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RNAstructure Classes
Version 6.2
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RNAstructure Classes
Version 6.2
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This is the complete list of members for design, 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 |
| bias_in_leaf_refinement | design | private |
| BreakPseudoknot(const bool minimum_energy=true, const int structurenumber=0, const bool useFastMethod=true) | RNA | |
| CalculateFreeEnergy(const int structurenumber=1, const bool UseSimpleMBLoopRules=false) | RNA | |
| ClearEnergies() | Thermodynamics | |
| ClearEnthalpies() | Thermodynamics | |
| closeenoughtocut(int i, int j, int nucstart, int nucend, int missingstart, int missingend, double CLOSENESS) | design | private |
| ContainsPseudoknot(const int structurenumber) | RNA | |
| copied | Thermodynamics | protected |
| CopyThermo(Thermodynamics ©) | RNA | |
| Thermodynamics::CopyThermo(const Thermodynamics ©) | Thermodynamics | protectedvirtual |
| 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 char *const alphabet) | design | |
| design_sequence(double &pernucdefect, const bool random, const bool bias, const char prob_info[], const int maxdepth=5, bool heuristic=false, int MaxRedesignC=10, int MaxMutateC=4, int MaxLeafRedesignC=3, long randomSeed=1L, bool allow_isolated=false) | design | |
| DetermineDrawingCoordinates(const int height, const int width, const int structurenumber=1) | RNA | |
| EnsureStructureCapcacity(const int minimumStructures) | RNA | |
| enthalpy | Thermodynamics | protected |
| ErrorCode | RNA | protected |
| ExteriorLoopCorrection(const int structurenumber, const bool UseSimpleMBLoopRules, int min_index, int max_index) | RNA | |
| FileReader(const char filename[], const RNAInputType fileType) | RNA | protected |
| FillSequence(int start, int end, int missingstart, int missingend, bool random, bool bias, 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, bool simple_iloops=true, bool disablecoax=false, bool allow_isolated=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 | |
| GetAlphabetName() const | Thermodynamics | |
| GetBackboneType() const | RNA | |
| GetCommentString(const int structurenumber=1) | RNA | |
| GetDatatable() | Thermodynamics | |
| GetDefect(int start, int end, int missingstart, int missingend, vector< double > &def, double &defect, RNA *fragment) | design | private |
| GetEnergyRead() const | Thermodynamics | |
| GetEnsembleDefect(const int structurenumber=1, const int start=0, const int end=0, const char filename[]="") | RNA | |
| GetEnsembleEnergy() | RNA | |
| GetEnthalpyTable(const char *alphabet=NULL) | Thermodynamics | |
| GetErrorCode() const | RNA | |
| GetErrorDetails() const | RNA | |
| GetErrorMessage(const int error) | RNA | static |
| GetErrorMessageString(const int error) const | 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 | |
| GetFullErrorMessage() const | 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 | |
| GetPairProbabilities(double *arr, const int size) | RNA | |
| GetPairProbability(const int i, const int j) | RNA | |
| GetProgress() | RNA | |
| GetSequence() const | RNA | |
| GetSequence(size_t start, size_t length=std::string::npos) const | RNA | |
| GetSequenceLength() const | RNA | |
| GetStructure() | RNA | |
| GetStructureNumber() const | RNA | |
| GetTemperature() const | Thermodynamics | |
| GetVprimeQ(const int i, const int j) | RNA | |
| GetW(const int i, const int j) | RNA | |
| init(const char *sequenceOrFileName, const RNAInputType fileType, const bool allowUnknownBases=false, const bool skipThermoTables=false) | RNA | protected |
| IsAlphabetRead() const | Thermodynamics | |
| isrna | Thermodynamics | |
| leafdesign(int start, int end, int missingstart, int missingend, bool random, bool bias, randomnumber *dice, vector< vector< string > > *Helices, vector< vector< string > > *Loops, double pernucdefect, Thermodynamics *thermo, bool allowisolated) | 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, bool allowisolated) | 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 |
| nominal_alphabetName | Thermodynamics | protected |
| nominal_temperature | Thermodynamics | protected |
| numbering | design | private |
| pairbias | design | private |
| PartitionFunction(const char savefile[]="", double temperature=-10.0, bool disablecoax=false, bool restoreSHAPE=true, bool allowisolated=false, int maxinter=30) | 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, double threshold=0) | RNA | |
| ProbKnotFromSample(int iterations=1, int MinHelixLength=1, double threshold=0) | RNA | |
| progress | RNA | protected |
| Q | RNA | protected |
| randomnuc(randomnumber *dice) | design | private |
| randompair(int *i, int *j, randomnumber *dice) | design | private |
| ReadConstraints(const char filename[]) | RNA | |
| ReadDMS(const char filename[], const bool bynt=false) | RNA | |
| ReadDSO(const char filename[]) | RNA | |
| ReadExperimentalPairBonus(const char filename[], double const experimentalOffset, double const experimentalScaling) | RNA | |
| ReadSHAPE(const char filename[], const double slope, const double intercept, RestraintType modifier=RESTRAINT_SHAPE, const bool IsPseudoEnergy=true) | RNA | |
| ReadSHAPE(const char filename[], const double dsSlope, const double dsIntercept, const double ssSlope, const double ssIntercept, RestraintType modifier=RESTRAINT_SHAPE) | RNA | |
| ReadSSO(const char filename[]) | RNA | |
| ReadThermodynamic(const char *directory=NULL, const char *alphabet=NULL, const double temperature=-1.0) | Thermodynamics | |
| ReFoldSingleStrand(const float percent=20, const int maximumstructures=20, const int window=5) | RNA | |
| ReloadDataTables(const double new_temperature=-1.0) | Thermodynamics | |
| RemoveBasePair(const int i, const int structurenumber=1) | RNA | |
| RemoveConstraints() | RNA | |
| RemovePairs(const int structurenumber=1, bool removeIfLastStructure=true) | RNA | |
| ResetError() | RNA | |
| RNA(const char sequence[], const bool IsRNA=true) | RNA | |
| RNA(const char filepathOrSequence[], const RNAInputType fileType, const char *const alphabetName, const bool allowUnknownBases=false, const bool skipThermoTables=false) | RNA | |
| RNA(const char filepathOrSequence[], const RNAInputType fileType, const Thermodynamics *copyThermo) | RNA | |
| RNA(const char filename[], const RNAInputType fileType, const bool IsRNA=true) | RNA | |
| RNA(const bool IsRNA=true) | RNA | |
| Rsample(const vector< double > &experimentalRestraints, RsampleData &refdata, const int randomSeed=0, const char savefile[]="", const double cparam=0.5, const double offset=1.10, const int numsamples=10000) | RNA | |
| SelectSequence(int **tree, bool random, bool bias, int depth, const double pernucdefect, long seed=1, bool allowisolated=false) | design | private |
| SelectSequenceHeuristic(int **tree, bool random, bool bias, int depth, const double pernucdefect, long seed=1, bool allowisolated=false) | design | private |
| SetConstraints(vector< int > ss) | RNA | |
| SetErrorDetails(const string &details) | RNA | |
| SetExtrinsic(int i, int j, double k) | RNA | |
| SetProgress(ProgressHandler &Progress) | RNA | |
| SetSequenceLabel(const string &label) | RNA | |
| SetTemperature(double temperature) | Thermodynamics | |
| singlebias | design | private |
| skipThermoTables | Thermodynamics | protected |
| 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 |
| Thermodynamics(const bool isRNA=true, const char *const alphabetName=NULL, const double temperature=310.15) | Thermodynamics | |
| Thermodynamics(const Thermodynamics ©Thermo) | Thermodynamics | |
| toint(char i) | design | private |
| tonuc(int i) | design | private |
| v | RNA | protected |
| VerifyThermodynamic() | Thermodynamics | |
| w | RNA | protected |
| w3 | RNA | protected |
| w5 | RNA | protected |
| wca | RNA | protected |
| wcoax | RNA | protected |
| wl | RNA | protected |
| wlc | RNA | protected |
| wmb | RNA | protected |
| wmbl | RNA | protected |
| WriteConstraints(const char filename[]) | RNA | |
| WriteCt(const char filename[], bool append=false, CTCommentProvider &commentProvider=CTComments::Energy) const | RNA | |
| WriteDotBracket(const char filename[], const int structurenumber=-1, const DotBracketFormat format=DBN_FMT_MULTI_TITLE, CTCommentProvider &commentProvider=CTComments::Energy) const | RNA | |
| WriteThermodynamicDetails(const char filename[], const bool UseSimpleMBLoopRules=false) | RNA | |
| ~RNA() | RNA | |
| ~Thermodynamics() | Thermodynamics |
1.8.13