberline {9.29.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}{81}{subsubsection.9.29.2.1}
\contentsline {subsubsection}{\numberline {9.29.2.2}destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}{82}{subsubsection.9.29.2.2}
\contentsline {subsubsection}{\numberline {9.29.2.3}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}List}{82}{subsubsection.9.29.2.3}
\contentsline {subsubsection}{\numberline {9.29.2.4}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}f5}{83}{subsubsection.9.29.2.4}
\contentsline {section}{\numberline {9.30}Calculate Partition Functions of a Distance Based Partitioning}{84}{section.9.30}
\contentsline {subsection}{\numberline {9.30.1}Detailed Description}{84}{subsection.9.30.1}
\contentsline {subsection}{\numberline {9.30.2}Function Documentation}{84}{subsection.9.30.2}
\contentsline {subsubsection}{\numberline {9.30.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}{84}{subsubsection.9.30.2.1}
\contentsline {subsubsection}{\numberline {9.30.2.2}get\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E}{85}{subsubsection.9.30.2.2}
\contentsline {subsubsection}{\numberline {9.30.2.3}destroy\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}variables}{85}{subsubsection.9.30.2.3}
\contentsline {subsubsection}{\numberline {9.30.2.4}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}List}{85}{subsubsection.9.30.2.4}
\contentsline {section}{\numberline {9.31}Stochastic Backtracking of Structures from Distance Based Partitioning}{87}{section.9.31}
\contentsline {subsection}{\numberline {9.31.1}Detailed Description}{87}{subsection.9.31.1}
\contentsline {subsection}{\numberline {9.31.2}Function Documentation}{87}{subsection.9.31.2}
\contentsline {subsubsection}{\numberline {9.31.2.1}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack}{87}{subsubsection.9.31.2.1}
\contentsline {subsubsection}{\numberline {9.31.2.2}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}pbacktrack5}{88}{subsubsection.9.31.2.2}
\contentsline {section}{\numberline {9.32}Compute the Density of States}{89}{section.9.32}
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\contentsline {subsubsection}{\numberline {11.34.2.2}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}{171}{subsubsection.11.34.2.2}
\contentsline {subsubsection}{\numberline {11.34.2.3}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}{171}{subsubsection.11.34.2.3}
\contentsline {subsubsection}{\numberline {11.34.2.4}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}E\discretionary {-}{}{}A\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}R}{171}{subsubsection.11.34.2.4}
\contentsline {subsubsection}{\numberline {11.34.2.5}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}{171}{subsubsection.11.34.2.5}
\contentsline {subsubsection}{\numberline {11.34.2.6}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 {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}T}{172}{subsubsection.11.34.2.6}
\contentsline {subsubsection}{\numberline {11.34.2.7}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 {-}{}{}T\discretionary {-}{}{}R\discretionary {-}{}{}U\discretionary {-}{}{}N\discretionary {-}{}{}C\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N}{172}{subsubsection.11.34.2.7}
\contentsline {subsubsection}{\numberline {11.34.2.8}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}{172}{subsubsection.11.34.2.8}
\contentsline {subsubsection}{\numberline {11.34.2.9}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}{172}{subsubsection.11.34.2.9}
\contentsline {subsubsection}{\numberline {11.34.2.10}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 {-}{}{}S\discretionary {-}{}{}K\discretionary {-}{}{}I\discretionary {-}{}{}P\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}L\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}K\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}E\discretionary {-}{}{}S}{172}{subsubsection.11.34.2.10}
\contentsline {subsubsection}{\numberline {11.34.2.11}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}L\discretionary {-}{}{}A\discretionary {-}{}{}N\discretionary {-}{}{}K\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}E}{172}{subsubsection.11.34.2.11}
\contentsline {subsubsection}{\numberline {11.34.2.12}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 {-}{}{}S\discretionary {-}{}{}K\discretionary {-}{}{}I\discretionary {-}{}{}P\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}M\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}S}{172}{subsubsection.11.34.2.12}
\contentsline {subsubsection}{\numberline {11.34.2.13}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}{172}{subsubsection.11.34.2.13}
\contentsline {subsubsection}{\numberline {11.34.2.14}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}{172}{subsubsection.11.34.2.14}
\contentsline {subsubsection}{\numberline {11.34.2.15}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}{172}{subsubsection.11.34.2.15}
\contentsline {subsubsection}{\numberline {11.34.2.16}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}{172}{subsubsection.11.34.2.16}
\contentsline {subsubsection}{\numberline {11.34.2.17}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 {-}{}{}N\discretionary {-}{}{}G\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K}{172}{subsubsection.11.34.2.17}
\contentsline {subsubsection}{\numberline {11.34.2.18}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 {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}D\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}R\discretionary {-}{}{}A\discretionary {-}{}{}C\discretionary {-}{}{}K}{173}{subsubsection.11.34.2.18}
\contentsline {subsubsection}{\numberline {11.34.2.19}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 {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}E}{173}{subsubsection.11.34.2.19}
\contentsline {subsubsection}{\numberline {11.34.2.20}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 {-}{}{}N\discretionary {-}{}{}O\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}H\discretionary {-}{}{}E\discretionary {-}{}{}A\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}R}{173}{subsubsection.11.34.2.20}
\contentsline {subsubsection}{\numberline {11.34.2.21}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}{173}{subsubsection.11.34.2.21}
\contentsline {subsubsection}{\numberline {11.34.2.22}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}{173}{subsubsection.11.34.2.22}
\contentsline {subsubsection}{\numberline {11.34.2.23}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}O\discretionary {-}{}{}P\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}M\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}L\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}E}{173}{subsubsection.11.34.2.23}
\contentsline {subsubsection}{\numberline {11.34.2.24}M\discretionary {-}{}{}I\discretionary {-}{}{}N2}{173}{subsubsection.11.34.2.24}
\contentsline {subsubsection}{\numberline {11.34.2.25}M\discretionary {-}{}{}A\discretionary {-}{}{}X2}{173}{subsubsection.11.34.2.25}
\contentsline {subsubsection}{\numberline {11.34.2.26}M\discretionary {-}{}{}I\discretionary {-}{}{}N3}{173}{subsubsection.11.34.2.26}
\contentsline {subsubsection}{\numberline {11.34.2.27}M\discretionary {-}{}{}A\discretionary {-}{}{}X3}{173}{subsubsection.11.34.2.27}
\contentsline {subsubsection}{\numberline {11.34.2.28}X\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}R}{173}{subsubsection.11.34.2.28}
\contentsline {subsubsection}{\numberline {11.34.2.29}S\discretionary {-}{}{}T\discretionary {-}{}{}R}{174}{subsubsection.11.34.2.29}
\contentsline {subsubsection}{\numberline {11.34.2.30}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}{174}{subsubsection.11.34.2.30}
\contentsline {subsubsection}{\numberline {11.34.2.31}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}{174}{subsubsection.11.34.2.31}
\contentsline {subsection}{\numberline {11.34.3}Function Documentation}{174}{subsection.11.34.3}
\contentsline {subsubsection}{\numberline {11.34.3.1}space}{174}{subsubsection.11.34.3.1}
\contentsline {subsubsection}{\numberline {11.34.3.2}xrealloc}{174}{subsubsection.11.34.3.2}
\contentsline {subsubsection}{\numberline {11.34.3.3}nrerror}{174}{subsubsection.11.34.3.3}
\contentsline {subsubsection}{\numberline {11.34.3.4}warn\discretionary {-}{}{}\_\discretionary {-}{}{}user}{175}{subsubsection.11.34.3.4}
\contentsline {subsubsection}{\numberline {11.34.3.5}urn}{175}{subsubsection.11.34.3.5}
\contentsline {subsubsection}{\numberline {11.34.3.6}int\discretionary {-}{}{}\_\discretionary {-}{}{}urn}{175}{subsubsection.11.34.3.6}
\contentsline {subsubsection}{\numberline {11.34.3.7}time\discretionary {-}{}{}\_\discretionary {-}{}{}stamp}{175}{subsubsection.11.34.3.7}
\contentsline {subsubsection}{\numberline {11.34.3.8}random\discretionary {-}{}{}\_\discretionary {-}{}{}string}{175}{subsubsection.11.34.3.8}
\contentsline {subsubsection}{\numberline {11.34.3.9}hamming}{176}{subsubsection.11.34.3.9}
\contentsline {subsubsection}{\numberline {11.34.3.10}hamming\discretionary {-}{}{}\_\discretionary {-}{}{}bound}{176}{subsubsection.11.34.3.10}
\contentsline {subsubsection}{\numberline {11.34.3.11}get\discretionary {-}{}{}\_\discretionary {-}{}{}line}{176}{subsubsection.11.34.3.11}
\contentsline {subsubsection}{\numberline {11.34.3.12}get\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}line}{176}{subsubsection.11.34.3.12}
\contentsline {subsubsection}{\numberline {11.34.3.13}read\discretionary {-}{}{}\_\discretionary {-}{}{}record}{177}{subsubsection.11.34.3.13}
\contentsline {subsubsection}{\numberline {11.34.3.14}pack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{178}{subsubsection.11.34.3.14}
\contentsline {subsubsection}{\numberline {11.34.3.15}unpack\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{178}{subsubsection.11.34.3.15}
\contentsline {subsubsection}{\numberline {11.34.3.16}make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}{178}{subsubsection.11.34.3.16}
\contentsline {subsubsection}{\numberline {11.34.3.17}copy\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}{179}{subsubsection.11.34.3.17}
\contentsline {subsubsection}{\numberline {11.34.3.18}alimake\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table}{179}{subsubsection.11.34.3.18}
\contentsline {subsubsection}{\numberline {11.34.3.19}make\discretionary {-}{}{}\_\discretionary {-}{}{}pair\discretionary {-}{}{}\_\discretionary {-}{}{}table\discretionary {-}{}{}\_\discretionary {-}{}{}snoop}{179}{subsubsection.11.34.3.19}
\contentsline {subsubsection}{\numberline {11.34.3.20}make\discretionary {-}{}{}\_\discretionary {-}{}{}loop\discretionary {-}{}{}\_\discretionary {-}{}{}index\discretionary {-}{}{}\_\discretionary {-}{}{}pt}{179}{subsubsection.11.34.3.20}
\contentsline {subsubsection}{\numberline {11.34.3.21}print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq}{179}{subsubsection.11.34.3.21}
\contentsline {subsubsection}{\numberline {11.34.3.22}print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}input\discretionary {-}{}{}\_\discretionary {-}{}{}seq\discretionary {-}{}{}\_\discretionary {-}{}{}str}{179}{subsubsection.11.34.3.22}
\contentsline {subsubsection}{\numberline {11.34.3.23}print\discretionary {-}{}{}\_\discretionary {-}{}{}tty\discretionary {-}{}{}\_\discretionary {-}{}{}constraint}{180}{subsubsection.11.34.3.23}
\contentsline {subsubsection}{\numberline {11.34.3.24}str\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}D\discretionary {-}{}{}N\discretionary {-}{}{}A2\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}{180}{subsubsection.11.34.3.24}
\contentsline {subsubsection}{\numberline {11.34.3.25}str\discretionary {-}{}{}\_\discretionary {-}{}{}uppercase}{180}{subsubsection.11.34.3.25}
\contentsline {subsubsection}{\numberline {11.34.3.26}get\discretionary {-}{}{}\_\discretionary {-}{}{}iindx}{180}{subsubsection.11.34.3.26}
\contentsline {subsubsection}{\numberline {11.34.3.27}get\discretionary {-}{}{}\_\discretionary {-}{}{}indx}{181}{subsubsection.11.34.3.27}
\contentsline {subsubsection}{\numberline {11.34.3.28}constrain\discretionary {-}{}{}\_\discretionary {-}{}{}ptypes}{181}{subsubsection.11.34.3.28}
\contentsline {subsection}{\numberline {11.34.4}Variable Documentation}{182}{subsection.11.34.4}
\contentsline {subsubsection}{\numberline {11.34.4.1}xsubi}{182}{subsubsection.11.34.4.1}
\contentsline {section}{\numberline {11.35}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.8.4\discretionary {-}{}{}\_\discretionary {-}{}{}epars.h File Reference}{182}{section.11.35}
\contentsline {subsection}{\numberline {11.35.1}Detailed Description}{182}{subsection.11.35.1}
\contentsline {section}{\numberline {11.36}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/lib/1.8.4\discretionary {-}{}{}\_\discretionary {-}{}{}intloops.h File Reference}{182}{section.11.36}
\contentsline {subsection}{\numberline {11.36.1}Detailed Description}{182}{subsection.11.36.1}
\contentsline {part}{Index}{183}{chapter*.131}