# HybridRNA Member List

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

AccessFold(const double gamma, const float percent, const int maximumstructures, const int window, const int maxinternalloopsize=30) | HybridRNA |
AddComment(const char comment[], const int structurenumber=1) | RNA |
BreakPseudoknot(const bool minimum_energy=true, const int structurenumber=0) | RNA |
CalculateFreeEnergy(const int structurenumber=1, const bool UseSimpleMBLoopRules=false) | RNA |
commonconstructor() | HybridRNA | `[private]`
ContainsPseudoknot(const int structurenumber) | RNA |
CopyThermodynamic(Thermodynamics *thermo) | Thermodynamics |
data | Thermodynamics | `[protected]`
DetermineDrawingCoordinates(const int height, const int width, const int structurenumber=1) | RNA |
energyread | Thermodynamics | `[protected]`
enthalpy | Thermodynamics | `[protected]`
ErrorCode | RNA | `[protected]`
FileReader(const char filename[], const int type) | RNA | `[protected]`
FoldBimolecular(const float percent, const int maximumstructures, const int window, const char savefile[]="", const int maxinternalloopsize=30) | HybridRNA |
FoldDuplex(const float percent, const int maximumstructures, const int window, const int maxinternalloopsize=30) | HybridRNA |
FoldSingleStrand(const float percent, const int maximumstructures, const int window, const char savefile[]="", const int maxinternalloopsize=30, bool mfeonly=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, const double deltaG) | RNA |
GetBackboneType() | RNA |
GetCommentString(const int structurenumber=1) | RNA |
GetDat(char *loop, char *stackf, char *tstackh, char *tstacki, char *tloop, char *miscloop, char *danglef, char *int22, char *int21, char *coax, char *tstackcoax, char *coaxstack, char *tstack, char *tstackm, char *triloop, char *int11, char *hexaloop, char *tstacki23, char *tstacki1n, char *datapath, bool isRNA, bool isEnthalpy=false) | Thermodynamics | `[protected]`
GetDatatable() | Thermodynamics |
GetEnergyRead() | Thermodynamics |
GetEnsembleEnergy() | RNA |
GetEnthalpyTable() | Thermodynamics |
GetErrorCode() | HybridRNA |
GetErrorMessage(const int error) | HybridRNA |
GetErrorMessageString(const int error) | 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 |
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 |
GetPairProbability(const int i, const int j) | RNA |
GetProgress() | RNA |
GetRNA1() | HybridRNA |
GetRNA2() | HybridRNA |
GetSequenceLength() | RNA |
GetStructure() | RNA |
GetStructureNumber() | RNA |
GetTemperature() | Thermodynamics |
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 |
isrna | Thermodynamics |
MaximizeExpectedAccuracy(const double maxPercent, const int maxStructures, const int window, const double gamma=1.0) | RNA |
PartitionFunction(const char savefile[]="", double temperature=-10.0) | RNA |
PartitionFunctionBimolecular(const char savefile[]="") | HybridRNA |
pfdata | RNA | `[protected]`
PredictProbablePairs(const float probability=0) | RNA |
ProbKnot(int iterations=1, int MinHelixLength=1) | RNA |
ProbKnotFromSample(int iterations=1, int MinHelixLength=1) | RNA |
progress | RNA | `[protected]`
Q | RNA | `[protected]`
ReadConstraints(const char filename[]) | RNA |
ReadDSO(const char filename[]) | RNA |
ReadExperimentalPairBonus(const char filename[], double const experimentalOffset, double const experimentalScaling) | RNA |
ReadSHAPE(const char filename[], const double parameter1, const double parameter2, std::string modifier="SHAPE", const bool IsPseudoEnergy=true) | RNA |
ReadSHAPE(const char filename[], const double parameter1, const double parameter2, const double ssm, const double ssb, std::string modifier="SHAPE") | RNA |
ReadSSO(const char filename[]) | RNA |
ReadThermodynamic(const char *pathname=NULL) | Thermodynamics |
ReFoldSingleStrand(const float percent, const int maximumstructures, const int window) | RNA |
RemoveBasePair(const int i, const int structurenumber=1) | RNA |
RemoveConstraints() | RNA |
RemovePairs(const int structurenumber=1) | RNA |
RNA(const char sequence[], const bool IsRNA=true) | RNA |
RNA(const char filename[], const int type, const bool IsRNA=true) | RNA |
RNA(const bool IsRNA=true) | RNA |
sequences | HybridRNA | `[private]`
SetExtrinsic(int i, int j, double k) | RNA |
SetForbidIntramolecular(const bool forbid) | HybridRNA |
SetModifier(std::string modifier) | RNA |
SetProgress(TProgressDialog &Progress) | HybridRNA |
SetTemperature(double temperature) | Thermodynamics |
SetupBimolecular() | HybridRNA | `[private]`
SpecifyPair(const int i, const int j, const int structurenumber=1) | RNA |
Stochastic(const int structures, const int seed=1) | RNA |
StopProgress() | HybridRNA |
temp | Thermodynamics | `[protected]`
Thermodynamics(const bool ISRNA=true) | Thermodynamics |
v | RNA | `[protected]`
w | RNA | `[protected]`
w3 | RNA | `[protected]`
w5 | RNA | `[protected]`
wca | RNA | `[protected]`
wcoax | RNA | `[protected]`
wl | RNA | `[protected]`
wmb | RNA | `[protected]`
wmbl | RNA | `[protected]`
WriteConstraints(const char filename[]) | RNA |
WriteCt(const char filename[], bool append=false) | RNA |
WriteDotBracket(const char filename[]) | RNA |
WriteThermodynamicDetails(const char filename[], const bool UseSimpleMBLoopRules=false) | RNA |
~HybridRNA() | HybridRNA |
~RNA() | RNA |
~Thermodynamics() | Thermodynamics |