RNAstructure Classes  Version 6.1
design Member List

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)designprivate
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)designprivate
ContainsPseudoknot(const int structurenumber)RNA
copiedThermodynamicsprotected
CopyThermo(Thermodynamics &copy)RNA
Thermodynamics::CopyThermo(const Thermodynamics &copy)Thermodynamicsprotectedvirtual
dataThermodynamicsprotected
Debug1(int start, int end, int missingstart, int missingend, char *sequence, RNA *fragment)designprivate
decompose(int nucstart, int nucend, int currentdepth, int maxdepth, int **tree, int missingstart=0, int missingend=0)designprivate
defectweighteddesignprivate
design(const char filename[], const char *const alphabet)design
design_sequence(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
EnsureStructureCapcacity(const int minimumStructures)RNA
enthalpyThermodynamicsprotected
ErrorCodeRNAprotected
FileReader(const char filename[], const RNAInputType fileType)RNAprotected
FillSequence(int start, int end, int missingstart, int missingend, bool random, randomnumber *dice, vector< vector< string > > &Helices, vector< vector< string > > &Loops)designprivate
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)designprivate
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)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)designprivate
GetEnergyRead() const Thermodynamics
GetEnsembleDefect(const int structurenumber=1)RNA
GetEnsembleEnergy()RNA
GetEnthalpyTable(const char *alphabet=NULL)Thermodynamics
GetErrorCode() const RNA
GetErrorDetails() const RNA
GetErrorMessage(const int error)RNAstatic
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
GetSequenceLength() const RNA
GetStructure()RNA
GetStructureNumber() const RNA
GetTemperature() const Thermodynamics
init(const char *sequenceOrFileName, const RNAInputType fileType, const bool allowUnknownBases=false, const bool skipThermoTables=false)RNAprotected
IsAlphabetRead() const Thermodynamics
isrnaThermodynamics
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)designprivate
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)designprivate
MapFragmenttoNuc(int j, int start, int missingstart, int missingend)designprivate
MapNuctoFragment(int j, int start, int missingstart, int missingend)designprivate
marktree(int beststart, int bestend, int nucstart, int nucend, int missingstart, int missingend, int currentdepth, int **tree)designprivate
MaximizeExpectedAccuracy(const double maxPercent=20, const int maxStructures=20, const int window=1, const double gamma=1.0)RNA
MaxLeafRedesigndesignprivate
MaxMutatedesignprivate
MaxRedesigndesignprivate
Mutation(int maxDefPos, int start, int missingstart, int missingend, char *sequence, vector< int > &Mutated)designprivate
nominal_alphabetNameThermodynamicsprotected
nominal_temperatureThermodynamicsprotected
numberingdesignprivate
PartitionFunction(const char savefile[]="", double temperature=-10.0, bool disablecoax=false, bool restoreSHAPE=true)RNA
pfdataRNAprotected
PlaceSeqOnStack(vector< int > *stackstart, vector< int > *stackend, vector< int > *stackmissingstart, vector< int > *stackmissingend, vector< int > *stackfragmentdepth)designprivate
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
ReadDMS(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 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, int depth, const double pernucdefect, long seed=1)designprivate
SelectSequenceHeuristic(int **tree, bool random, int depth, const double pernucdefect, long seed=1)designprivate
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
skipThermoTablesThermodynamicsprotected
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)designprivate
StoreMutation(int start, int end, int missingstart, int missingend, char *sequence)designprivate
Thermodynamics(const bool isRNA=true, const char *const alphabetName=NULL, const double temperature=310.15)Thermodynamics
Thermodynamics(const Thermodynamics &copyThermo)Thermodynamics
toint(char i)designprivate
tonuc(int i)designprivate
vRNAprotected
VerifyThermodynamic()Thermodynamics
wRNAprotected
w3RNAprotected
w5RNAprotected
wcaRNAprotected
wcoaxRNAprotected
wlRNAprotected
wmbRNAprotected
wmblRNAprotected
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