, 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] |
| Debug1(int start, int end, int missingstart, int missingend, char *sequence, RNA *fragment) | design | [private] |
| decompose(int nucstart, int nucend, int currentdepth, int maxdepth, int **tree, int missingstart=0, int missingend=0) | design | [private] |
| defectweighted | design | [private] |
| design(const char filename[], const bool IsRNA=true) | design | |
| design_sequence(const double pernucdefect, const bool random, const int maxdepth=5, bool heuristic=false, int MaxRedesignC=10, int MaxMutateC=4, int MaxLeafRedesignC=3, long randomSeed=1L) | 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, vector< vector< string > > &Helices, vector< vector< string > > &Loops) | 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=20, const int maximumstructures=20, const int window=5, 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=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) | Thermodynamics | [protected] |
| GetDatatable() | Thermodynamics | |
| GetDefect(int start, int end, int missingstart, int missingend, vector< double > &def, double &defect, RNA *fragment) | design | [private] |
| 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 | |
| leafdesign(int start, int end, int missingstart, int missingend, bool random, randomnumber *dice, vector< vector< string > > *Helices, vector< vector< string > > *Loops, double pernucdefect, Thermodynamics *thermo) | design | [private] |
| LeafOptimize(const double pernucdefect, randomnumber &dice, double &defect, vector< double > &def, RNA *fragment, int start, int end, int missingstart, int missingend, char *sequence, Thermodynamics *thermo) | design | [private] |
| MapFragmenttoNuc(int j, int start, int missingstart, int missingend) | design | [private] |
| 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 currentdepth, int **tree) | design | [private] |
| MaximizeExpectedAccuracy(const double maxPercent=20, const int maxStructures=20, const int window=1, const double gamma=1.0) | RNA | |
| MaxLeafRedesign | design | [private] |
| MaxMutate | design | [private] |
| MaxRedesign | design | [private] |
| Mutation(int maxDefPos, int start, int missingstart, int missingend, char *sequence, vector< int > &Mutated) | design | [private] |
| numbering | design | [private] |
| PartitionFunction(const char savefile[]="", double temperature=-10.0) | RNA | |
| pfdata | RNA | [protected] |
| PlaceSeqOnStack(vector< int > *stackstart, vector< int > *stackend, vector< int > *stackmissingstart, vector< int > *stackmissingend, vector< int > *stackfragmentdepth) | design | [private] |
| 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=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 | |
| SelectSequence(int **tree, bool random, int depth, const double pernucdefect, long seed=1) | design | [private] |
| SelectSequenceHeuristic(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 | |
| SpecifyRedesignLimits(int leaf, int parent, int mutate) | design | |
| SpecifyWeightedDefect(bool DefectWeighted) | design | |
| Stochastic(const int structures=1000, const int seed=1) | RNA | |
| StopProgress() | RNA | |
| StoreBestSequence(int start, int end, int missingstart, int missingend, char **sequence, int fragmentdepth) | design | [private] |
| StoreMutation(int start, int end, int missingstart, int missingend, char *sequence) | design | [private] |
| temp | Thermodynamics | [protected] |
| Thermodynamics(const bool ISRNA=true) | Thermodynamics | |
| toint(char i) | design | [private] |
| tonuc(int i) | design | [private] |
| 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 | |
| ~RNA() | RNA | |
| ~Thermodynamics() | Thermodynamics | |
