# Oligowalk_object Member List

This is the complete list of members for Oligowalk_object, 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 |
CommonConstructor() | Oligowalk_object | `[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]`
FoldSingleStrand(const float percent, const int maximumstructures, const int window, const char savefile[]="", const int maxinternalloopsize=30, bool mfeonly=false) | 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, const double deltaG) | RNA |
GetBackboneType() | RNA |
GetBreakTargetDG(const int index) | Oligowalk_object |
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 |
GetDuplexDG(const int index) | Oligowalk_object |
GetEnergyRead() | Thermodynamics |
GetEnsembleEnergy() | RNA |
GetEnthalpyTable() | Thermodynamics |
GetErrorCode() | RNA |
GetErrorMessage(const int error) | Oligowalk_object |
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 |
GetOligoOligoDG(const int index) | Oligowalk_object |
GetOligoSelfDG(const int index) | Oligowalk_object |
GetOverallDG(const int index) | Oligowalk_object |
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 |
GetTm(const int index) | Oligowalk_object |
isrna | Thermodynamics |
length | Oligowalk_object | `[private]`
MaximizeExpectedAccuracy(const double maxPercent, const int maxStructures, const int window, const double gamma=1.0) | RNA |
numofsubstructures | Oligowalk_object | `[private]`
OligoScreen(const char infilename[], const char outfilename[]) | Oligowalk_object |
Oligowalk(const int oligo_length, const bool isDNA, const int option, const double oligo_concentration, const int usesub, const int start, const int stop) | Oligowalk_object |
Oligowalk_object(const char sequence[]) | Oligowalk_object |
Oligowalk_object(const char filename[], const int type) | Oligowalk_object |
Oligowalk_object(const bool IsRNA=true) | Oligowalk_object |
PartitionFunction(const char savefile[]="", double temperature=-10.0) | RNA |
pfdata | RNA | `[protected]`
PredictProbablePairs(const float probability=0) | RNA |
prefilter | Oligowalk_object | `[private]`
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 |
SetExtrinsic(int i, int j, double k) | RNA |
SetModifier(std::string modifier) | 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, const int seed=1) | RNA |
StopProgress() | RNA |
table | Oligowalk_object | `[private]`
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 |
WriteReport(const char outputfilename[], const int oligo_length, const bool isDNA, const int option, const double oligo_concentration, const int usesub, const int start, const int stop) | Oligowalk_object |
WriteThermodynamicDetails(const char filename[], const bool UseSimpleMBLoopRules=false) | RNA |
~Oligowalk_object() | Oligowalk_object |
~RNA() | RNA |
~Thermodynamics() | Thermodynamics |