RNAstructure Classes  Version 5.8.1
RNA Member List

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

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
ContainsPseudoknot(const int structurenumber)RNA
CopyThermodynamic(Thermodynamics *thermo)Thermodynamics
ctRNAprivate
dataThermodynamicsprotected
DetermineDrawingCoordinates(const int height, const int width, const int structurenumber=1)RNA
drawallocatedRNAprivate
energyallocatedRNAprivate
energyreadThermodynamicsprotected
enthalpyThermodynamicsprotected
ErrorCodeRNAprotected
evRNAprivate
ewRNAprivate
ew2RNAprivate
ew3RNAprivate
ew5RNAprivate
ewmbRNAprivate
ewmb2RNAprivate
fceRNAprivate
FileReader(const char filename[], const int type)RNAprotected
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)RNA
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
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)Thermodynamicsprotected
GetDatatable()Thermodynamics
GetEnergyRead()Thermodynamics
GetEnsembleEnergy()RNA
GetEnthalpyTable()Thermodynamics
GetErrorCode()RNA
GetErrorMessage(const int error)RNA
GetErrorMessageString(const int error)RNA
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
GetSequenceLength()RNA
GetStructure()RNA
GetStructureNumber()RNA
GetTemperature()Thermodynamics
isrnaThermodynamics
lfceRNAprivate
MaximizeExpectedAccuracy(const double maxPercent=20, const int maxStructures=20, const int window=1, const double gamma=1.0)RNA
modRNAprivate
PartitionFunction(const char savefile[]="", double temperature=-10.0)RNA
partitionfunctionallocatedRNAprivate
pfdataRNAprotected
PredictProbablePairs(const float probability=0)RNA
ProbKnot(int iterations=1, int MinHelixLength=1)RNA
ProbKnotFromSample(int iterations=1, int MinHelixLength=1)RNA
progressRNAprotected
QRNAprotected
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=20, const int maximumstructures=20, const int window=5)RNA
RemoveBasePair(const int i, const int structurenumber=1)RNA
RemoveConstraints()RNA
RemovePairs(const int structurenumber=1)RNA
ResetError()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
SetExtrinsic(int i, int j, double k)RNA
SetProgress(TProgressDialog &Progress)RNA
SetTemperature(double temperature)Thermodynamics
SpecifyPair(const int i, const int j, const int structurenumber=1)RNA
Stochastic(const int structures=1000, const int seed=1)RNA
StopProgress()RNA
structurecoordinatesRNAprivate
tempThermodynamicsprotected
Thermodynamics(const bool ISRNA=true)Thermodynamics
vRNAprotected
vminRNAprivate
wRNAprotected
w3RNAprotected
w5RNAprotected
wcaRNAprotected
wcoaxRNAprotected
wlRNAprotected
wmbRNAprotected
wmblRNAprotected
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
~RNA()RNA
~Thermodynamics()Thermodynamics