| RNAstructure Classes Version 6.2

HybridRNA Member List

This is the complete list of members for HybridRNA, including all inherited members.

AccessFold(const double gamma=0.4, const float percent=50, const int maximumstructures=20, const int window=0, const int maxinternalloopsize=30) | HybridRNA |
AddComment(const char comment[], const int structurenumber=1) | RNA |
BreakPseudoknot(const bool minimum_energy=true, const int structurenumber=0, const bool useFastMethod=true) | RNA |
CalculateFreeEnergy(const int structurenumber=1, const bool UseSimpleMBLoopRules=false) | RNA |
ClearEnergies() | Thermodynamics |
ClearEnthalpies() | Thermodynamics |
commonconstructor(const char fileNameOrsequence1[], const int fileType1, const char fileNameOrsequence2[], const int fileType2) | HybridRNA | private
ContainsPseudoknot(const int structurenumber) | RNA |
copied | Thermodynamics | protected
CopyThermo(Thermodynamics &copy) | RNA |
Thermodynamics::CopyThermo(const Thermodynamics &copy) | Thermodynamics | protected virtual
data | Thermodynamics | protected
DetermineDrawingCoordinates(const int height, const int width, const int structurenumber=1) | RNA |
EnsureStructureCapcacity(const int minimumStructures) | RNA |
enthalpy | Thermodynamics | protected
ErrorCode | RNA | protected
ExteriorLoopCorrection(const int structurenumber, const bool UseSimpleMBLoopRules, int min_index, int max_index) | RNA |
FileReader(const char filename[], const RNAInputType fileType) | RNA | protected
FoldBimolecular(const float percent=10, const int maximumstructures=20, const int window=0, const char savefile[]="", const int maxinternalloopsize=30) | HybridRNA |
FoldDuplex(const float percent=40, const int maximumstructures=10, const int window=0, const int maxinternalloopsize=30) | HybridRNA |
FoldSingleStrand(const float percent=20, const int maximumstructures=20, const int window=5, const char savefile[]="", const int maxinternalloopsize=30, bool mfeonly=false, bool simple_iloops=true, bool disablecoax=false, bool allow_isolated=false) | RNA |
forbidunimolecular | HybridRNA | private
ForceDoubleStranded(const int i) | RNA |
ForceFMNCleavage(const int i) | RNA |
ForceMaximumPairingDistance(const int distance) | RNA |
ForceModification(const int i) | RNA |
ForcePair(const int i, const int j) | RNA |
ForceProhibitPair(const int i, const int j) | RNA |
ForceSingleStranded(const int i) | RNA |
GenerateAllSuboptimalStructures(const float percent=5, const double deltaG=0.6) | RNA |
GetAlphabetName() const | Thermodynamics |
GetBackboneType() const | RNA |
GetCommentString(const int structurenumber=1) | RNA |
GetDatatable() | Thermodynamics |
GetEnergyRead() const | Thermodynamics |
GetEnsembleDefect(const int structurenumber=1, const int start=0, const int end=0, const char filename[]="") | RNA |
GetEnsembleEnergy() | RNA |
GetEnthalpyTable(const char *alphabet=NULL) | Thermodynamics |
GetErrorCode() | HybridRNA |
RNA::GetErrorCode() const | RNA |
GetErrorDetails() const | RNA |
GetErrorMessage(const int error) | HybridRNA |
GetErrorMessageString(const int error) const | RNA |
GetForbidIntramolecular() | HybridRNA |
GetForcedDoubleStranded(const int constraintnumber) | RNA |
GetForcedFMNCleavage(const int constraintnumber) | RNA |
GetForcedModification(const int constraintnumber) | RNA |
GetForcedPair(const int constraintnumber, const bool fiveprime) | RNA |
GetForcedProhibitedPair(const int constraintnumber, const bool fiveprime) | RNA |
GetForcedSingleStranded(const int constraintnumber) | RNA |
GetFreeEnergy(const int structurenumber) | RNA |
GetFullErrorMessage() const | RNA |
GetLabelXCoordinate(const int i) | RNA |
GetLabelYCoordinate(const int i) | RNA |
GetMaximumPairingDistance() | RNA |
GetNucleotide(const int i) | RNA |
GetNucleotideXCoordinate(const int i) | RNA |
GetNucleotideYCoordinate(const int i) | RNA |
GetNumberOfForcedDoubleStranded() | RNA |
GetNumberOfForcedFMNCleavages() | RNA |
GetNumberOfForcedModifications() | RNA |
GetNumberOfForcedPairs() | RNA |
GetNumberOfForcedProhibitedPairs() | RNA |
GetNumberOfForcedSingleStranded() | RNA |
GetPair(const int i, const int structurenumber=1) | RNA |
GetPairEnergy(const int i, const int j) | RNA |
GetPairProbabilities(double *arr, const int size) | RNA |
GetPairProbability(const int i, const int j) | RNA |
GetProgress() | RNA |
GetRNA1() | HybridRNA |
GetRNA2() | HybridRNA |
GetSequence() const | RNA |
GetSequence(size_t start, size_t length=std::string::npos) const | RNA |
GetSequenceLength() const | RNA |
GetStructure() | RNA |
GetStructureNumber() const | RNA |
GetTemperature() const | Thermodynamics |
GetVprimeQ(const int i, const int j) | RNA |
GetW(const int i, const int j) | RNA |
HybridRNA(const char filename1[], const int type1, const char filename2[], const int type2, Thermodynamics *copyThermo) | HybridRNA |
HybridRNA(const char sequence1[], const char sequence2[], const bool IsRNA=true) | HybridRNA |
HybridRNA(const char filename1[], const int type1, const char filename2[], const int type2, const bool IsRNA=true) | HybridRNA |
HybridRNA(const char filename1[], const int type1, const char filename2[], const int type2, const char *alphabet) | HybridRNA |
init(const char *sequenceOrFileName, const RNAInputType fileType, const bool allowUnknownBases=false, const bool skipThermoTables=false) | RNA | protected
IsAlphabetRead() const | Thermodynamics |
isrna | Thermodynamics |
MaximizeExpectedAccuracy(const double maxPercent=20, const int maxStructures=20, const int window=1, const double gamma=1.0) | RNA |
nominal_alphabetName | Thermodynamics | protected
nominal_temperature | Thermodynamics | protected
PartitionFunction(const char savefile[]="", double temperature=-10.0, bool disablecoax=false, bool restoreSHAPE=true, bool allowisolated=false, int maxinter=30) | RNA |
PartitionFunctionBimolecular(const char savefile[]="") | HybridRNA |
pfdata | RNA | protected
PredictProbablePairs(const float probability=0) | RNA |
ProbKnot(int iterations=1, int MinHelixLength=1, double threshold=0) | RNA |
ProbKnotFromSample(int iterations=1, int MinHelixLength=1, double threshold=0) | RNA |
progress | RNA | protected
Q | RNA | protected
ReadConstraints(const char filename[]) | RNA |
ReadDMS(const char filename[], const bool bynt=false) | RNA |
ReadDSO(const char filename[]) | RNA |
ReadExperimentalPairBonus(const char filename[], double const experimentalOffset, double const experimentalScaling) | RNA |
ReadSHAPE(const char filename[], const double slope, const double intercept, RestraintType modifier=RESTRAINT_SHAPE, const bool IsPseudoEnergy=true) | RNA |
ReadSHAPE(const char filename[], const double dsSlope, const double dsIntercept, const double ssSlope, const double ssIntercept, RestraintType modifier=RESTRAINT_SHAPE) | RNA |
ReadSSO(const char filename[]) | RNA |
ReadThermodynamic(const char *directory=NULL, const char *alphabet=NULL, const double temperature=-1.0) | Thermodynamics |
ReFoldSingleStrand(const float percent=20, const int maximumstructures=20, const int window=5) | RNA |
ReloadDataTables(const double new_temperature=-1.0) | Thermodynamics |
RemoveBasePair(const int i, const int structurenumber=1) | RNA |
RemoveConstraints() | RNA |
RemovePairs(const int structurenumber=1, bool removeIfLastStructure=true) | RNA |
ResetError() | RNA |
RNA(const char sequence[], const bool IsRNA=true) | RNA |
RNA(const char filepathOrSequence[], const RNAInputType fileType, const char *const alphabetName, const bool allowUnknownBases=false, const bool skipThermoTables=false) | RNA |
RNA(const char filepathOrSequence[], const RNAInputType fileType, const Thermodynamics *copyThermo) | RNA |
RNA(const char filename[], const RNAInputType fileType, const bool IsRNA=true) | RNA |
RNA(const bool IsRNA=true) | RNA |
Rsample(const vector< double > &experimentalRestraints, RsampleData &refdata, const int randomSeed=0, const char savefile[]="", const double cparam=0.5, const double offset=1.10, const int numsamples=10000) | RNA |
sequences | HybridRNA | private
SetConstraints(vector< int > ss) | RNA |
SetErrorDetails(const string &details) | RNA |
SetExtrinsic(int i, int j, double k) | RNA |
SetForbidIntramolecular(const bool forbid) | HybridRNA |
SetProgress(ProgressHandler &Progress) | HybridRNA |
SetSequenceLabel(const string &label) | RNA |
SetTemperature(double temperature) | Thermodynamics |
SetupBimolecular() | HybridRNA | private
skipThermoTables | Thermodynamics | protected
SpecifyPair(const int i, const int j, const int structurenumber=1) | RNA |
Stochastic(const int structures=1000, const int seed=1) | RNA |
StopProgress() | HybridRNA |
Thermodynamics(const bool isRNA=true, const char *const alphabetName=NULL, const double temperature=310.15) | Thermodynamics |
Thermodynamics(const Thermodynamics &copyThermo) | Thermodynamics |
v | RNA | protected
VerifyThermodynamic() | Thermodynamics |
w | RNA | protected
w3 | RNA | protected
w5 | RNA | protected
wca | RNA | protected
wcoax | RNA | protected
wl | RNA | protected
wlc | RNA | protected
wmb | RNA | protected
wmbl | RNA | protected
WriteConstraints(const char filename[]) | RNA |
WriteCt(const char filename[], bool append=false, CTCommentProvider &commentProvider=CTComments::Energy) const | RNA |
WriteDotBracket(const char filename[], const int structurenumber=-1, const DotBracketFormat format=DBN_FMT_MULTI_TITLE, CTCommentProvider &commentProvider=CTComments::Energy) const | RNA |
WriteThermodynamicDetails(const char filename[], const bool UseSimpleMBLoopRules=false) | RNA |
~HybridRNA() | HybridRNA |
~RNA() | RNA |
~Thermodynamics() | Thermodynamics |