\indexentry{RNA Secondary Structure Folding@{RNA Secondary Structure Folding}|hyperpage}{31}
\indexentry{Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (MFE) Structures}|hyperpage}{33}
\indexentry{mfe\_\discretionary {-}{}{}fold@{mfe\_\discretionary {-}{}{}fold}!fold\_\discretionary {-}{}{}par@{fold\_\discretionary {-}{}{}par}|hyperpage}{34}
\indexentry{fold\_\discretionary {-}{}{}par@{fold\_\discretionary {-}{}{}par}!mfe_fold@{mfe\_\discretionary {-}{}{}fold}|hyperpage}{34}
\indexentry{mfe\_\discretionary {-}{}{}fold@{mfe\_\discretionary {-}{}{}fold}!fold@{fold}|hyperpage}{35}
\indexentry{fold@{fold}!mfe_fold@{mfe\_\discretionary {-}{}{}fold}|hyperpage}{35}
\indexentry{mfe\_\discretionary {-}{}{}fold@{mfe\_\discretionary {-}{}{}fold}!circfold@{circfold}|hyperpage}{35}
\indexentry{circfold@{circfold}!mfe_fold@{mfe\_\discretionary {-}{}{}fold}|hyperpage}{35}
\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{37}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}|hyperpage}{39}
\indexentry{pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{39}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{39}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{39}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}|hyperpage}{40}
\indexentry{pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{40}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays@{free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}|hyperpage}{41}
\indexentry{free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays@{free\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{41}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}|hyperpage}{42}
\indexentry{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{42}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!export\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}bppm}|hyperpage}{42}
\indexentry{export\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}bppm}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{42}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr@{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}|hyperpage}{42}
\indexentry{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr@{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}pr}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{42}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays@{get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}|hyperpage}{43}
\indexentry{get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays@{get\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}arrays}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{43}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}|hyperpage}{43}
\indexentry{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{43}
\indexentry{pf\_\discretionary {-}{}{}fold@{pf\_\discretionary {-}{}{}fold}!mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}|hyperpage}{43}
\indexentry{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}distance\_\discretionary {-}{}{}pr}!pf_fold@{pf\_\discretionary {-}{}{}fold}|hyperpage}{43}
\indexentry{Compute the structure with maximum expected accuracy (MEA)@{Compute the structure with maximum expected accuracy (MEA)}|hyperpage}{45}
\indexentry{Compute the centroid structure@{Compute the centroid structure}|hyperpage}{46}
\indexentry{centroid\_\discretionary {-}{}{}fold@{centroid\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl@{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}|hyperpage}{46}
\indexentry{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl@{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pl}!centroid_fold@{centroid\_\discretionary {-}{}{}fold}|hyperpage}{46}
\indexentry{centroid\_\discretionary {-}{}{}fold@{centroid\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr@{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}|hyperpage}{46}
\indexentry{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr@{get\_\discretionary {-}{}{}centroid\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pr}!centroid_fold@{centroid\_\discretionary {-}{}{}fold}|hyperpage}{46}
\indexentry{Enumerating Suboptimal Structures@{Enumerating Suboptimal Structures}|hyperpage}{48}
\indexentry{Suboptimal structures according to Zuker et al. 1989@{Suboptimal structures according to Zuker et al. 1989}|hyperpage}{49}
\indexentry{subopt\_\discretionary {-}{}{}zuker@{subopt\_\discretionary {-}{}{}zuker}!zukersubopt@{zukersubopt}|hyperpage}{49}
\indexentry{zukersubopt@{zukersubopt}!subopt_zuker@{subopt\_\discretionary {-}{}{}zuker}|hyperpage}{49}
\indexentry{Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the MFE}|hyperpage}{50}
\indexentry{subopt\_\discretionary {-}{}{}wuchty@{subopt\_\discretionary {-}{}{}wuchty}!subopt@{subopt}|hyperpage}{50}
\indexentry{subopt@{subopt}!subopt_wuchty@{subopt\_\discretionary {-}{}{}wuchty}|hyperpage}{50}
\indexentry{subopt\_\discretionary {-}{}{}wuchty@{subopt\_\discretionary {-}{}{}wuchty}!subopt\_\discretionary {-}{}{}circ@{subopt\_\discretionary {-}{}{}circ}|hyperpage}{51}
\indexentry{subopt\_\discretionary {-}{}{}circ@{subopt\_\discretionary {-}{}{}circ}!subopt_wuchty@{subopt\_\discretionary {-}{}{}wuchty}|hyperpage}{51}
\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{52}
\indexentry{subopt\_\discretionary {-}{}{}stochbt@{subopt\_\discretionary {-}{}{}stochbt}!pbacktrack@{pbacktrack}|hyperpage}{52}
\indexentry{pbacktrack@{pbacktrack}!subopt_stochbt@{subopt\_\discretionary {-}{}{}stochbt}|hyperpage}{52}
\indexentry{subopt\_\discretionary {-}{}{}stochbt@{subopt\_\discretionary {-}{}{}stochbt}!pbacktrack\_\discretionary {-}{}{}circ@{pbacktrack\_\discretionary {-}{}{}circ}|hyperpage}{53}
\indexentry{pbacktrack\_\discretionary {-}{}{}circ@{pbacktrack\_\discretionary {-}{}{}circ}!subopt_stochbt@{subopt\_\discretionary {-}{}{}stochbt}|hyperpage}{53}
\indexentry{subopt\_\discretionary {-}{}{}stochbt@{subopt\_\discretionary {-}{}{}stochbt}!st\_\discretionary {-}{}{}back@{st\_\discretionary {-}{}{}back}|hyperpage}{53}
\indexentry{st\_\discretionary {-}{}{}back@{st\_\discretionary {-}{}{}back}!subopt_stochbt@{subopt\_\discretionary {-}{}{}stochbt}|hyperpage}{53}
\indexentry{Calculate Secondary Structures of two RNAs upon Dimerization@{Calculate Secondary Structures of two RNAs upon Dimerization}|hyperpage}{54}
\indexentry{MFE Structures of two hybridized Sequences@{MFE Structures of two hybridized Sequences}|hyperpage}{55}
\indexentry{mfe\_\discretionary {-}{}{}cofold@{mfe\_\discretionary {-}{}{}cofold}!cofold@{cofold}|hyperpage}{55}
\indexentry{cofold@{cofold}!mfe_cofold@{mfe\_\discretionary {-}{}{}cofold}|hyperpage}{55}
\indexentry{mfe\_\discretionary {-}{}{}cofold@{mfe\_\discretionary {-}{}{}cofold}!export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq@{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}|hyperpage}{56}
\indexentry{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq@{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays\_\discretionary {-}{}{}gq}!mfe_cofold@{mfe\_\discretionary {-}{}{}cofold}|hyperpage}{56}
\indexentry{mfe\_\discretionary {-}{}{}cofold@{mfe\_\discretionary {-}{}{}cofold}!export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays@{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}|hyperpage}{56}
\indexentry{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays@{export\_\discretionary {-}{}{}cofold\_\discretionary {-}{}{}arrays}!mfe_cofold@{mfe\_\discretionary {-}{}{}cofold}|hyperpage}{56}
\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{58}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{59}
\indexentry{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{59}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}|hyperpage}{59}
\indexentry{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{59}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}|hyperpage}{60}
\indexentry{export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}co\_\discretionary {-}{}{}bppm}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{60}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}|hyperpage}{60}
\indexentry{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{60}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par@{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}|hyperpage}{61}
\indexentry{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par@{update\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}params\_\discretionary {-}{}{}par}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{61}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!compute\_\discretionary {-}{}{}probabilities@{compute\_\discretionary {-}{}{}probabilities}|hyperpage}{61}
\indexentry{compute\_\discretionary {-}{}{}probabilities@{compute\_\discretionary {-}{}{}probabilities}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{61}
\indexentry{pf\_\discretionary {-}{}{}cofold@{pf\_\discretionary {-}{}{}cofold}!get\_\discretionary {-}{}{}concentrations@{get\_\discretionary {-}{}{}concentrations}|hyperpage}{61}
\indexentry{get\_\discretionary {-}{}{}concentrations@{get\_\discretionary {-}{}{}concentrations}!pf_cofold@{pf\_\discretionary {-}{}{}cofold}|hyperpage}{61}
\indexentry{Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}|hyperpage}{63}
\indexentry{up\_\discretionary {-}{}{}cofold@{up\_\discretionary {-}{}{}cofold}!pf\_\discretionary {-}{}{}unstru@{pf\_\discretionary {-}{}{}unstru}|hyperpage}{63}
\indexentry{pf\_\discretionary {-}{}{}unstru@{pf\_\discretionary {-}{}{}unstru}!up_cofold@{up\_\discretionary {-}{}{}cofold}|hyperpage}{63}
\indexentry{up\_\discretionary {-}{}{}cofold@{up\_\discretionary {-}{}{}cofold}!pf\_\discretionary {-}{}{}interact@{pf\_\discretionary {-}{}{}interact}|hyperpage}{64}
\indexentry{pf\_\discretionary {-}{}{}interact@{pf\_\discretionary {-}{}{}interact}!up_cofold@{up\_\discretionary {-}{}{}cofold}|hyperpage}{64}
\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{66}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}mpi@{get\_\discretionary {-}{}{}mpi}|hyperpage}{67}
\indexentry{get\_\discretionary {-}{}{}mpi@{get\_\discretionary {-}{}{}mpi}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{67}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}|hyperpage}{67}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}alistruct}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{67}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence@{encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}|hyperpage}{68}
\indexentry{encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence@{encode\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}sequence}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{68}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays@{alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}|hyperpage}{68}
\indexentry{alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays@{alloc\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{68}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays@{free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}|hyperpage}{69}
\indexentry{free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays@{free\_\discretionary {-}{}{}sequence\_\discretionary {-}{}{}arrays}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{69}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays@{get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}|hyperpage}{69}
\indexentry{get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays@{get\_\discretionary {-}{}{}alipf\_\discretionary {-}{}{}arrays}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{69}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!cv\_\discretionary {-}{}{}fact@{cv\_\discretionary {-}{}{}fact}|hyperpage}{70}
\indexentry{cv\_\discretionary {-}{}{}fact@{cv\_\discretionary {-}{}{}fact}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{70}
\indexentry{consensus\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}fold}!nc\_\discretionary {-}{}{}fact@{nc\_\discretionary {-}{}{}fact}|hyperpage}{70}
\indexentry{nc\_\discretionary {-}{}{}fact@{nc\_\discretionary {-}{}{}fact}!consensus_fold@{consensus\_\discretionary {-}{}{}fold}|hyperpage}{70}
\indexentry{MFE Consensus Structures for Sequence Alignment(s)@{MFE Consensus Structures for Sequence Alignment(s)}|hyperpage}{71}
\indexentry{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}!alifold@{alifold}|hyperpage}{71}
\indexentry{alifold@{alifold}!consensus_mfe_fold@{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}|hyperpage}{71}
\indexentry{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}!circalifold@{circalifold}|hyperpage}{71}
\indexentry{circalifold@{circalifold}!consensus_mfe_fold@{consensus\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}|hyperpage}{71}
\indexentry{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}|hyperpage}{73}
\indexentry{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}|hyperpage}{73}
\indexentry{alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par@{alipf\_\discretionary {-}{}{}fold\_\discretionary {-}{}{}par}!consensus_pf_fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{73}
\indexentry{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!alipf\_\discretionary {-}{}{}fold@{alipf\_\discretionary {-}{}{}fold}|hyperpage}{73}
\indexentry{alipf\_\discretionary {-}{}{}fold@{alipf\_\discretionary {-}{}{}fold}!consensus_pf_fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{73}
\indexentry{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold@{alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}|hyperpage}{74}
\indexentry{alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold@{alipf\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}fold}!consensus_pf_fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{74}
\indexentry{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}|hyperpage}{74}
\indexentry{export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm@{export\_\discretionary {-}{}{}ali\_\discretionary {-}{}{}bppm}!consensus_pf_fold@{consensus\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{74}
\indexentry{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)@{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}|hyperpage}{75}
\indexentry{consensus\_\discretionary {-}{}{}stochbt@{consensus\_\discretionary {-}{}{}stochbt}!alipbacktrack@{alipbacktrack}|hyperpage}{75}
\indexentry{alipbacktrack@{alipbacktrack}!consensus_stochbt@{consensus\_\discretionary {-}{}{}stochbt}|hyperpage}{75}
\indexentry{Predicting Locally stable structures of large sequences@{Predicting Locally stable structures of large sequences}|hyperpage}{76}
\indexentry{Local MFE structure Prediction and Z-\/scores@{Local MFE structure Prediction and Z-\/scores}|hyperpage}{77}
\indexentry{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}!Lfold@{Lfold}|hyperpage}{77}
\indexentry{Lfold@{Lfold}!local_mfe_fold@{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}|hyperpage}{77}
\indexentry{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}!Lfoldz@{Lfoldz}|hyperpage}{77}
\indexentry{Lfoldz@{Lfoldz}!local_mfe_fold@{local\_\discretionary {-}{}{}mfe\_\discretionary {-}{}{}fold}|hyperpage}{77}
\indexentry{Partition functions for locally stable secondary structures@{Partition functions for locally stable secondary structures}|hyperpage}{78}
\indexentry{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP@{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}|hyperpage}{78}
\indexentry{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP@{update\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}paramsLP}!local_pf_fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{78}
\indexentry{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!pfl\_\discretionary {-}{}{}fold@{pfl\_\discretionary {-}{}{}fold}|hyperpage}{78}
\indexentry{pfl\_\discretionary {-}{}{}fold@{pfl\_\discretionary {-}{}{}fold}!local_pf_fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{78}
\indexentry{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!putoutpU\_\discretionary {-}{}{}prob@{putoutpU\_\discretionary {-}{}{}prob}|hyperpage}{79}
\indexentry{putoutpU\_\discretionary {-}{}{}prob@{putoutpU\_\discretionary {-}{}{}prob}!local_pf_fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{79}
\indexentry{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin@{putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}|hyperpage}{79}
\indexentry{putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin@{putoutpU\_\discretionary {-}{}{}prob\_\discretionary {-}{}{}bin}!local_pf_fold@{local\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{79}
\indexentry{Local MFE consensus structures for Sequence Alignments@{Local MFE consensus structures for Sequence Alignments}|hyperpage}{81}
\indexentry{local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold@{local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}!aliLfold@{aliLfold}|hyperpage}{81}
\indexentry{aliLfold@{aliLfold}!local_consensus_fold@{local\_\discretionary {-}{}{}consensus\_\discretionary {-}{}{}fold}|hyperpage}{81}
\indexentry{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}|hyperpage}{82}
\indexentry{energy\_\discretionary {-}{}{}parameters@{energy\_\discretionary {-}{}{}parameters}!scale\_\discretionary {-}{}{}parameters@{scale\_\discretionary {-}{}{}parameters}|hyperpage}{83}
\indexentry{scale\_\discretionary {-}{}{}parameters@{scale\_\discretionary {-}{}{}parameters}!energy_parameters@{energy\_\discretionary {-}{}{}parameters}|hyperpage}{83}
\indexentry{energy\_\discretionary {-}{}{}parameters@{energy\_\discretionary {-}{}{}parameters}!get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters@{get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}|hyperpage}{83}
\indexentry{get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters@{get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}parameters}!energy_parameters@{energy\_\discretionary {-}{}{}parameters}|hyperpage}{83}
\indexentry{energy\_\discretionary {-}{}{}parameters@{energy\_\discretionary {-}{}{}parameters}!get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters@{get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}|hyperpage}{83}
\indexentry{get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters@{get\_\discretionary {-}{}{}scaled\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}parameters}!energy_parameters@{energy\_\discretionary {-}{}{}parameters}|hyperpage}{83}
\indexentry{energy\_\discretionary {-}{}{}parameters@{energy\_\discretionary {-}{}{}parameters}!get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors@{get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}|hyperpage}{84}
\indexentry{get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors@{get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factors}!energy_parameters@{energy\_\discretionary {-}{}{}parameters}|hyperpage}{84}
\indexentry{energy\_\discretionary {-}{}{}parameters@{energy\_\discretionary {-}{}{}parameters}!get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy@{get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}|hyperpage}{84}
\indexentry{get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy@{get\_\discretionary {-}{}{}boltzmann\_\discretionary {-}{}{}factor\_\discretionary {-}{}{}copy}!energy_parameters@{energy\_\discretionary {-}{}{}parameters}|hyperpage}{84}
\indexentry{Reading/Writing energy parameter sets from/to File@{Reading/Writing energy parameter sets from/to File}|hyperpage}{86}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}!read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}|hyperpage}{86}
\indexentry{read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{read\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}!energy_parameters_rw@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}|hyperpage}{86}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}!write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}|hyperpage}{86}
\indexentry{write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{write\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}!energy_parameters_rw@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}rw}|hyperpage}{86}
\indexentry{Converting energy parameter files@{Converting energy parameter files}|hyperpage}{88}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ALL}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}HP}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}STACK}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}HP}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}1N}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}23}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}MULTI}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MM\_\discretionary {-}{}{}EXT}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}|hyperpage}{89}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE5}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{89}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DANGLE3}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}11}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}21}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT\_\discretionary {-}{}{}22}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}BULGE}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}INT}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}ML}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}MISC}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}SPECIAL\_\discretionary {-}{}{}HP}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}|hyperpage}{90}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}VANILLA}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{90}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}|hyperpage}{91}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}NINIO}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{91}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}|hyperpage}{91}
\indexentry{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP@{VRNA\_\discretionary {-}{}{}CONVERT\_\discretionary {-}{}{}OUTPUT\_\discretionary {-}{}{}DUMP}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{91}
\indexentry{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}!convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}|hyperpage}{91}
\indexentry{convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file@{convert\_\discretionary {-}{}{}parameter\_\discretionary {-}{}{}file}!energy_parameters_convert@{energy\_\discretionary {-}{}{}parameters\_\discretionary {-}{}{}convert}|hyperpage}{91}
\indexentry{Energy evaluation@{Energy evaluation}|hyperpage}{93}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}|hyperpage}{94}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure}!eval@{eval}|hyperpage}{94}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}|hyperpage}{94}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}!eval@{eval}|hyperpage}{94}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}|hyperpage}{94}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}structure}!eval@{eval}|hyperpage}{94}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}|hyperpage}{95}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}par}!eval@{eval}|hyperpage}{95}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}|hyperpage}{95}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}structure\_\discretionary {-}{}{}pt}!eval@{eval}|hyperpage}{95}
\indexentry{eval@{eval}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}|hyperpage}{96}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt\_\discretionary {-}{}{}par}!eval@{eval}|hyperpage}{96}
\indexentry{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}|hyperpage}{97}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{97}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{97}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!final\_\discretionary {-}{}{}cost@{final\_\discretionary {-}{}{}cost}|hyperpage}{98}
\indexentry{final\_\discretionary {-}{}{}cost@{final\_\discretionary {-}{}{}cost}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!give\_\discretionary {-}{}{}up@{give\_\discretionary {-}{}{}up}|hyperpage}{98}
\indexentry{give\_\discretionary {-}{}{}up@{give\_\discretionary {-}{}{}up}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{inverse\_\discretionary {-}{}{}fold@{inverse\_\discretionary {-}{}{}fold}!inv\_\discretionary {-}{}{}verbose@{inv\_\discretionary {-}{}{}verbose}|hyperpage}{98}
\indexentry{inv\_\discretionary {-}{}{}verbose@{inv\_\discretionary {-}{}{}verbose}!inverse_fold@{inverse\_\discretionary {-}{}{}fold}|hyperpage}{98}
\indexentry{Classified Dynamic Programming@{Classified Dynamic Programming}|hyperpage}{99}
\indexentry{Distance based partitioning of the Secondary Structure Space@{Distance based partitioning of the Secondary Structure Space}|hyperpage}{100}
\indexentry{Calculating MFE representatives of a Distance Based Partitioning@{Calculating MFE representatives of a Distance Based Partitioning}|hyperpage}{101}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}!get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables@{get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}|hyperpage}{102}
\indexentry{get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables@{get\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}!kl_neighborhood_mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}|hyperpage}{102}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}!destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables@{destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}|hyperpage}{102}
\indexentry{destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables@{destroy\_\discretionary {-}{}{}TwoDfold\_\discretionary {-}{}{}variables}!kl_neighborhood_mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}|hyperpage}{102}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}!TwoDfoldList@{TwoDfoldList}|hyperpage}{102}
\indexentry{TwoDfoldList@{TwoDfoldList}!kl_neighborhood_mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}|hyperpage}{102}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}!TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5@{TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}|hyperpage}{103}
\indexentry{TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5@{TwoDfold\_\discretionary {-}{}{}backtrack\_\discretionary {-}{}{}f5}!kl_neighborhood_mfe@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}mfe}|hyperpage}{103}
\indexentry{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}|hyperpage}{104}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}!get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables@{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}|hyperpage}{105}
\indexentry{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables@{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}!kl_neighborhood_pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}|hyperpage}{105}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}!get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE@{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}|hyperpage}{105}
\indexentry{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE@{get\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables\_\discretionary {-}{}{}from\_\discretionary {-}{}{}MFE}!kl_neighborhood_pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}|hyperpage}{105}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}!destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables@{destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}|hyperpage}{105}
\indexentry{destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables@{destroy\_\discretionary {-}{}{}TwoDpfold\_\discretionary {-}{}{}variables}!kl_neighborhood_pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}|hyperpage}{105}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}!TwoDpfoldList@{TwoDpfoldList}|hyperpage}{106}
\indexentry{TwoDpfoldList@{TwoDpfoldList}!kl_neighborhood_pf@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}pf}|hyperpage}{106}
\indexentry{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}|hyperpage}{107}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}!TwoDpfold\_\discretionary {-}{}{}pbacktrack@{TwoDpfold\_\discretionary {-}{}{}pbacktrack}|hyperpage}{107}
\indexentry{TwoDpfold\_\discretionary {-}{}{}pbacktrack@{TwoDpfold\_\discretionary {-}{}{}pbacktrack}!kl_neighborhood_stochbt@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}|hyperpage}{107}
\indexentry{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}!TwoDpfold\_\discretionary {-}{}{}pbacktrack5@{TwoDpfold\_\discretionary {-}{}{}pbacktrack5}|hyperpage}{108}
\indexentry{TwoDpfold\_\discretionary {-}{}{}pbacktrack5@{TwoDpfold\_\discretionary {-}{}{}pbacktrack5}!kl_neighborhood_stochbt@{kl\_\discretionary {-}{}{}neighborhood\_\discretionary {-}{}{}stochbt}|hyperpage}{108}
\indexentry{Compute the Density of States@{Compute the Density of States}|hyperpage}{109}
\indexentry{dos@{dos}!density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states@{density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}|hyperpage}{109}
\indexentry{density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states@{density\_\discretionary {-}{}{}of\_\discretionary {-}{}{}states}!dos@{dos}|hyperpage}{109}
\indexentry{Parsing and Comparing -\/ Functions to Manipulate Structures@{Parsing and Comparing -\/ Functions to Manipulate Structures}|hyperpage}{110}
\indexentry{bondT@{bondT}|hyperpage}{111}
\indexentry{bondTEn@{bondTEn}|hyperpage}{112}
\indexentry{cofoldF@{cofoldF}|hyperpage}{113}
\indexentry{ConcEnt@{ConcEnt}|hyperpage}{114}
\indexentry{constrain@{constrain}|hyperpage}{115}
\indexentry{COORDINATE@{COORDINATE}|hyperpage}{116}
\indexentry{cpair@{cpair}|hyperpage}{117}
\indexentry{duplexT@{duplexT}|hyperpage}{118}
\indexentry{dupVar@{dupVar}|hyperpage}{119}
\indexentry{folden@{folden}|hyperpage}{120}
\indexentry{interact@{interact}|hyperpage}{121}
\indexentry{intermediate\_\discretionary {-}{}{}t@{intermediate\_\discretionary {-}{}{}t}|hyperpage}{122}
\indexentry{INTERVAL@{INTERVAL}|hyperpage}{123}
\indexentry{LIST@{LIST}|hyperpage}{124}
\indexentry{LST\_\discretionary {-}{}{}BUCKET@{LST\_\discretionary {-}{}{}BUCKET}|hyperpage}{125}
\indexentry{model\_\discretionary {-}{}{}detailsT@{model\_\discretionary {-}{}{}detailsT}|hyperpage}{126}
\indexentry{model\_\discretionary {-}{}{}detailsT@{model\_\discretionary {-}{}{}detailsT}!dangles@{dangles}|hyperpage}{126}
\indexentry{dangles@{dangles}!model_detailsT@{model\_\discretionary {-}{}{}detailsT}|hyperpage}{126}
\indexentry{move\_\discretionary {-}{}{}t@{move\_\discretionary {-}{}{}t}|hyperpage}{128}
\indexentry{PAIR@{PAIR}|hyperpage}{129}
\indexentry{pair\_\discretionary {-}{}{}info@{pair\_\discretionary {-}{}{}info}|hyperpage}{130}
\indexentry{pairpro@{pairpro}|hyperpage}{131}
\indexentry{paramT@{paramT}|hyperpage}{132}
\indexentry{path\_\discretionary {-}{}{}t@{path\_\discretionary {-}{}{}t}|hyperpage}{133}
\indexentry{pf\_\discretionary {-}{}{}paramT@{pf\_\discretionary {-}{}{}paramT}|hyperpage}{134}
\indexentry{pf\_\discretionary {-}{}{}paramT@{pf\_\discretionary {-}{}{}paramT}!alpha@{alpha}|hyperpage}{134}
\indexentry{alpha@{alpha}!pf_paramT@{pf\_\discretionary {-}{}{}paramT}|hyperpage}{134}
\indexentry{plist@{plist}|hyperpage}{136}
\indexentry{Postorder\_\discretionary {-}{}{}list@{Postorder\_\discretionary {-}{}{}list}|hyperpage}{137}
\indexentry{pu\_\discretionary {-}{}{}contrib@{pu\_\discretionary {-}{}{}contrib}|hyperpage}{138}
\indexentry{pu\_\discretionary {-}{}{}out@{pu\_\discretionary {-}{}{}out}|hyperpage}{139}
\indexentry{sect@{sect}|hyperpage}{140}
\indexentry{snoopT@{snoopT}|hyperpage}{141}
\indexentry{SOLUTION@{SOLUTION}|hyperpage}{142}
\indexentry{struct\_\discretionary {-}{}{}en@{struct\_\discretionary {-}{}{}en}|hyperpage}{143}
\indexentry{svm\_\discretionary {-}{}{}model@{svm\_\discretionary {-}{}{}model}|hyperpage}{144}
\indexentry{swString@{swString}|hyperpage}{145}
\indexentry{Tree@{Tree}|hyperpage}{146}
\indexentry{TwoDfold\_\discretionary {-}{}{}solution@{TwoDfold\_\discretionary {-}{}{}solution}|hyperpage}{147}
\indexentry{TwoDfold\_\discretionary {-}{}{}vars@{TwoDfold\_\discretionary {-}{}{}vars}|hyperpage}{148}
\indexentry{TwoDpfold\_\discretionary {-}{}{}solution@{TwoDpfold\_\discretionary {-}{}{}solution}|hyperpage}{150}
\indexentry{TwoDpfold\_\discretionary {-}{}{}vars@{TwoDpfold\_\discretionary {-}{}{}vars}|hyperpage}{151}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dfold.h}|hyperpage}{153}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/2Dpfold.h}|hyperpage}{155}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}|hyperpage}{156}
\indexentry{alifold.h@{alifold.h}!update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}|hyperpage}{158}
\indexentry{update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params@{update\_\discretionary {-}{}{}alifold\_\discretionary {-}{}{}params}!alifold.h@{alifold.h}|hyperpage}{158}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h}|hyperpage}{159}
\indexentry{cofold.h@{cofold.h}!get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes@{get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}|hyperpage}{160}
\indexentry{get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes@{get\_\discretionary {-}{}{}monomere\_\discretionary {-}{}{}mfes}!cofold.h@{cofold.h}|hyperpage}{160}
\indexentry{cofold.h@{cofold.h}!initialize\_\discretionary {-}{}{}cofold@{initialize\_\discretionary {-}{}{}cofold}|hyperpage}{160}
\indexentry{initialize\_\discretionary {-}{}{}cofold@{initialize\_\discretionary {-}{}{}cofold}!cofold.h@{cofold.h}|hyperpage}{160}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\discretionary {-}{}{}epars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/convert\_\discretionary {-}{}{}epars.h}|hyperpage}{161}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\discretionary {-}{}{}structures.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/data\_\discretionary {-}{}{}structures.h}|hyperpage}{162}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\discretionary {-}{}{}vars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/dist\_\discretionary {-}{}{}vars.h}|hyperpage}{165}
\indexentry{dist\_\discretionary {-}{}{}vars.h@{dist\_\discretionary {-}{}{}vars.h}!edit\_\discretionary {-}{}{}backtrack@{edit\_\discretionary {-}{}{}backtrack}|hyperpage}{165}
\indexentry{edit\_\discretionary {-}{}{}backtrack@{edit\_\discretionary {-}{}{}backtrack}!dist_vars.h@{dist\_\discretionary {-}{}{}vars.h}|hyperpage}{165}
\indexentry{dist\_\discretionary {-}{}{}vars.h@{dist\_\discretionary {-}{}{}vars.h}!cost\_\discretionary {-}{}{}matrix@{cost\_\discretionary {-}{}{}matrix}|hyperpage}{165}
\indexentry{cost\_\discretionary {-}{}{}matrix@{cost\_\discretionary {-}{}{}matrix}!dist_vars.h@{dist\_\discretionary {-}{}{}vars.h}|hyperpage}{165}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/duplex.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/duplex.h}|hyperpage}{167}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/edit\_\discretionary {-}{}{}cost.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/edit\_\discretionary {-}{}{}cost.h}|hyperpage}{168}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\discretionary {-}{}{}const.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!GASCONST@{GASCONST}|hyperpage}{169}
\indexentry{GASCONST@{GASCONST}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!K0@{K0}|hyperpage}{169}
\indexentry{K0@{K0}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!INF@{INF}|hyperpage}{169}
\indexentry{INF@{INF}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!FORBIDDEN@{FORBIDDEN}|hyperpage}{169}
\indexentry{FORBIDDEN@{FORBIDDEN}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{169}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!BONUS@{BONUS}|hyperpage}{170}
\indexentry{BONUS@{BONUS}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{170}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!NBPAIRS@{NBPAIRS}|hyperpage}{170}
\indexentry{NBPAIRS@{NBPAIRS}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{170}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!TURN@{TURN}|hyperpage}{170}
\indexentry{TURN@{TURN}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{170}
\indexentry{energy\_\discretionary {-}{}{}const.h@{energy\_\discretionary {-}{}{}const.h}!MAXLOOP@{MAXLOOP}|hyperpage}{170}
\indexentry{MAXLOOP@{MAXLOOP}!energy_const.h@{energy\_\discretionary {-}{}{}const.h}|hyperpage}{170}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h}|hyperpage}{171}
\indexentry{findpath.h@{findpath.h}!find\_\discretionary {-}{}{}saddle@{find\_\discretionary {-}{}{}saddle}|hyperpage}{171}
\indexentry{find\_\discretionary {-}{}{}saddle@{find\_\discretionary {-}{}{}saddle}!findpath.h@{findpath.h}|hyperpage}{171}
\indexentry{findpath.h@{findpath.h}!get\_\discretionary {-}{}{}path@{get\_\discretionary {-}{}{}path}|hyperpage}{172}
\indexentry{get\_\discretionary {-}{}{}path@{get\_\discretionary {-}{}{}path}!findpath.h@{findpath.h}|hyperpage}{172}
\indexentry{findpath.h@{findpath.h}!free\_\discretionary {-}{}{}path@{free\_\discretionary {-}{}{}path}|hyperpage}{172}
\indexentry{free\_\discretionary {-}{}{}path@{free\_\discretionary {-}{}{}path}!findpath.h@{findpath.h}|hyperpage}{172}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h}|hyperpage}{173}
\indexentry{fold.h@{fold.h}!parenthesis\_\discretionary {-}{}{}structure@{parenthesis\_\discretionary {-}{}{}structure}|hyperpage}{175}
\indexentry{parenthesis\_\discretionary {-}{}{}structure@{parenthesis\_\discretionary {-}{}{}structure}!fold.h@{fold.h}|hyperpage}{175}
\indexentry{fold.h@{fold.h}!parenthesis\_\discretionary {-}{}{}zuker@{parenthesis\_\discretionary {-}{}{}zuker}|hyperpage}{175}
\indexentry{parenthesis\_\discretionary {-}{}{}zuker@{parenthesis\_\discretionary {-}{}{}zuker}!fold.h@{fold.h}|hyperpage}{175}
\indexentry{fold.h@{fold.h}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}|hyperpage}{175}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move}!fold.h@{fold.h}|hyperpage}{175}
\indexentry{fold.h@{fold.h}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}|hyperpage}{176}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}move\_\discretionary {-}{}{}pt}!fold.h@{fold.h}|hyperpage}{176}
\indexentry{fold.h@{fold.h}!loop\_\discretionary {-}{}{}energy@{loop\_\discretionary {-}{}{}energy}|hyperpage}{176}
\indexentry{loop\_\discretionary {-}{}{}energy@{loop\_\discretionary {-}{}{}energy}!fold.h@{fold.h}|hyperpage}{176}
\indexentry{fold.h@{fold.h}!assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db@{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}|hyperpage}{177}
\indexentry{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db@{assign\_\discretionary {-}{}{}plist\_\discretionary {-}{}{}from\_\discretionary {-}{}{}db}!fold.h@{fold.h}|hyperpage}{177}
\indexentry{fold.h@{fold.h}!LoopEnergy@{LoopEnergy}|hyperpage}{177}
\indexentry{LoopEnergy@{LoopEnergy}!fold.h@{fold.h}|hyperpage}{177}
\indexentry{fold.h@{fold.h}!HairpinE@{HairpinE}|hyperpage}{177}
\indexentry{HairpinE@{HairpinE}!fold.h@{fold.h}|hyperpage}{177}
\indexentry{fold.h@{fold.h}!initialize\_\discretionary {-}{}{}fold@{initialize\_\discretionary {-}{}{}fold}|hyperpage}{177}
\indexentry{initialize\_\discretionary {-}{}{}fold@{initialize\_\discretionary {-}{}{}fold}!fold.h@{fold.h}|hyperpage}{177}
\indexentry{fold.h@{fold.h}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}|hyperpage}{177}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct}!fold.h@{fold.h}|hyperpage}{177}
\indexentry{fold.h@{fold.h}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}|hyperpage}{178}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}struct\_\discretionary {-}{}{}pt}!fold.h@{fold.h}|hyperpage}{178}
\indexentry{fold.h@{fold.h}!energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}|hyperpage}{179}
\indexentry{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct@{energy\_\discretionary {-}{}{}of\_\discretionary {-}{}{}circ\_\discretionary {-}{}{}struct}!fold.h@{fold.h}|hyperpage}{179}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold\_\discretionary {-}{}{}vars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold\_\discretionary {-}{}{}vars.h}|hyperpage}{180}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details@{set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}|hyperpage}{182}
\indexentry{set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details@{set\_\discretionary {-}{}{}model\_\discretionary {-}{}{}details}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{182}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!noLonelyPairs@{noLonelyPairs}|hyperpage}{182}
\indexentry{noLonelyPairs@{noLonelyPairs}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{182}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!dangles@{dangles}|hyperpage}{182}
\indexentry{dangles@{dangles}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{182}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!tetra\_\discretionary {-}{}{}loop@{tetra\_\discretionary {-}{}{}loop}|hyperpage}{183}
\indexentry{tetra\_\discretionary {-}{}{}loop@{tetra\_\discretionary {-}{}{}loop}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!energy\_\discretionary {-}{}{}set@{energy\_\discretionary {-}{}{}set}|hyperpage}{183}
\indexentry{energy\_\discretionary {-}{}{}set@{energy\_\discretionary {-}{}{}set}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!oldAliEn@{oldAliEn}|hyperpage}{183}
\indexentry{oldAliEn@{oldAliEn}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!ribo@{ribo}|hyperpage}{183}
\indexentry{ribo@{ribo}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!RibosumFile@{RibosumFile}|hyperpage}{183}
\indexentry{RibosumFile@{RibosumFile}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!nonstandards@{nonstandards}|hyperpage}{183}
\indexentry{nonstandards@{nonstandards}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!temperature@{temperature}|hyperpage}{183}
\indexentry{temperature@{temperature}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!james\_\discretionary {-}{}{}rule@{james\_\discretionary {-}{}{}rule}|hyperpage}{183}
\indexentry{james\_\discretionary {-}{}{}rule@{james\_\discretionary {-}{}{}rule}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!logML@{logML}|hyperpage}{183}
\indexentry{logML@{logML}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!cut\_\discretionary {-}{}{}point@{cut\_\discretionary {-}{}{}point}|hyperpage}{183}
\indexentry{cut\_\discretionary {-}{}{}point@{cut\_\discretionary {-}{}{}point}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{183}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!base\_\discretionary {-}{}{}pair@{base\_\discretionary {-}{}{}pair}|hyperpage}{184}
\indexentry{base\_\discretionary {-}{}{}pair@{base\_\discretionary {-}{}{}pair}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{184}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!pr@{pr}|hyperpage}{184}
\indexentry{pr@{pr}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{184}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!iindx@{iindx}|hyperpage}{184}
\indexentry{iindx@{iindx}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{184}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!pf\_\discretionary {-}{}{}scale@{pf\_\discretionary {-}{}{}scale}|hyperpage}{184}
\indexentry{pf\_\discretionary {-}{}{}scale@{pf\_\discretionary {-}{}{}scale}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{184}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!do\_\discretionary {-}{}{}backtrack@{do\_\discretionary {-}{}{}backtrack}|hyperpage}{184}
\indexentry{do\_\discretionary {-}{}{}backtrack@{do\_\discretionary {-}{}{}backtrack}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{184}
\indexentry{fold\_\discretionary {-}{}{}vars.h@{fold\_\discretionary {-}{}{}vars.h}!backtrack\_\discretionary {-}{}{}type@{backtrack\_\discretionary {-}{}{}type}|hyperpage}{185}
\indexentry{backtrack\_\discretionary {-}{}{}type@{backtrack\_\discretionary {-}{}{}type}!fold_vars.h@{fold\_\discretionary {-}{}{}vars.h}|hyperpage}{185}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/gquad.h}|hyperpage}{186}
\indexentry{gquad.h@{gquad.h}!get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix@{get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix}|hyperpage}{186}
\indexentry{get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix@{get\_\discretionary {-}{}{}gquad\_\discretionary {-}{}{}matrix}!gquad.h@{gquad.h}|hyperpage}{186}
\indexentry{gquad.h@{gquad.h}!parse\_\discretionary {-}{}{}gquad@{parse\_\discretionary {-}{}{}gquad}|hyperpage}{187}
\indexentry{parse\_\discretionary {-}{}{}gquad@{parse\_\discretionary {-}{}{}gquad}!gquad.h@{gquad.h}|hyperpage}{187}
\indexentry{gquad.h@{gquad.h}!backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop@{backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop}|hyperpage}{187}
\indexentry{backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop@{backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop}!gquad.h@{gquad.h}|hyperpage}{187}
\indexentry{gquad.h@{gquad.h}!backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L@{backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L}|hyperpage}{187}
\indexentry{backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L@{backtrack\_\discretionary {-}{}{}GQuad\_\discretionary {-}{}{}IntLoop\_\discretionary {-}{}{}L}!gquad.h@{gquad.h}|hyperpage}{187}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/inverse.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/inverse.h}|hyperpage}{189}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/Lfold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/Lfold.h}|hyperpage}{190}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/loop\_\discretionary {-}{}{}energies.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/loop\_\discretionary {-}{}{}energies.h}|hyperpage}{191}
\indexentry{loop\_\discretionary {-}{}{}energies.h@{loop\_\discretionary {-}{}{}energies.h}!E\_\discretionary {-}{}{}IntLoop@{E\_\discretionary {-}{}{}IntLoop}|hyperpage}{192}
\indexentry{E\_\discretionary {-}{}{}IntLoop@{E\_\discretionary {-}{}{}IntLoop}!loop_energies.h@{loop\_\discretionary {-}{}{}energies.h}|hyperpage}{192}
\indexentry{loop\_\discretionary {-}{}{}energies.h@{loop\_\discretionary {-}{}{}energies.h}!E\_\discretionary {-}{}{}Hairpin@{E\_\discretionary {-}{}{}Hairpin}|hyperpage}{193}
\indexentry{E\_\discretionary {-}{}{}Hairpin@{E\_\discretionary {-}{}{}Hairpin}!loop_energies.h@{loop\_\discretionary {-}{}{}energies.h}|hyperpage}{193}
\indexentry{loop\_\discretionary {-}{}{}energies.h@{loop\_\discretionary {-}{}{}energies.h}!E\_\discretionary {-}{}{}Stem@{E\_\discretionary {-}{}{}Stem}|hyperpage}{194}
\indexentry{E\_\discretionary {-}{}{}Stem@{E\_\discretionary {-}{}{}Stem}!loop_energies.h@{loop\_\discretionary {-}{}{}energies.h}|hyperpage}{194}
\indexentry{loop\_\discretionary {-}{}{}energies.h@{loop\_\discretionary {-}{}{}energies.h}!exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem@{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}|hyperpage}{195}
\indexentry{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem@{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Stem}!loop_energies.h@{loop\_\discretionary {-}{}{}energies.h}|hyperpage}{195}
\indexentry{loop\_\discretionary {-}{}{}energies.h@{loop\_\discretionary {-}{}{}energies.h}!exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin@{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}|hyperpage}{195}
\indexentry{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin@{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}Hairpin}!loop_energies.h@{loop\_\discretionary {-}{}{}energies.h}|hyperpage}{195}
\indexentry{loop\_\discretionary {-}{}{}energies.h@{loop\_\discretionary {-}{}{}energies.h}!exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop@{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}|hyperpage}{196}
\indexentry{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop@{exp\_\discretionary {-}{}{}E\_\discretionary {-}{}{}IntLoop}!loop_energies.h@{loop\_\discretionary {-}{}{}energies.h}|hyperpage}{196}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/LPfold.h}|hyperpage}{198}
\indexentry{LPfold.h@{LPfold.h}!init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP@{init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}|hyperpage}{199}
\indexentry{init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP@{init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}foldLP}!LPfold.h@{LPfold.h}|hyperpage}{199}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/MEA.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/MEA.h}|hyperpage}{200}
\indexentry{MEA.h@{MEA.h}!MEA@{MEA}|hyperpage}{200}
\indexentry{MEA@{MEA}!MEA.h@{MEA.h}|hyperpage}{200}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/mm.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/mm.h}|hyperpage}{201}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/naview.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/naview.h}|hyperpage}{202}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/params.h}|hyperpage}{203}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func.h}|hyperpage}{205}
\indexentry{part\_\discretionary {-}{}{}func.h@{part\_\discretionary {-}{}{}func.h}!init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{207}
\indexentry{init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{init\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!part_func.h@{part\_\discretionary {-}{}{}func.h}|hyperpage}{207}
\indexentry{part\_\discretionary {-}{}{}func.h@{part\_\discretionary {-}{}{}func.h}!centroid@{centroid}|hyperpage}{207}
\indexentry{centroid@{centroid}!part_func.h@{part\_\discretionary {-}{}{}func.h}|hyperpage}{207}
\indexentry{part\_\discretionary {-}{}{}func.h@{part\_\discretionary {-}{}{}func.h}!mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}|hyperpage}{207}
\indexentry{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist@{mean\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}dist}!part_func.h@{part\_\discretionary {-}{}{}func.h}|hyperpage}{207}
\indexentry{part\_\discretionary {-}{}{}func.h@{part\_\discretionary {-}{}{}func.h}!expLoopEnergy@{expLoopEnergy}|hyperpage}{207}
\indexentry{expLoopEnergy@{expLoopEnergy}!part_func.h@{part\_\discretionary {-}{}{}func.h}|hyperpage}{207}
\indexentry{part\_\discretionary {-}{}{}func.h@{part\_\discretionary {-}{}{}func.h}!expHairpinEnergy@{expHairpinEnergy}|hyperpage}{207}
\indexentry{expHairpinEnergy@{expHairpinEnergy}!part_func.h@{part\_\discretionary {-}{}{}func.h}|hyperpage}{207}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}|hyperpage}{208}
\indexentry{part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h@{part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}!get\_\discretionary {-}{}{}plist@{get\_\discretionary {-}{}{}plist}|hyperpage}{209}
\indexentry{get\_\discretionary {-}{}{}plist@{get\_\discretionary {-}{}{}plist}!part_func_co.h@{part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}|hyperpage}{209}
\indexentry{part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h@{part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}!init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}|hyperpage}{209}
\indexentry{init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold@{init\_\discretionary {-}{}{}co\_\discretionary {-}{}{}pf\_\discretionary {-}{}{}fold}!part_func_co.h@{part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}co.h}|hyperpage}{209}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\discretionary {-}{}{}func\_\discretionary {-}{}{}up.h}|hyperpage}{211}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot\_\discretionary {-}{}{}layouts.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/plot\_\discretionary {-}{}{}layouts.h}|hyperpage}{212}
\indexentry{plot\_\discretionary {-}{}{}layouts.h@{plot\_\discretionary {-}{}{}layouts.h}!VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE@{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}|hyperpage}{213}
\indexentry{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE@{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}SIMPLE}!plot_layouts.h@{plot\_\discretionary {-}{}{}layouts.h}|hyperpage}{213}
\indexentry{plot\_\discretionary {-}{}{}layouts.h@{plot\_\discretionary {-}{}{}layouts.h}!VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW@{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}|hyperpage}{213}
\indexentry{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW@{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}NAVIEW}!plot_layouts.h@{plot\_\discretionary {-}{}{}layouts.h}|hyperpage}{213}
\indexentry{plot\_\discretionary {-}{}{}layouts.h@{plot\_\discretionary {-}{}{}layouts.h}!VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR@{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}|hyperpage}{213}
\indexentry{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR@{VRNA\_\discretionary {-}{}{}PLOT\_\discretionary {-}{}{}TYPE\_\discretionary {-}{}{}CIRCULAR}!plot_layouts.h@{plot\_\discretionary {-}{}{}layouts.h}|hyperpage}{213}
\indexentry{plot\_\discretionary {-}{}{}layouts.h@{plot\_\discretionary {-}{}{}layouts.h}!simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates@{simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}|hyperpage}{214}
\indexentry{simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates@{simple\_\discretionary {-}{}{}xy\_\discretionary {-}{}{}coordinates}!plot_layouts.h@{plot\_\discretionary {-}{}{}layouts.h}|hyperpage}{214}
\indexentry{plot\_\discretionary {-}{}{}layouts.h@{plot\_\discretionary {-}{}{}layouts.h}!simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates@{simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}|hyperpage}{214}
\indexentry{simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates@{simple\_\discretionary {-}{}{}circplot\_\discretionary {-}{}{}coordinates}!plot_layouts.h@{plot\_\discretionary {-}{}{}layouts.h}|hyperpage}{214}
\indexentry{plot\_\discretionary {-}{}{}layouts.h@{plot\_\discretionary {-}{}{}layouts.h}!rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type@{rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}|hyperpage}{215}
\indexentry{rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type@{rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}type}!plot_layouts.h@{plot\_\discretionary {-}{}{}layouts.h}|hyperpage}{215}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h}|hyperpage}{216}
\indexentry{profiledist.h@{profiledist.h}!profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance@{profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}|hyperpage}{216}
\indexentry{profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance@{profile\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}!profiledist.h@{profiledist.h}|hyperpage}{216}
\indexentry{profiledist.h@{profiledist.h}!Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm@{Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}|hyperpage}{216}
\indexentry{Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm@{Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile\_\discretionary {-}{}{}bppm}!profiledist.h@{profiledist.h}|hyperpage}{216}
\indexentry{profiledist.h@{profiledist.h}!free\_\discretionary {-}{}{}profile@{free\_\discretionary {-}{}{}profile}|hyperpage}{217}
\indexentry{free\_\discretionary {-}{}{}profile@{free\_\discretionary {-}{}{}profile}!profiledist.h@{profiledist.h}|hyperpage}{217}
\indexentry{profiledist.h@{profiledist.h}!Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile@{Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}|hyperpage}{217}
\indexentry{Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile@{Make\_\discretionary {-}{}{}bp\_\discretionary {-}{}{}profile}!profiledist.h@{profiledist.h}|hyperpage}{217}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS\_\discretionary {-}{}{}dot.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/PS\_\discretionary {-}{}{}dot.h}|hyperpage}{218}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot@{PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}|hyperpage}{219}
\indexentry{PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot@{PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{219}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a@{PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}|hyperpage}{219}
\indexentry{PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a@{PS\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}a}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{219}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!gmlRNA@{gmlRNA}|hyperpage}{220}
\indexentry{gmlRNA@{gmlRNA}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{220}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot@{ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}|hyperpage}{220}
\indexentry{ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot@{ssv\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{220}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot@{svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}|hyperpage}{220}
\indexentry{svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot@{svg\_\discretionary {-}{}{}rna\_\discretionary {-}{}{}plot}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{220}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!xrna\_\discretionary {-}{}{}plot@{xrna\_\discretionary {-}{}{}plot}|hyperpage}{221}
\indexentry{xrna\_\discretionary {-}{}{}plot@{xrna\_\discretionary {-}{}{}plot}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{221}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list@{PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}|hyperpage}{221}
\indexentry{PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list@{PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot\_\discretionary {-}{}{}list}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{221}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln@{aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln}|hyperpage}{221}
\indexentry{aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln@{aliPS\_\discretionary {-}{}{}color\_\discretionary {-}{}{}aln}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{221}
\indexentry{PS\_\discretionary {-}{}{}dot.h@{PS\_\discretionary {-}{}{}dot.h}!PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot@{PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}|hyperpage}{222}
\indexentry{PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot@{PS\_\discretionary {-}{}{}dot\_\discretionary {-}{}{}plot}!PS_dot.h@{PS\_\discretionary {-}{}{}dot.h}|hyperpage}{222}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/read\_\discretionary {-}{}{}epars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/read\_\discretionary {-}{}{}epars.h}|hyperpage}{223}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/RNAstruct.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/RNAstruct.h}|hyperpage}{224}
\indexentry{RNAstruct.h@{RNAstruct.h}!b2HIT@{b2HIT}|hyperpage}{225}
\indexentry{b2HIT@{b2HIT}!RNAstruct.h@{RNAstruct.h}|hyperpage}{225}
\indexentry{RNAstruct.h@{RNAstruct.h}!b2C@{b2C}|hyperpage}{225}
\indexentry{b2C@{b2C}!RNAstruct.h@{RNAstruct.h}|hyperpage}{225}
\indexentry{RNAstruct.h@{RNAstruct.h}!b2Shapiro@{b2Shapiro}|hyperpage}{226}
\indexentry{b2Shapiro@{b2Shapiro}!RNAstruct.h@{RNAstruct.h}|hyperpage}{226}
\indexentry{RNAstruct.h@{RNAstruct.h}!add\_\discretionary {-}{}{}root@{add\_\discretionary {-}{}{}root}|hyperpage}{226}
\indexentry{add\_\discretionary {-}{}{}root@{add\_\discretionary {-}{}{}root}!RNAstruct.h@{RNAstruct.h}|hyperpage}{226}
\indexentry{RNAstruct.h@{RNAstruct.h}!expand\_\discretionary {-}{}{}Shapiro@{expand\_\discretionary {-}{}{}Shapiro}|hyperpage}{226}
\indexentry{expand\_\discretionary {-}{}{}Shapiro@{expand\_\discretionary {-}{}{}Shapiro}!RNAstruct.h@{RNAstruct.h}|hyperpage}{226}
\indexentry{RNAstruct.h@{RNAstruct.h}!expand\_\discretionary {-}{}{}Full@{expand\_\discretionary {-}{}{}Full}|hyperpage}{226}
\indexentry{expand\_\discretionary {-}{}{}Full@{expand\_\discretionary {-}{}{}Full}!RNAstruct.h@{RNAstruct.h}|hyperpage}{226}
\indexentry{RNAstruct.h@{RNAstruct.h}!unexpand\_\discretionary {-}{}{}Full@{unexpand\_\discretionary {-}{}{}Full}|hyperpage}{227}
\indexentry{unexpand\_\discretionary {-}{}{}Full@{unexpand\_\discretionary {-}{}{}Full}!RNAstruct.h@{RNAstruct.h}|hyperpage}{227}
\indexentry{RNAstruct.h@{RNAstruct.h}!unweight@{unweight}|hyperpage}{227}
\indexentry{unweight@{unweight}!RNAstruct.h@{RNAstruct.h}|hyperpage}{227}
\indexentry{RNAstruct.h@{RNAstruct.h}!unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F@{unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}|hyperpage}{227}
\indexentry{unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F@{unexpand\_\discretionary {-}{}{}aligned\_\discretionary {-}{}{}F}!RNAstruct.h@{RNAstruct.h}|hyperpage}{227}
\indexentry{RNAstruct.h@{RNAstruct.h}!parse\_\discretionary {-}{}{}structure@{parse\_\discretionary {-}{}{}structure}|hyperpage}{227}
\indexentry{parse\_\discretionary {-}{}{}structure@{parse\_\discretionary {-}{}{}structure}!RNAstruct.h@{RNAstruct.h}|hyperpage}{227}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/stringdist.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/stringdist.h}|hyperpage}{229}
\indexentry{stringdist.h@{stringdist.h}!Make\_\discretionary {-}{}{}swString@{Make\_\discretionary {-}{}{}swString}|hyperpage}{229}
\indexentry{Make\_\discretionary {-}{}{}swString@{Make\_\discretionary {-}{}{}swString}!stringdist.h@{stringdist.h}|hyperpage}{229}
\indexentry{stringdist.h@{stringdist.h}!string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance@{string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}|hyperpage}{229}
\indexentry{string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance@{string\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}!stringdist.h@{stringdist.h}|hyperpage}{229}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/subopt.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/subopt.h}|hyperpage}{231}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/treedist.h}|hyperpage}{232}
\indexentry{treedist.h@{treedist.h}!make\_\discretionary {-}{}{}tree@{make\_\discretionary {-}{}{}tree}|hyperpage}{232}
\indexentry{make\_\discretionary {-}{}{}tree@{make\_\discretionary {-}{}{}tree}!treedist.h@{treedist.h}|hyperpage}{232}
\indexentry{treedist.h@{treedist.h}!tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance@{tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}|hyperpage}{232}
\indexentry{tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance@{tree\_\discretionary {-}{}{}edit\_\discretionary {-}{}{}distance}!treedist.h@{treedist.h}|hyperpage}{232}
\indexentry{treedist.h@{treedist.h}!free\_\discretionary {-}{}{}tree@{free\_\discretionary {-}{}{}tree}|hyperpage}{233}
\indexentry{free\_\discretionary {-}{}{}tree@{free\_\discretionary {-}{}{}tree}!treedist.h@{treedist.h}|hyperpage}{233}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/utils.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/utils.h}|hyperpage}{234}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR}|hyperpage}{237}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}ERROR}!utils.h@{utils.h}|hyperpage}{237}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT}|hyperpage}{237}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}QUIT}!utils.h@{utils.h}|hyperpage}{237}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC}|hyperpage}{237}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}MISC}!utils.h@{utils.h}|hyperpage}{237}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}|hyperpage}{237}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}FASTA\_\discretionary {-}{}{}HEADER}!utils.h@{utils.h}|hyperpage}{237}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}|hyperpage}{237}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}SEQUENCE}!utils.h@{utils.h}|hyperpage}{237}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}|hyperpage}{237}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}CONSTRAINT}!utils.h@{utils.h}|hyperpage}{237}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION}|hyperpage}{237}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}TRUNCATION}!utils.h@{utils.h}|hyperpage}{237}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}REST}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}SPAN}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINES}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}BLANK\_\discretionary {-}{}{}LINE}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}NOSKIP\_\discretionary {-}{}{}COMMENTS}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT@{VRNA\_\discretionary {-}{}{}INPUT\_\discretionary {-}{}{}COMMENT}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}PIPE}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}DOT}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}X}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK}|hyperpage}{238}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ANG\_\discretionary {-}{}{}BRACK}!utils.h@{utils.h}|hyperpage}{238}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK}|hyperpage}{239}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}RND\_\discretionary {-}{}{}BRACK}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE}|hyperpage}{239}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}MULTILINE}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER}|hyperpage}{239}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}NO\_\discretionary {-}{}{}HEADER}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL}|hyperpage}{239}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}ALL}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G}|hyperpage}{239}
\indexentry{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G@{VRNA\_\discretionary {-}{}{}CONSTRAINT\_\discretionary {-}{}{}G}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE@{VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}|hyperpage}{239}
\indexentry{VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE@{VRNA\_\discretionary {-}{}{}OPTION\_\discretionary {-}{}{}MULTILINE}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!MIN2@{MIN2}|hyperpage}{239}
\indexentry{MIN2@{MIN2}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!MAX2@{MAX2}|hyperpage}{239}
\indexentry{MAX2@{MAX2}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!MIN3@{MIN3}|hyperpage}{239}
\indexentry{MIN3@{MIN3}!utils.h@{utils.h}|hyperpage}{239}
\indexentry{utils.h@{utils.h}!MAX3@{MAX3}|hyperpage}{240}
\indexentry{MAX3@{MAX3}!utils.h@{utils.h}|hyperpage}{240}
\indexentry{utils.h@{utils.h}!XSTR@{XSTR}|hyperpage}{240}
\indexentry{XSTR@{XSTR}!utils.h@{utils.h}|hyperpage}{240}
\indexentry{utils.h@{utils.h}!STR@{STR}|hyperpage}{240}
\indexentry{STR@{STR}!utils.h@{utils.h}|hyperpage}{240}
\indexentry{utils.h@{utils.h}!FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH@{FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}|hyperpage}{240}
\indexentry{FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH@{FILENAME\_\discretionary {-}{}{}MAX\_\discretionary {-}{}{}LENGTH}!utils.h@{utils.h}|hyperpage}{240}
\indexentry{utils.h@{utils.h}!FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH@{FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}|hyperpage}{240}
\indexentry{FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH@{FILENAME\_\discretionary {-}{}{}ID\_\discretionary {-}{}{}LENGTH}!utils.h@{utils.h}|hyperpage}{240}
\indexentry{utils.h@{utils.h}!space@{space}|hyperpage}{240}
\indexentry{space@{space}!utils.h@{utils.h}|hyperpage}{240}
\indexentry{utils.h@{utils.h}!xrealloc@{xrealloc}|hyperpage}{240}
\indexentry{xrealloc@{xrealloc}!utils.h@{utils.h}|hyperpage}{240}
\indexentry{utils.h@{utils.h}!nrerror@{nrerror}|hyperpage}{241}
\indexentry{nrerror@{nrerror}!utils.h@{utils.h}|hyperpage}{241}
\indexentry{utils.h@{utils.h}!warn\_\discretionary {-}{}{}user@{warn\_\discretionary {-}{}{}user}|hyperpage}{241}
\indexentry{warn\_\discretionary {-}{}{}user@{warn\_\discretionary {-}{}{}user}!utils.h@{utils.h}|hyperpage}{241}
\indexentry{utils.h@{utils.h}!urn@{urn}|hyperpage}{241}
\indexentry{urn@{urn}!utils.h@{utils.h}|hyperpage}{241}
\indexentry{utils.h@{utils.h}!int\_\discretionary {-}{}{}urn@{int\_\discretionary {-}{}{}urn}|hyperpage}{241}
\indexentry{int\_\discretionary {-}{}{}urn@{int\_\discretionary {-}{}{}urn}!utils.h@{utils.h}|hyperpage}{241}
\indexentry{utils.h@{utils.h}!time\_\discretionary {-}{}{}stamp@{time\_\discretionary {-}{}{}stamp}|hyperpage}{242}
\indexentry{time\_\discretionary {-}{}{}stamp@{time\_\discretionary {-}{}{}stamp}!utils.h@{utils.h}|hyperpage}{242}
\indexentry{utils.h@{utils.h}!random\_\discretionary {-}{}{}string@{random\_\discretionary {-}{}{}string}|hyperpage}{242}
\indexentry{random\_\discretionary {-}{}{}string@{random\_\discretionary {-}{}{}string}!utils.h@{utils.h}|hyperpage}{242}
\indexentry{utils.h@{utils.h}!hamming@{hamming}|hyperpage}{242}
\indexentry{hamming@{hamming}!utils.h@{utils.h}|hyperpage}{242}
\indexentry{utils.h@{utils.h}!hamming\_\discretionary {-}{}{}bound@{hamming\_\discretionary {-}{}{}bound}|hyperpage}{242}
\indexentry{hamming\_\discretionary {-}{}{}bound@{hamming\_\discretionary {-}{}{}bound}!utils.h@{utils.h}|hyperpage}{242}
\indexentry{utils.h@{utils.h}!get\_\discretionary {-}{}{}line@{get\_\discretionary {-}{}{}line}|hyperpage}{243}
\indexentry{get\_\discretionary {-}{}{}line@{get\_\discretionary {-}{}{}line}!utils.h@{utils.h}|hyperpage}{243}
\indexentry{utils.h@{utils.h}!get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line@{get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}|hyperpage}{243}
\indexentry{get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line@{get\_\discretionary {-}{}{}input\_\discretionary {-}{}{}line}!utils.h@{utils.h}|hyperpage}{243}
\indexentry{utils.h@{utils.h}!read\_\discretionary {-}{}{}record@{read\_\discretionary {-}{}{}record}|hyperpage}{244}
\indexentry{read\_\discretionary {-}{}{}record@{read\_\discretionary {-}{}{}record}!utils.h@{utils.h}|hyperpage}{244}
\indexentry{utils.h@{utils.h}!pack\_\discretionary {-}{}{}structure@{pack\_\discretionary {-}{}{}structure}|hyperpage}{245}
\indexentry{pack\_\discretionary {-}{}{}structure@{pack\_\discretionary {-}{}{}structure}!utils.h@{utils.h}|hyperpage}{245}
\indexentry{utils.h@{utils.h}!unpack\_\discretionary {-}{}{}structure@{unpack\_\discretionary {-}{}{}structure}|hyperpage}{245}
\indexentry{unpack\_\discretionary {-}{}{}structure@{unpack\_\discretionary {-}{}{}structure}!utils.h@{utils.h}|hyperpage}{245}
\indexentry{utils.h@{utils.h}!make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table@{make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}|hyperpage}{246}
\indexentry{make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table@{make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}!utils.h@{utils.h}|hyperpage}{246}
\indexentry{utils.h@{utils.h}!copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table@{copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}|hyperpage}{246}
\indexentry{copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table@{copy\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}!utils.h@{utils.h}|hyperpage}{246}
\indexentry{utils.h@{utils.h}!alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table@{alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}|hyperpage}{246}
\indexentry{alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table@{alimake\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table}!utils.h@{utils.h}|hyperpage}{246}
\indexentry{utils.h@{utils.h}!make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop@{make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}|hyperpage}{246}
\indexentry{make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop@{make\_\discretionary {-}{}{}pair\_\discretionary {-}{}{}table\_\discretionary {-}{}{}snoop}!utils.h@{utils.h}|hyperpage}{246}
\indexentry{utils.h@{utils.h}!make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt@{make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt}|hyperpage}{246}
\indexentry{make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt@{make\_\discretionary {-}{}{}loop\_\discretionary {-}{}{}index\_\discretionary {-}{}{}pt}!utils.h@{utils.h}|hyperpage}{246}
\indexentry{utils.h@{utils.h}!print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq@{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}|hyperpage}{247}
\indexentry{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq@{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq}!utils.h@{utils.h}|hyperpage}{247}
\indexentry{utils.h@{utils.h}!print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str@{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}|hyperpage}{247}
\indexentry{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str@{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}input\_\discretionary {-}{}{}seq\_\discretionary {-}{}{}str}!utils.h@{utils.h}|hyperpage}{247}
\indexentry{utils.h@{utils.h}!print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint@{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}|hyperpage}{247}
\indexentry{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint@{print\_\discretionary {-}{}{}tty\_\discretionary {-}{}{}constraint}!utils.h@{utils.h}|hyperpage}{247}
\indexentry{utils.h@{utils.h}!str\_\discretionary {-}{}{}DNA2RNA@{str\_\discretionary {-}{}{}DNA2RNA}|hyperpage}{247}
\indexentry{str\_\discretionary {-}{}{}DNA2RNA@{str\_\discretionary {-}{}{}DNA2RNA}!utils.h@{utils.h}|hyperpage}{247}
\indexentry{utils.h@{utils.h}!str\_\discretionary {-}{}{}uppercase@{str\_\discretionary {-}{}{}uppercase}|hyperpage}{247}
\indexentry{str\_\discretionary {-}{}{}uppercase@{str\_\discretionary {-}{}{}uppercase}!utils.h@{utils.h}|hyperpage}{247}
\indexentry{utils.h@{utils.h}!get\_\discretionary {-}{}{}iindx@{get\_\discretionary {-}{}{}iindx}|hyperpage}{248}
\indexentry{get\_\discretionary {-}{}{}iindx@{get\_\discretionary {-}{}{}iindx}!utils.h@{utils.h}|hyperpage}{248}
\indexentry{utils.h@{utils.h}!get\_\discretionary {-}{}{}indx@{get\_\discretionary {-}{}{}indx}|hyperpage}{248}
\indexentry{get\_\discretionary {-}{}{}indx@{get\_\discretionary {-}{}{}indx}!utils.h@{utils.h}|hyperpage}{248}
\indexentry{utils.h@{utils.h}!constrain\_\discretionary {-}{}{}ptypes@{constrain\_\discretionary {-}{}{}ptypes}|hyperpage}{248}
\indexentry{constrain\_\discretionary {-}{}{}ptypes@{constrain\_\discretionary {-}{}{}ptypes}!utils.h@{utils.h}|hyperpage}{248}
\indexentry{utils.h@{utils.h}!xsubi@{xsubi}|hyperpage}{249}
\indexentry{xsubi@{xsubi}!utils.h@{utils.h}|hyperpage}{249}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}epars.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}epars.h}|hyperpage}{250}
\indexentry{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}intloops.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/1.8.4\_\discretionary {-}{}{}intloops.h}|hyperpage}{251}