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| design (const char filename[], const bool IsRNA=true) |
| Constructor. Programmer provides a filename for a ct file. More...
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int | 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) |
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void | SpecifyRedesignLimits (int leaf, int parent, int mutate) |
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void | SpecifyWeightedDefect (bool DefectWeighted) |
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| RNA (const char sequence[], const bool IsRNA=true) |
| Constructor - user provides a sequence as a c string. More...
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| RNA (const char filename[], const int type, const bool IsRNA=true) |
| Constructor - user provides a filename for existing file as a c string. More...
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| RNA (const bool IsRNA=true) |
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int | GetErrorCode () |
| Return an error code, where a return of zero is no error. More...
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char * | GetErrorMessage (const int error) |
| Return error messages based on code from GetErrorCode and other error codes. More...
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std::string | GetErrorMessageString (const int error) |
| Return error messages based on code from GetErrorCode and other error codes. More...
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void | ResetError () |
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int | SpecifyPair (const int i, const int j, const int structurenumber=1) |
| Specify a base pair between nucleotides i and j. More...
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int | RemovePairs (const int structurenumber=1) |
| Remove all the current base pairs in a specified structure. More...
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int | RemoveBasePair (const int i, const int structurenumber=1) |
| Remove a specified pair in a specified structure. More...
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double | CalculateFreeEnergy (const int structurenumber=1, const bool UseSimpleMBLoopRules=false) |
| Return the predicted Gibb's free energy change for structure # structurenumber, defaulted to 1. More...
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int | WriteThermodynamicDetails (const char filename[], const bool UseSimpleMBLoopRules=false) |
| Calculate the folding free energy change for all structures and write the details of the calculation to a file. More...
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int | 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) |
| Predict the lowest free energy secondary structure and generate suboptimal structures using a heuristic. More...
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int | GenerateAllSuboptimalStructures (const float percent=5, const double deltaG=0.6) |
| Predict the lowest free energy secondary structure and generate all suboptimal structures. More...
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int | MaximizeExpectedAccuracy (const double maxPercent=20, const int maxStructures=20, const int window=1, const double gamma=1.0) |
| Predict the structure with maximum expected accuracy and suboptimal structures. More...
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int | PartitionFunction (const char savefile[]="", double temperature=-10.0) |
| Predict the partition function for a sequence. More...
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int | PredictProbablePairs (const float probability=0) |
| Predict structures containing highly probable pairs. More...
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int | ProbKnot (int iterations=1, int MinHelixLength=1) |
| Predict maximum expected accuracy structures that contain pseudoknots from either a sequence or a partition function save file. More...
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int | ProbKnotFromSample (int iterations=1, int MinHelixLength=1) |
| Predict maximum expected accuracy structures that contain pseudoknots from a file containing ensemble of structures. More...
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int | ReFoldSingleStrand (const float percent=20, const int maximumstructures=20, const int window=5) |
| Re-predict the lowest free energy secondary structure and generate suboptimal structures using a heuristic. More...
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int | Stochastic (const int structures=1000, const int seed=1) |
| Sample structures from the Boltzman ensemable. More...
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int | ForceDoubleStranded (const int i) |
| Force a nucleotide to be double stranded (base paired). More...
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int | ForceFMNCleavage (const int i) |
| Indicate a nucleotide that is accessible to FMN cleavage (a U in GU pair). More...
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int | ForceMaximumPairingDistance (const int distance) |
| Force a maximum distance between apired nucleotides. More...
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int | ForceModification (const int i) |
| Force modification for a nucleotide. More...
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int | ForcePair (const int i, const int j) |
| Force a pair between two nucleotides. More...
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int | ForceProhibitPair (const int i, const int j) |
| Prohibit a pair between two nucleotides. More...
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int | ForceSingleStranded (const int i) |
| Force a nucleotide to be single stranded. More...
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int | GetForcedDoubleStranded (const int constraintnumber) |
| Return a nucleotide that is forced double stranded. More...
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int | GetForcedFMNCleavage (const int constraintnumber) |
| Return a nucleotide that is accessible to FMN cleavage. More...
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int | GetForcedModification (const int constraintnumber) |
| Return a nucleotide that is accessible to modification. More...
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int | GetForcedPair (const int constraintnumber, const bool fiveprime) |
| Return a nucleotide in a forced pair. More...
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int | GetForcedProhibitedPair (const int constraintnumber, const bool fiveprime) |
| Return a nucleotide in a prohibited pair. More...
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int | GetForcedSingleStranded (const int constraintnumber) |
| Return a nucleotide that is forced single stranded. More...
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int | GetMaximumPairingDistance () |
| Return the maximum pairing distance. More...
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int | GetNumberOfForcedDoubleStranded () |
| Return the number of nucletides forced to be paired. More...
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int | GetNumberOfForcedFMNCleavages () |
| Return the number of nucleotides accessible to FMN cleavage. More...
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int | GetNumberOfForcedModifications () |
| Return the number of nucleotides accessible to chemical modification. More...
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int | GetNumberOfForcedPairs () |
| Return the number of forced base pairs. More...
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int | GetNumberOfForcedProhibitedPairs () |
| Return the number of prohibited base pairs. More...
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int | GetNumberOfForcedSingleStranded () |
| Return the number of nucleotides that are not allowed to pair. More...
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int | ReadConstraints (const char filename[]) |
| Read a set of folding constraints to disk in a plain text file. More...
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int | ReadSHAPE (const char filename[], const double parameter1, const double parameter2, std::string modifier="SHAPE", const bool IsPseudoEnergy=true) |
| Read SHAPE data from disk. More...
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int | ReadSHAPE (const char filename[], const double parameter1, const double parameter2, const double ssm, const double ssb, std::string modifier="SHAPE") |
| Read SHAPE data from disk including single-stranded SHAPE pseudo free energys. More...
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int | ReadDSO (const char filename[]) |
| Read double strand offset data from disk. More...
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int | ReadSSO (const char filename[]) |
| Read single strand offset data from disk. More...
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int | ReadExperimentalPairBonus (const char filename[], double const experimentalOffset, double const experimentalScaling) |
| Read experimental pair bonuses from disk. More...
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void | RemoveConstraints () |
| Remove all folding constraints. More...
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int | SetExtrinsic (int i, int j, double k) |
| Add extrinsic restraints for partition function calculations. More...
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int | WriteConstraints (const char filename[]) |
| Write the current set of folding constraints to disk in a plain text file. More...
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int | AddComment (const char comment[], const int structurenumber=1) |
| Add a comment associated with a structure. More...
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int | WriteCt (const char filename[], bool append=false) |
| Write a ct file of the structures. More...
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int | WriteDotBracket (const char filename[]) |
| Write dot-bracket file of structures. More...
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int | BreakPseudoknot (const bool minimum_energy=true, const int structurenumber=0) |
| Break any pseudoknots that might be in a structure. More...
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bool | ContainsPseudoknot (const int structurenumber) |
| Report if there are any pseudoknots in a structure. More...
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double | GetEnsembleEnergy () |
| Get the ensemble folding free energy change. More...
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double | GetFreeEnergy (const int structurenumber) |
| Get the folding free energy change for a predicted structure. More...
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int | GetPair (const int i, const int structurenumber=1) |
| Get the nucleotide to which the specified nucleotide is paired. More...
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double | GetPairEnergy (const int i, const int j) |
| Get the lowest folding free energy possible for a structure containing pair i-j. More...
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double | GetPairProbability (const int i, const int j) |
| Get a base pair probability. More...
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int | GetStructureNumber () |
| Get the total number of specified or predicted structures. More...
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int | DetermineDrawingCoordinates (const int height, const int width, const int structurenumber=1) |
| Determine the coordinates for drawing a secondary structure. More...
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std::string | GetCommentString (const int structurenumber=1) |
| Provide the comment from the ct file as a string. More...
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int | GetNucleotideXCoordinate (const int i) |
| Get the X coordinate for nucleotide i for drawing a structure. More...
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int | GetNucleotideYCoordinate (const int i) |
| Get the Y coordinate for nucleotide i for drawing a structure. More...
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int | GetLabelXCoordinate (const int i) |
| Get the X coordinate for placing the nucleotide index label specified by i. More...
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int | GetLabelYCoordinate (const int i) |
| Get the Y coordinate for placing the nucleotide index label specified by i. More...
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char | GetNucleotide (const int i) |
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int | GetSequenceLength () |
| Get the total length of the sequence. More...
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bool | GetBackboneType () |
| Get the backbone type. More...
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structure * | GetStructure () |
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void | SetProgress (TProgressDialog &Progress) |
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void | StopProgress () |
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TProgressDialog * | GetProgress () |
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| ~RNA () |
| Destructor. More...
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| Thermodynamics (const bool ISRNA=true) |
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int | SetTemperature (double temperature) |
| Set the temperature of folding in K. More...
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double | GetTemperature () |
| Get the current folding temperature in K. More...
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int | ReadThermodynamic (const char *pathname=NULL) |
| Function to read the thermodynamic parameters. More...
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datatable * | GetDatatable () |
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datatable * | GetEnthalpyTable () |
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void | CopyThermodynamic (Thermodynamics *thermo) |
| Copy thermodynamic parameters from an instance of Thermodynamics class. More...
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bool | GetEnergyRead () |
| Return whether this instance of Thermodynamics has the paremters populated (either from disk or from another Thermodynamics class). More...
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| ~Thermodynamics () |
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void | decompose (int nucstart, int nucend, int currentdepth, int maxdepth, int **tree, int missingstart=0, int missingend=0) |
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bool | closeenoughtocut (int i, int j, int nucstart, int nucend, int missingstart, int missingend, double CLOSENESS) |
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void | marktree (int beststart, int bestend, int nucstart, int nucend, int missingstart, int missingend, int currentdepth, int **tree) |
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void | bestdecomposition (int nuctstart, int nucend, int currentstart, int currentend, int *beststart, int *bestend, int missingstart, int missingend) |
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double | SelectSequence (int **tree, bool random, int depth, const double pernucdefect, long seed=1) |
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double | SelectSequenceHeuristic (int **tree, bool random, int depth, const double pernucdefect, long seed=1) |
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void | 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) |
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void | FillSequence (int start, int end, int missingstart, int missingend, bool random, randomnumber *dice, vector< vector< string > > &Helices, vector< vector< string > > &Loops) |
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int | MapNuctoFragment (int j, int start, int missingstart, int missingend) |
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int | MapFragmenttoNuc (int j, int start, int missingstart, int missingend) |
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void | Mutation (int maxDefPos, int start, int missingstart, int missingend, char *sequence, vector< int > &Mutated) |
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void | GetDefect (int start, int end, int missingstart, int missingend, vector< double > &def, double &defect, RNA *fragment) |
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void | Debug1 (int start, int end, int missingstart, int missingend, char *sequence, RNA *fragment) |
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void | PlaceSeqOnStack (vector< int > *stackstart, vector< int > *stackend, vector< int > *stackmissingstart, vector< int > *stackmissingend, vector< int > *stackfragmentdepth) |
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void | StoreMutation (int start, int end, int missingstart, int missingend, char *sequence) |
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void | StoreBestSequence (int start, int end, int missingstart, int missingend, char **sequence, int fragmentdepth) |
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char | tonuc (int i) |
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int | toint (char i) |
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double | 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) |
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void | 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) |
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