, including all inherited members.
AddComment(const char comment[], const int structurenumber=1) | RNA | |
bestdecomposition(int nuctstart, int nucend, int currentstart, int currentend, int *beststart, int *bestend, int missingstart, int missingend) | design | [private] |
BreakPseudoknot(const bool minimum_energy=true, const int structurenumber=0) | RNA | |
CalculateFreeEnergy(const int structurenumber=1, const bool UseSimpleMBLoopRules=false) | RNA | |
closeenoughtocut(int i, int j, int nucstart, int nucend, int missingstart, int missingend, double CLOSENESS) | design | [private] |
ContainsPseudoknot(const int structurenumber) | RNA | |
CopyThermodynamic(Thermodynamics *thermo) | Thermodynamics | |
data | Thermodynamics | [protected] |
decompose(int nucstart, int nucend, int currentdepth, int maxdepth, int numbering, int **tree, int missingstart=0, int missingend=0) | design | [private] |
design(const char filename[], const bool IsRNA=true) | design | |
design_sequence(const double pernucdefect, const bool random, const int maxdepth=5) | design | |
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] |
FillSequence(int start, int end, int missingstart, int missingend, bool random, randomnumber *dice) | design | [private] |
FindFragments(int **tree, int level, int start, int stop, int missingstart, int missingstop, vector< int > *stackstart, vector< int > *stackend, vector< int > *stackmissingstart, vector< int > *stackmissingend, vector< int > *stackfragmentdepth) | design | [private] |
FoldSingleStrand(const float percent, const int maximumstructures, const int window, const char savefile[]="", const int maxinternalloopsize=30) | 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 | |
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() | 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 | |
isrna | Thermodynamics | |
MapNuctoFragment(int j, int start, int missingstart, int missingend) | design | [private] |
marktree(int beststart, int bestend, int nucstart, int nucend, int missingstart, int missingend, int numbering, int currentdepth, int **tree) | design | [private] |
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 | |
PredictProbablePairs(const float probability=0) | RNA | |
ProbKnot(int iterations=1, int MinHelixLength=1) | RNA | |
progress | 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, const bool IsPseudoEnergy=true) | RNA | |
ReadSHAPE(const char filename[], const double parameter1, const double parameter2, const double ssm, const double ssb) | 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 | |
SelectSequence(int **tree, bool random, int depth, const double pernucdefect, long seed=1) | design | [private] |
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, const int seed=1) | RNA | |
StopProgress() | RNA | |
temp | Thermodynamics | [protected] |
Thermodynamics(const bool ISRNA=true) | Thermodynamics | |
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 | |