| RNAstructure Classes Version 6.2

ProbScan Member List

This is the complete list of members for ProbScan, including all inherited members.

AddComment(const char comment[], const int structurenumber=1) | RNA |
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 |
CheckPair(const int i, const int j) | RNA |
ClearEnergies() | Thermodynamics |
ClearEnthalpies() | Thermodynamics |
construct_mb_element_array(const multibranch_loop_t &) | ProbScan | private
ContainsPseudoknot(const int structurenumber) | RNA |
copied | Thermodynamics | protected
CopyThermo(Thermodynamics &copy) | RNA |
Thermodynamics::CopyThermo(const Thermodynamics &copy) | Thermodynamics | protected virtual
ct | RNA | private
data | Thermodynamics | protected
DetermineDrawingCoordinates(const int height, const int width, const int structurenumber=1) | RNA |
drawallocated | RNA | private
energyallocated | RNA | private
EnsureStructureCapcacity(const int minimumStructures) | RNA |
enthalpy | Thermodynamics | protected
equilibrium_constant_for_multibranch_loop(const multibranch_loop_t &) | ProbScan | private
ErrorCode | RNA | protected
ev | RNA | private
ew | RNA | private
ew2 | RNA | private
ew3 | RNA | private
ew5 | RNA | private
ewmb | RNA | private
ewmb2 | RNA | private
ExteriorLoopCorrection(const int structurenumber, const bool UseSimpleMBLoopRules, int min_index, int max_index) | RNA |
fce | RNA | private
FileReader(const char filename[], const RNAInputType fileType) | RNA | protected
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 |
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 |
lastErrorDetails | RNA | private
lfce | RNA | private
MaximizeExpectedAccuracy(const double maxPercent=20, const int maxStructures=20, const int window=1, const double gamma=1.0) | RNA |
mod | RNA | private
nominal_alphabetName | Thermodynamics | protected
nominal_temperature | Thermodynamics | protected
PartitionFunction(const char savefile[]="", double temperature=-10.0, bool disablecoax=false, bool restoreSHAPE=true, bool allowisolated=false, int maxinter=30) | RNA |
partitionfunctionallocated | RNA | private
pfdata | RNA | protected
PredictProbablePairs(const float probability=0) | RNA |
probability_of_all_hairpins(int min, int max, double threshold) | ProbScan |
probability_of_all_helices(double threshold, int length) | ProbScan |
probability_of_all_internal_loops(double threshold, std::string mode=std::string("both")) | ProbScan |
probability_of_hairpin(int i, int j) | ProbScan |
probability_of_helix(const int i, const int j, const int how_many_stacks) | ProbScan |
probability_of_internal_loop(int i, int j, int k, int l) | ProbScan |
probability_of_multibranch_loop(const multibranch_loop_t &mb) | ProbScan |
probability_of_stack(int i, int j) | ProbScan |
probability_of_stemloop(int i, int j, int ip, int jp) | ProbScan |
ProbKnot(int iterations=1, int MinHelixLength=1, double threshold=0) | RNA |
ProbKnotFromSample(int iterations=1, int MinHelixLength=1, double threshold=0) | RNA |
ProbScan(std::string sequence, const char *const alphabetName="rna") | ProbScan |
ProbScan(const char filename[], bool from_sequence_file, const char *const alphabetName="rna") | ProbScan |
progress | RNA | protected
Q | RNA | protected
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 |
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 |
skipThermoTables | Thermodynamics | protected
SpecifyPair(const int i, const int j, const int structurenumber=1) | RNA |
Stochastic(const int structures=1000, const int seed=1) | RNA |
StopProgress() | RNA |
structurecoordinates | RNA | private
Thermodynamics(const bool isRNA=true, const char *const alphabetName=NULL, const double temperature=310.15) | Thermodynamics |
Thermodynamics(const Thermodynamics &copyThermo) | Thermodynamics |
v | RNA | protected
VerifyThermodynamic() | Thermodynamics |
vmin | RNA | private
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 |