Add missing doc files

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / refman.toc

diff --git a/binaries/src/ViennaRNA/doc/latex/refman.toc b/binaries/src/ViennaRNA/doc/latex/refman.toc
new file mode 100644 (file)
index 0000000..945f189
--- /dev/null
+++ b/binaries/src/ViennaRNA/doc/latex/refman.toc
@@ -0,0 +1,530 @@
+\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}
+\contentsline {subsection}{\numberline {9.32.1}Detailed Description}{89}{subsection.9.32.1}
+\contentsline {subsection}{\numberline {9.32.2}Variable Documentation}{89}{subsection.9.32.2}
+\contentsline {subsubsection}{\numberline {9.32.2.1}density\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}states}{89}{subsubsection.9.32.2.1}
+\contentsline {section}{\numberline {9.33}Parsing and Comparing -\/ Functions to Manipulate Structures}{90}{section.9.33}
+\contentsline {chapter}{\numberline {10}Data Structure Documentation}{91}{chapter.10}
+\contentsline {section}{\numberline {10.1}bond\discretionary {-}{}{}T Struct Reference}{91}{section.10.1}
+\contentsline {subsection}{\numberline {10.1.1}Detailed Description}{91}{subsection.10.1.1}
+\contentsline {section}{\numberline {10.2}bond\discretionary {-}{}{}T\discretionary {-}{}{}En Struct Reference}{91}{section.10.2}
+\contentsline {subsection}{\numberline {10.2.1}Detailed Description}{91}{subsection.10.2.1}
+\contentsline {section}{\numberline {10.3}cofold\discretionary {-}{}{}F Struct Reference}{91}{section.10.3}
+\contentsline {section}{\numberline {10.4}Conc\discretionary {-}{}{}Ent Struct Reference}{92}{section.10.4}
+\contentsline {section}{\numberline {10.5}constrain Struct Reference}{92}{section.10.5}
+\contentsline {subsection}{\numberline {10.5.1}Detailed Description}{92}{subsection.10.5.1}
+\contentsline {section}{\numberline {10.6}C\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}D\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}T\discretionary {-}{}{}E Struct Reference}{92}{section.10.6}
+\contentsline {subsection}{\numberline {10.6.1}Detailed Description}{92}{subsection.10.6.1}
+\contentsline {section}{\numberline {10.7}cpair Struct Reference}{93}{section.10.7}
+\contentsline {subsection}{\numberline {10.7.1}Detailed Description}{93}{subsection.10.7.1}
+\contentsline {section}{\numberline {10.8}duplex\discretionary {-}{}{}T Struct Reference}{93}{section.10.8}
+\contentsline {section}{\numberline {10.9}dup\discretionary {-}{}{}Var Struct Reference}{93}{section.10.9}
+\contentsline {section}{\numberline {10.10}folden Struct Reference}{93}{section.10.10}
+\contentsline {section}{\numberline {10.11}interact Struct Reference}{93}{section.10.11}
+\contentsline {section}{\numberline {10.12}intermediate\discretionary {-}{}{}\_\discretionary {-}{}{}t Struct Reference}{94}{section.10.12}
+\contentsline {section}{\numberline {10.13}I\discretionary {-}{}{}N\discretionary {-}{}{}T\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}V\discretionary {-}{}{}A\discretionary {-}{}{}L Struct Reference}{94}{section.10.13}
+\contentsline {subsection}{\numberline {10.13.1}Detailed Description}{95}{subsection.10.13.1}
+\contentsline {section}{\numberline {10.14}L\discretionary {-}{}{}I\discretionary {-}{}{}S\discretionary {-}{}{}T Struct Reference}{95}{section.10.14}
+\contentsline {section}{\numberline {10.15}L\discretionary {-}{}{}S\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}B\discretionary {-}{}{}U\discretionary {-}{}{}C\discretionary {-}{}{}K\discretionary {-}{}{}E\discretionary {-}{}{}T Struct Reference}{95}{section.10.15}
+\contentsline {section}{\numberline {10.16}model\discretionary {-}{}{}\_\discretionary {-}{}{}details\discretionary {-}{}{}T Struct Reference}{96}{section.10.16}
+\contentsline {subsection}{\numberline {10.16.1}Detailed Description}{96}{subsection.10.16.1}
+\contentsline {subsection}{\numberline {10.16.2}Field Documentation}{96}{subsection.10.16.2}
+\contentsline {subsubsection}{\numberline {10.16.2.1}dangles}{96}{subsubsection.10.16.2.1}
+\contentsline {section}{\numberline {10.17}move\discretionary {-}{}{}\_\discretionary {-}{}{}t Struct Reference}{96}{section.10.17}
+\contentsline {section}{\numberline {10.18}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R Struct Reference}{97}{section.10.18}
+\contentsline {subsection}{\numberline {10.18.1}Detailed Description}{97}{subsection.10.18.1}
+\contentsline {section}{\numberline {10.19}pair\discretionary {-}{}{}\_\discretionary {-}{}{}info Struct Reference}{97}{section.10.19}
+\contentsline {subsection}{\numberline {10.19.1}Detailed Description}{97}{subsection.10.19.1}
+\contentsline {section}{\numberline {10.20}pairpro Struct Reference}{98}{section.10.20}
+\contentsline {section}{\numberline {10.21}param\discretionary {-}{}{}T Struct Reference}{98}{section.10.21}
+\contentsline {subsection}{\numberline {10.21.1}Detailed Description}{99}{subsection.10.21.1}
+\contentsline {section}{\numberline {10.22}path\discretionary {-}{}{}\_\discretionary {-}{}{}t Struct Reference}{99}{section.10.22}
+\contentsline {section}{\numberline {10.23}pf\discretionary {-}{}{}\_\discretionary {-}{}{}param\discretionary {-}{}{}T Struct Reference}{99}{section.10.23}
+\contentsline {subsection}{\numberline {10.23.1}Detailed Description}{100}{subsection.10.23.1}
+\contentsline {subsection}{\numberline {10.23.2}Field Documentation}{100}{subsection.10.23.2}
+\contentsline {subsubsection}{\numberline {10.23.2.1}alpha}{100}{subsubsection.10.23.2.1}
+\contentsline {section}{\numberline {10.24}plist Struct Reference}{100}{section.10.24}
+\contentsline {subsection}{\numberline {10.24.1}Detailed Description}{100}{subsection.10.24.1}
+\contentsline {section}{\numberline {10.25}Postorder\discretionary {-}{}{}\_\discretionary {-}{}{}list Struct Reference}{100}{section.10.25}
+\contentsline {section}{\numberline {10.26}pu\discretionary {-}{}{}\_\discretionary {-}{}{}contrib Struct Reference}{100}{section.10.26}
+\contentsline {subsection}{\numberline {10.26.1}Detailed Description}{101}{subsection.10.26.1}
+\contentsline {section}{\numberline {10.27}pu\discretionary {-}{}{}\_\discretionary {-}{}{}out Struct Reference}{101}{section.10.27}
+\contentsline {subsection}{\numberline {10.27.1}Detailed Description}{101}{subsection.10.27.1}
+\contentsline {section}{\numberline {10.28}sect Struct Reference}{101}{section.10.28}
+\contentsline {subsection}{\numberline {10.28.1}Detailed Description}{101}{subsection.10.28.1}
+\contentsline {section}{\numberline {10.29}snoop\discretionary {-}{}{}T Struct Reference}{102}{section.10.29}
+\contentsline {section}{\numberline {10.30}S\discretionary {-}{}{}O\discretionary {-}{}{}L\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}I\discretionary {-}{}{}O\discretionary {-}{}{}N Struct Reference}{102}{section.10.30}
+\contentsline {subsection}{\numberline {10.30.1}Detailed Description}{102}{subsection.10.30.1}
+\contentsline {section}{\numberline {10.31}struct\discretionary {-}{}{}\_\discretionary {-}{}{}en Struct Reference}{102}{section.10.31}
+\contentsline {section}{\numberline {10.32}svm\discretionary {-}{}{}\_\discretionary {-}{}{}model Struct Reference}{102}{section.10.32}
+\contentsline {section}{\numberline {10.33}sw\discretionary {-}{}{}String Struct Reference}{102}{section.10.33}
+\contentsline {section}{\numberline {10.34}Tree Struct Reference}{103}{section.10.34}
+\contentsline {section}{\numberline {10.35}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution Struct Reference}{103}{section.10.35}
+\contentsline {subsection}{\numberline {10.35.1}Detailed Description}{103}{subsection.10.35.1}
+\contentsline {section}{\numberline {10.36}Two\discretionary {-}{}{}Dfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars Struct Reference}{104}{section.10.36}
+\contentsline {subsection}{\numberline {10.36.1}Detailed Description}{105}{subsection.10.36.1}
+\contentsline {section}{\numberline {10.37}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}solution Struct Reference}{105}{section.10.37}
+\contentsline {subsection}{\numberline {10.37.1}Detailed Description}{105}{subsection.10.37.1}
+\contentsline {section}{\numberline {10.38}Two\discretionary {-}{}{}Dpfold\discretionary {-}{}{}\_\discretionary {-}{}{}vars Struct Reference}{106}{section.10.38}
+\contentsline {subsection}{\numberline {10.38.1}Detailed Description}{107}{subsection.10.38.1}
+\contentsline {chapter}{\numberline {11}File Documentation}{109}{chapter.11}
+\contentsline {section}{\numberline {11.1}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dfold.h File Reference}{109}{section.11.1}
+\contentsline {section}{\numberline {11.2}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/2\discretionary {-}{}{}Dpfold.h File Reference}{110}{section.11.2}
+\contentsline {section}{\numberline {11.3}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/alifold.h File Reference}{111}{section.11.3}
+\contentsline {subsection}{\numberline {11.3.1}Detailed Description}{112}{subsection.11.3.1}
+\contentsline {subsection}{\numberline {11.3.2}Function Documentation}{112}{subsection.11.3.2}
+\contentsline {subsubsection}{\numberline {11.3.2.1}update\discretionary {-}{}{}\_\discretionary {-}{}{}alifold\discretionary {-}{}{}\_\discretionary {-}{}{}params}{112}{subsubsection.11.3.2.1}
+\contentsline {section}{\numberline {11.4}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/cofold.h File Reference}{113}{section.11.4}
+\contentsline {subsection}{\numberline {11.4.1}Detailed Description}{114}{subsection.11.4.1}
+\contentsline {subsection}{\numberline {11.4.2}Function Documentation}{114}{subsection.11.4.2}
+\contentsline {subsubsection}{\numberline {11.4.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}monomere\discretionary {-}{}{}\_\discretionary {-}{}{}mfes}{114}{subsubsection.11.4.2.1}
+\contentsline {subsubsection}{\numberline {11.4.2.2}initialize\discretionary {-}{}{}\_\discretionary {-}{}{}cofold}{114}{subsubsection.11.4.2.2}
+\contentsline {section}{\numberline {11.5}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/convert\discretionary {-}{}{}\_\discretionary {-}{}{}epars.h File Reference}{114}{section.11.5}
+\contentsline {subsection}{\numberline {11.5.1}Detailed Description}{115}{subsection.11.5.1}
+\contentsline {section}{\numberline {11.6}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/data\discretionary {-}{}{}\_\discretionary {-}{}{}structures.h File Reference}{115}{section.11.6}
+\contentsline {subsection}{\numberline {11.6.1}Detailed Description}{117}{subsection.11.6.1}
+\contentsline {section}{\numberline {11.7}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/dist\discretionary {-}{}{}\_\discretionary {-}{}{}vars.h File Reference}{117}{section.11.7}
+\contentsline {subsection}{\numberline {11.7.1}Detailed Description}{118}{subsection.11.7.1}
+\contentsline {subsection}{\numberline {11.7.2}Variable Documentation}{118}{subsection.11.7.2}
+\contentsline {subsubsection}{\numberline {11.7.2.1}edit\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}{118}{subsubsection.11.7.2.1}
+\contentsline {subsubsection}{\numberline {11.7.2.2}cost\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}{118}{subsubsection.11.7.2.2}
+\contentsline {section}{\numberline {11.8}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/duplex.h File Reference}{118}{section.11.8}
+\contentsline {subsection}{\numberline {11.8.1}Detailed Description}{119}{subsection.11.8.1}
+\contentsline {section}{\numberline {11.9}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/edit\discretionary {-}{}{}\_\discretionary {-}{}{}cost.h File Reference}{119}{section.11.9}
+\contentsline {subsection}{\numberline {11.9.1}Detailed Description}{119}{subsection.11.9.1}
+\contentsline {section}{\numberline {11.10}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/energy\discretionary {-}{}{}\_\discretionary {-}{}{}const.h File Reference}{119}{section.11.10}
+\contentsline {subsection}{\numberline {11.10.1}Detailed Description}{120}{subsection.11.10.1}
+\contentsline {subsection}{\numberline {11.10.2}Macro Definition Documentation}{120}{subsection.11.10.2}
+\contentsline {subsubsection}{\numberline {11.10.2.1}G\discretionary {-}{}{}A\discretionary {-}{}{}S\discretionary {-}{}{}C\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}S\discretionary {-}{}{}T}{120}{subsubsection.11.10.2.1}
+\contentsline {subsubsection}{\numberline {11.10.2.2}K0}{120}{subsubsection.11.10.2.2}
+\contentsline {subsubsection}{\numberline {11.10.2.3}I\discretionary {-}{}{}N\discretionary {-}{}{}F}{120}{subsubsection.11.10.2.3}
+\contentsline {subsubsection}{\numberline {11.10.2.4}F\discretionary {-}{}{}O\discretionary {-}{}{}R\discretionary {-}{}{}B\discretionary {-}{}{}I\discretionary {-}{}{}D\discretionary {-}{}{}D\discretionary {-}{}{}E\discretionary {-}{}{}N}{120}{subsubsection.11.10.2.4}
+\contentsline {subsubsection}{\numberline {11.10.2.5}B\discretionary {-}{}{}O\discretionary {-}{}{}N\discretionary {-}{}{}U\discretionary {-}{}{}S}{120}{subsubsection.11.10.2.5}
+\contentsline {subsubsection}{\numberline {11.10.2.6}N\discretionary {-}{}{}B\discretionary {-}{}{}P\discretionary {-}{}{}A\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}S}{120}{subsubsection.11.10.2.6}
+\contentsline {subsubsection}{\numberline {11.10.2.7}T\discretionary {-}{}{}U\discretionary {-}{}{}R\discretionary {-}{}{}N}{120}{subsubsection.11.10.2.7}
+\contentsline {subsubsection}{\numberline {11.10.2.8}M\discretionary {-}{}{}A\discretionary {-}{}{}X\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}O\discretionary {-}{}{}P}{120}{subsubsection.11.10.2.8}
+\contentsline {section}{\numberline {11.11}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/findpath.h File Reference}{120}{section.11.11}
+\contentsline {subsection}{\numberline {11.11.1}Detailed Description}{121}{subsection.11.11.1}
+\contentsline {subsection}{\numberline {11.11.2}Function Documentation}{121}{subsection.11.11.2}
+\contentsline {subsubsection}{\numberline {11.11.2.1}find\discretionary {-}{}{}\_\discretionary {-}{}{}saddle}{121}{subsubsection.11.11.2.1}
+\contentsline {subsubsection}{\numberline {11.11.2.2}get\discretionary {-}{}{}\_\discretionary {-}{}{}path}{122}{subsubsection.11.11.2.2}
+\contentsline {subsubsection}{\numberline {11.11.2.3}free\discretionary {-}{}{}\_\discretionary {-}{}{}path}{122}{subsubsection.11.11.2.3}
+\contentsline {section}{\numberline {11.12}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/fold.h File Reference}{122}{section.11.12}
+\contentsline {subsection}{\numberline {11.12.1}Detailed Description}{124}{subsection.11.12.1}
+\contentsline {subsection}{\numberline {11.12.2}Function Documentation}{124}{subsection.11.12.2}
+\contentsline {subsubsection}{\numberline {11.12.2.1}parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{124}{subsubsection.11.12.2.1}
+\contentsline {subsubsection}{\numberline {11.12.2.2}parenthesis\discretionary {-}{}{}\_\discretionary {-}{}{}zuker}{125}{subsubsection.11.12.2.2}
+\contentsline {subsubsection}{\numberline {11.12.2.3}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move}{125}{subsubsection.11.12.2.3}
+\contentsline {subsubsection}{\numberline {11.12.2.4}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}move\discretionary {-}{}{}\_\discretionary {-}{}{}pt}{125}{subsubsection.11.12.2.4}
+\contentsline {subsubsection}{\numberline {11.12.2.5}loop\discretionary {-}{}{}\_\discretionary {-}{}{}energy}{125}{subsubsection.11.12.2.5}
+\contentsline {subsubsection}{\numberline {11.12.2.6}assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}db}{126}{subsubsection.11.12.2.6}
+\contentsline {subsubsection}{\numberline {11.12.2.7}Loop\discretionary {-}{}{}Energy}{126}{subsubsection.11.12.2.7}
+\contentsline {subsubsection}{\numberline {11.12.2.8}Hairpin\discretionary {-}{}{}E}{126}{subsubsection.11.12.2.8}
+\contentsline {subsubsection}{\numberline {11.12.2.9}initialize\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{126}{subsubsection.11.12.2.9}
+\contentsline {subsubsection}{\numberline {11.12.2.10}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct}{126}{subsubsection.11.12.2.10}
+\contentsline {subsubsection}{\numberline {11.12.2.11}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pt}{127}{subsubsection.11.12.2.11}
+\contentsline {subsubsection}{\numberline {11.12.2.12}energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}struct}{127}{subsubsection.11.12.2.12}
+\contentsline {section}{\numberline {11.13}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/fold\discretionary {-}{}{}\_\discretionary {-}{}{}vars.h File Reference}{128}{section.11.13}
+\contentsline {subsection}{\numberline {11.13.1}Detailed Description}{130}{subsection.11.13.1}
+\contentsline {subsection}{\numberline {11.13.2}Function Documentation}{130}{subsection.11.13.2}
+\contentsline {subsubsection}{\numberline {11.13.2.1}set\discretionary {-}{}{}\_\discretionary {-}{}{}model\discretionary {-}{}{}\_\discretionary {-}{}{}details}{130}{subsubsection.11.13.2.1}
+\contentsline {subsection}{\numberline {11.13.3}Variable Documentation}{130}{subsection.11.13.3}
+\contentsline {subsubsection}{\numberline {11.13.3.1}no\discretionary {-}{}{}Lonely\discretionary {-}{}{}Pairs}{130}{subsubsection.11.13.3.1}
+\contentsline {subsubsection}{\numberline {11.13.3.2}dangles}{130}{subsubsection.11.13.3.2}
+\contentsline {subsubsection}{\numberline {11.13.3.3}tetra\discretionary {-}{}{}\_\discretionary {-}{}{}loop}{131}{subsubsection.11.13.3.3}
+\contentsline {subsubsection}{\numberline {11.13.3.4}energy\discretionary {-}{}{}\_\discretionary {-}{}{}set}{131}{subsubsection.11.13.3.4}
+\contentsline {subsubsection}{\numberline {11.13.3.5}old\discretionary {-}{}{}Ali\discretionary {-}{}{}En}{131}{subsubsection.11.13.3.5}
+\contentsline {subsubsection}{\numberline {11.13.3.6}ribo}{131}{subsubsection.11.13.3.6}
+\contentsline {subsubsection}{\numberline {11.13.3.7}Ribosum\discretionary {-}{}{}File}{131}{subsubsection.11.13.3.7}
+\contentsline {subsubsection}{\numberline {11.13.3.8}nonstandards}{131}{subsubsection.11.13.3.8}
+\contentsline {subsubsection}{\numberline {11.13.3.9}temperature}{131}{subsubsection.11.13.3.9}
+\contentsline {subsubsection}{\numberline {11.13.3.10}james\discretionary {-}{}{}\_\discretionary {-}{}{}rule}{131}{subsubsection.11.13.3.10}
+\contentsline {subsubsection}{\numberline {11.13.3.11}log\discretionary {-}{}{}M\discretionary {-}{}{}L}{132}{subsubsection.11.13.3.11}
+\contentsline {subsubsection}{\numberline {11.13.3.12}cut\discretionary {-}{}{}\_\discretionary {-}{}{}point}{132}{subsubsection.11.13.3.12}
+\contentsline {subsubsection}{\numberline {11.13.3.13}base\discretionary {-}{}{}\_\discretionary {-}{}{}pair}{132}{subsubsection.11.13.3.13}
+\contentsline {subsubsection}{\numberline {11.13.3.14}pr}{132}{subsubsection.11.13.3.14}
+\contentsline {subsubsection}{\numberline {11.13.3.15}iindx}{132}{subsubsection.11.13.3.15}
+\contentsline {subsubsection}{\numberline {11.13.3.16}pf\discretionary {-}{}{}\_\discretionary {-}{}{}scale}{132}{subsubsection.11.13.3.16}
+\contentsline {subsubsection}{\numberline {11.13.3.17}do\discretionary {-}{}{}\_\discretionary {-}{}{}backtrack}{132}{subsubsection.11.13.3.17}
+\contentsline {subsubsection}{\numberline {11.13.3.18}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}type}{133}{subsubsection.11.13.3.18}
+\contentsline {section}{\numberline {11.14}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/gquad.h File Reference}{133}{section.11.14}
+\contentsline {subsection}{\numberline {11.14.1}Detailed Description}{133}{subsection.11.14.1}
+\contentsline {subsection}{\numberline {11.14.2}Function Documentation}{134}{subsection.11.14.2}
+\contentsline {subsubsection}{\numberline {11.14.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}gquad\discretionary {-}{}{}\_\discretionary {-}{}{}matrix}{134}{subsubsection.11.14.2.1}
+\contentsline {subsubsection}{\numberline {11.14.2.2}parse\discretionary {-}{}{}\_\discretionary {-}{}{}gquad}{134}{subsubsection.11.14.2.2}
+\contentsline {subsubsection}{\numberline {11.14.2.3}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}{134}{subsubsection.11.14.2.3}
+\contentsline {subsubsection}{\numberline {11.14.2.4}backtrack\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}G\discretionary {-}{}{}Quad\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}L}{135}{subsubsection.11.14.2.4}
+\contentsline {section}{\numberline {11.15}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/inverse.h File Reference}{135}{section.11.15}
+\contentsline {subsection}{\numberline {11.15.1}Detailed Description}{135}{subsection.11.15.1}
+\contentsline {section}{\numberline {11.16}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}Lfold.h File Reference}{135}{section.11.16}
+\contentsline {subsection}{\numberline {11.16.1}Detailed Description}{136}{subsection.11.16.1}
+\contentsline {section}{\numberline {11.17}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/loop\discretionary {-}{}{}\_\discretionary {-}{}{}energies.h File Reference}{136}{section.11.17}
+\contentsline {subsection}{\numberline {11.17.1}Detailed Description}{136}{subsection.11.17.1}
+\contentsline {subsection}{\numberline {11.17.2}Function Documentation}{137}{subsection.11.17.2}
+\contentsline {subsubsection}{\numberline {11.17.2.1}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}{137}{subsubsection.11.17.2.1}
+\contentsline {subsubsection}{\numberline {11.17.2.2}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}{138}{subsubsection.11.17.2.2}
+\contentsline {subsubsection}{\numberline {11.17.2.3}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}{138}{subsubsection.11.17.2.3}
+\contentsline {subsubsection}{\numberline {11.17.2.4}exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Stem}{139}{subsubsection.11.17.2.4}
+\contentsline {subsubsection}{\numberline {11.17.2.5}exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Hairpin}{140}{subsubsection.11.17.2.5}
+\contentsline {subsubsection}{\numberline {11.17.2.6}exp\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Int\discretionary {-}{}{}Loop}{140}{subsubsection.11.17.2.6}
+\contentsline {section}{\numberline {11.18}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}L\discretionary {-}{}{}Pfold.h File Reference}{141}{section.11.18}
+\contentsline {subsection}{\numberline {11.18.1}Detailed Description}{142}{subsection.11.18.1}
+\contentsline {subsection}{\numberline {11.18.2}Function Documentation}{142}{subsection.11.18.2}
+\contentsline {subsubsection}{\numberline {11.18.2.1}init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}L\discretionary {-}{}{}P}{142}{subsubsection.11.18.2.1}
+\contentsline {section}{\numberline {11.19}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A.h File Reference}{142}{section.11.19}
+\contentsline {subsection}{\numberline {11.19.1}Detailed Description}{143}{subsection.11.19.1}
+\contentsline {subsection}{\numberline {11.19.2}Function Documentation}{143}{subsection.11.19.2}
+\contentsline {subsubsection}{\numberline {11.19.2.1}M\discretionary {-}{}{}E\discretionary {-}{}{}A}{143}{subsubsection.11.19.2.1}
+\contentsline {section}{\numberline {11.20}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/mm.h File Reference}{144}{section.11.20}
+\contentsline {subsection}{\numberline {11.20.1}Detailed Description}{144}{subsection.11.20.1}
+\contentsline {section}{\numberline {11.21}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/naview.h File Reference}{144}{section.11.21}
+\contentsline {section}{\numberline {11.22}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/params.h File Reference}{145}{section.11.22}
+\contentsline {section}{\numberline {11.23}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func.h File Reference}{146}{section.11.23}
+\contentsline {subsection}{\numberline {11.23.1}Detailed Description}{148}{subsection.11.23.1}
+\contentsline {subsection}{\numberline {11.23.2}Function Documentation}{148}{subsection.11.23.2}
+\contentsline {subsubsection}{\numberline {11.23.2.1}init\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{148}{subsubsection.11.23.2.1}
+\contentsline {subsubsection}{\numberline {11.23.2.2}centroid}{148}{subsubsection.11.23.2.2}
+\contentsline {subsubsection}{\numberline {11.23.2.3}mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}dist}{148}{subsubsection.11.23.2.3}
+\contentsline {subsubsection}{\numberline {11.23.2.4}exp\discretionary {-}{}{}Loop\discretionary {-}{}{}Energy}{148}{subsubsection.11.23.2.4}
+\contentsline {subsubsection}{\numberline {11.23.2.5}exp\discretionary {-}{}{}Hairpin\discretionary {-}{}{}Energy}{148}{subsubsection.11.23.2.5}
+\contentsline {section}{\numberline {11.24}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}co.h File Reference}{148}{section.11.24}
+\contentsline {subsection}{\numberline {11.24.1}Detailed Description}{150}{subsection.11.24.1}
+\contentsline {subsection}{\numberline {11.24.2}Function Documentation}{150}{subsection.11.24.2}
+\contentsline {subsubsection}{\numberline {11.24.2.1}get\discretionary {-}{}{}\_\discretionary {-}{}{}plist}{150}{subsubsection.11.24.2.1}
+\contentsline {subsubsection}{\numberline {11.24.2.2}init\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}{150}{subsubsection.11.24.2.2}
+\contentsline {section}{\numberline {11.25}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/part\discretionary {-}{}{}\_\discretionary {-}{}{}func\discretionary {-}{}{}\_\discretionary {-}{}{}up.h File Reference}{150}{section.11.25}
+\contentsline {subsection}{\numberline {11.25.1}Detailed Description}{151}{subsection.11.25.1}
+\contentsline {section}{\numberline {11.26}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/plot\discretionary {-}{}{}\_\discretionary {-}{}{}layouts.h File Reference}{152}{section.11.26}
+\contentsline {subsection}{\numberline {11.26.1}Detailed Description}{153}{subsection.11.26.1}
+\contentsline {subsection}{\numberline {11.26.2}Macro Definition Documentation}{153}{subsection.11.26.2}
+\contentsline {subsubsection}{\numberline {11.26.2.1}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}T\discretionary {-}{}{}Y\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}S\discretionary {-}{}{}I\discretionary {-}{}{}M\discretionary {-}{}{}P\discretionary {-}{}{}L\discretionary {-}{}{}E}{153}{subsubsection.11.26.2.1}
+\contentsline {subsubsection}{\numberline {11.26.2.2}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}T\discretionary {-}{}{}Y\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}V\discretionary {-}{}{}I\discretionary {-}{}{}E\discretionary {-}{}{}W}{153}{subsubsection.11.26.2.2}
+\contentsline {subsubsection}{\numberline {11.26.2.3}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}P\discretionary {-}{}{}L\discretionary {-}{}{}O\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}T\discretionary {-}{}{}Y\discretionary {-}{}{}P\discretionary {-}{}{}E\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}C\discretionary {-}{}{}I\discretionary {-}{}{}R\discretionary {-}{}{}C\discretionary {-}{}{}U\discretionary {-}{}{}L\discretionary {-}{}{}A\discretionary {-}{}{}R}{154}{subsubsection.11.26.2.3}
+\contentsline {subsection}{\numberline {11.26.3}Function Documentation}{154}{subsection.11.26.3}
+\contentsline {subsubsection}{\numberline {11.26.3.1}simple\discretionary {-}{}{}\_\discretionary {-}{}{}xy\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}{154}{subsubsection.11.26.3.1}
+\contentsline {subsubsection}{\numberline {11.26.3.2}simple\discretionary {-}{}{}\_\discretionary {-}{}{}circplot\discretionary {-}{}{}\_\discretionary {-}{}{}coordinates}{154}{subsubsection.11.26.3.2}
+\contentsline {subsection}{\numberline {11.26.4}Variable Documentation}{155}{subsection.11.26.4}
+\contentsline {subsubsection}{\numberline {11.26.4.1}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}type}{155}{subsubsection.11.26.4.1}
+\contentsline {section}{\numberline {11.27}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/profiledist.h File Reference}{155}{section.11.27}
+\contentsline {subsection}{\numberline {11.27.1}Function Documentation}{156}{subsection.11.27.1}
+\contentsline {subsubsection}{\numberline {11.27.1.1}profile\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}{156}{subsubsection.11.27.1.1}
+\contentsline {subsubsection}{\numberline {11.27.1.2}Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}{156}{subsubsection.11.27.1.2}
+\contentsline {subsubsection}{\numberline {11.27.1.3}free\discretionary {-}{}{}\_\discretionary {-}{}{}profile}{156}{subsubsection.11.27.1.3}
+\contentsline {subsubsection}{\numberline {11.27.1.4}Make\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}profile}{156}{subsubsection.11.27.1.4}
+\contentsline {section}{\numberline {11.28}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot.h File Reference}{157}{section.11.28}
+\contentsline {subsection}{\numberline {11.28.1}Detailed Description}{158}{subsection.11.28.1}
+\contentsline {subsection}{\numberline {11.28.2}Function Documentation}{158}{subsection.11.28.2}
+\contentsline {subsubsection}{\numberline {11.28.2.1}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{158}{subsubsection.11.28.2.1}
+\contentsline {subsubsection}{\numberline {11.28.2.2}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}a}{158}{subsubsection.11.28.2.2}
+\contentsline {subsubsection}{\numberline {11.28.2.3}gml\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A}{158}{subsubsection.11.28.2.3}
+\contentsline {subsubsection}{\numberline {11.28.2.4}ssv\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{159}{subsubsection.11.28.2.4}
+\contentsline {subsubsection}{\numberline {11.28.2.5}svg\discretionary {-}{}{}\_\discretionary {-}{}{}rna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{159}{subsubsection.11.28.2.5}
+\contentsline {subsubsection}{\numberline {11.28.2.6}xrna\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{159}{subsubsection.11.28.2.6}
+\contentsline {subsubsection}{\numberline {11.28.2.7}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot\discretionary {-}{}{}\_\discretionary {-}{}{}list}{160}{subsubsection.11.28.2.7}
+\contentsline {subsubsection}{\numberline {11.28.2.8}ali\discretionary {-}{}{}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}color\discretionary {-}{}{}\_\discretionary {-}{}{}aln}{160}{subsubsection.11.28.2.8}
+\contentsline {subsubsection}{\numberline {11.28.2.9}P\discretionary {-}{}{}S\discretionary {-}{}{}\_\discretionary {-}{}{}dot\discretionary {-}{}{}\_\discretionary {-}{}{}plot}{160}{subsubsection.11.28.2.9}
+\contentsline {section}{\numberline {11.29}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/read\discretionary {-}{}{}\_\discretionary {-}{}{}epars.h File Reference}{160}{section.11.29}
+\contentsline {section}{\numberline {11.30}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}Astruct.h File Reference}{161}{section.11.30}
+\contentsline {subsection}{\numberline {11.30.1}Detailed Description}{162}{subsection.11.30.1}
+\contentsline {subsection}{\numberline {11.30.2}Function Documentation}{162}{subsection.11.30.2}
+\contentsline {subsubsection}{\numberline {11.30.2.1}b2\discretionary {-}{}{}H\discretionary {-}{}{}I\discretionary {-}{}{}T}{162}{subsubsection.11.30.2.1}
+\contentsline {subsubsection}{\numberline {11.30.2.2}b2\discretionary {-}{}{}C}{162}{subsubsection.11.30.2.2}
+\contentsline {subsubsection}{\numberline {11.30.2.3}b2\discretionary {-}{}{}Shapiro}{162}{subsubsection.11.30.2.3}
+\contentsline {subsubsection}{\numberline {11.30.2.4}add\discretionary {-}{}{}\_\discretionary {-}{}{}root}{163}{subsubsection.11.30.2.4}
+\contentsline {subsubsection}{\numberline {11.30.2.5}expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Shapiro}{163}{subsubsection.11.30.2.5}
+\contentsline {subsubsection}{\numberline {11.30.2.6}expand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}{163}{subsubsection.11.30.2.6}
+\contentsline {subsubsection}{\numberline {11.30.2.7}unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}Full}{163}{subsubsection.11.30.2.7}
+\contentsline {subsubsection}{\numberline {11.30.2.8}unweight}{164}{subsubsection.11.30.2.8}
+\contentsline {subsubsection}{\numberline {11.30.2.9}unexpand\discretionary {-}{}{}\_\discretionary {-}{}{}aligned\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}F}{164}{subsubsection.11.30.2.9}
+\contentsline {subsubsection}{\numberline {11.30.2.10}parse\discretionary {-}{}{}\_\discretionary {-}{}{}structure}{164}{subsubsection.11.30.2.10}
+\contentsline {section}{\numberline {11.31}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/stringdist.h File Reference}{164}{section.11.31}
+\contentsline {subsection}{\numberline {11.31.1}Detailed Description}{165}{subsection.11.31.1}
+\contentsline {subsection}{\numberline {11.31.2}Function Documentation}{165}{subsection.11.31.2}
+\contentsline {subsubsection}{\numberline {11.31.2.1}Make\discretionary {-}{}{}\_\discretionary {-}{}{}sw\discretionary {-}{}{}String}{165}{subsubsection.11.31.2.1}
+\contentsline {subsubsection}{\numberline {11.31.2.2}string\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}{165}{subsubsection.11.31.2.2}
+\contentsline {section}{\numberline {11.32}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/subopt.h File Reference}{166}{section.11.32}
+\contentsline {subsection}{\numberline {11.32.1}Detailed Description}{167}{subsection.11.32.1}
+\contentsline {section}{\numberline {11.33}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/treedist.h File Reference}{167}{section.11.33}
+\contentsline {subsection}{\numberline {11.33.1}Detailed Description}{167}{subsection.11.33.1}
+\contentsline {subsection}{\numberline {11.33.2}Function Documentation}{168}{subsection.11.33.2}
+\contentsline {subsubsection}{\numberline {11.33.2.1}make\discretionary {-}{}{}\_\discretionary {-}{}{}tree}{168}{subsubsection.11.33.2.1}
+\contentsline {subsubsection}{\numberline {11.33.2.2}tree\discretionary {-}{}{}\_\discretionary {-}{}{}edit\discretionary {-}{}{}\_\discretionary {-}{}{}distance}{168}{subsubsection.11.33.2.2}
+\contentsline {subsubsection}{\numberline {11.33.2.3}free\discretionary {-}{}{}\_\discretionary {-}{}{}tree}{168}{subsubsection.11.33.2.3}
+\contentsline {section}{\numberline {11.34}/home/asherstnev/\discretionary {-}{}{}Projects/\discretionary {-}{}{}Java.projects/jabaws/secure-\/git/develop/binaries/src/\discretionary {-}{}{}Vienna\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A/\discretionary {-}{}{}H/utils.h File Reference}{168}{section.11.34}
+\contentsline {subsection}{\numberline {11.34.1}Detailed Description}{171}{subsection.11.34.1}
+\contentsline {subsection}{\numberline {11.34.2}Macro Definition Documentation}{171}{subsection.11.34.2}
+\contentsline {subsubsection}{\numberline {11.34.2.1}V\discretionary {-}{}{}R\discretionary {-}{}{}N\discretionary {-}{}{}A\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}I\discretionary {-}{}{}N\discretionary {-}{}{}P\discretionary {-}{}{}U\discretionary {-}{}{}T\discretionary {-}{}{}\_\discretionary {-}{}{}\discretionary {-}{}{}E\discretionary {-}{}{}R\discretionary {-}{}{}R\discretionary {-}{}{}O\discretionary {-}{}{}R}{171}{subsubsection.11.34.2.1}
+\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}