RNAstructure Classes  Version 6.1
Oligowalk_object Class Reference

Oligowalk_object Class. More...

#include <Oligowalk_object.h>

Inheritance diagram for Oligowalk_object:
RNA Thermodynamics

Public Member Functions

 Oligowalk_object (const char sequence[])
 Constructor - user provides a sequence as a c string. More...
 
 Oligowalk_object (const char filename[], const int type)
 Constructor - user provides a filename for existing file as a c string. More...
 
 Oligowalk_object (const bool IsRNA=true)
 Default Constructor - user provides nothing. More...
 
int Oligowalk (const int oligo_length, const bool isDNA, const int option, const double oligo_concentration, const int usesub, const int start, const int stop)
 
double GetBreakTargetDG (const int index)
 
double GetDuplexDG (const int index)
 
double GetOligoOligoDG (const int index)
 
double GetOligoSelfDG (const int index)
 
double GetOverallDG (const int index)
 
double GetTm (const int index)
 
int WriteReport (const char outputfilename[], const int oligo_length, const bool isDNA, const int option, const double oligo_concentration, const int usesub, const int start, const int stop)
 
int OligoScreen (const char infilename[], const char outfilename[])
 This function runs OligoScreen. More...
 
const char * GetErrorMessage (const int error)
 
 ~Oligowalk_object ()
 This is the destructor. More...
 
- Public Member Functions inherited from RNA
 RNA (const char sequence[], const bool IsRNA=true)
 Constructor - user provides a sequence as a c string. More...
 
 RNA (const char filepathOrSequence[], const RNAInputType fileType, const char *const alphabetName, const bool allowUnknownBases=false, const bool skipThermoTables=false)
 
 RNA (const char filepathOrSequence[], const RNAInputType fileType, const Thermodynamics *copyThermo)
 
 RNA (const char filename[], const RNAInputType fileType, const bool IsRNA=true)
 Constructor - user provides a filename for existing file as a c string. More...
 
 RNA (const bool IsRNA=true)
 
int GetErrorCode () const
 Return an error code, where a return of zero is no error. More...
 
string GetFullErrorMessage () const
 
const string GetErrorDetails () const
 Returns extended details about the last error. (e.g. error messages produced during file read operations that are otherwise lost.) More...
 
void SetErrorDetails (const string &details)
 Set extended details about the last error. (e.g. error messages produced during file read operations that are otherwise lost.) More...
 
void SetSequenceLabel (const string &label)
 Set the name of the sequence. (This must be called before structure prediction for it to affect the resulting structures.) More...
 
string GetErrorMessageString (const int error) const
 Return error messages based on code from GetErrorCode and other error codes. More...
 
void ResetError ()
 
void EnsureStructureCapcacity (const int minimumStructures)
 Ensure that at a minumum number of structures have been created. More...
 
int SpecifyPair (const int i, const int j, const int structurenumber=1)
 Specify a base pair between nucleotides i and j. More...
 
int RemovePairs (const int structurenumber=1, bool removeIfLastStructure=true)
 Remove all the current base pairs in a specified structure. More...
 
int RemoveBasePair (const int i, const int structurenumber=1)
 Remove a specified pair in a specified structure. More...
 
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...
 
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...
 
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, bool disablecoax=false)
 Predict the lowest free energy secondary structure and generate suboptimal structures using a heuristic. More...
 
int GenerateAllSuboptimalStructures (const float percent=5, const double deltaG=0.6)
 Predict the lowest free energy secondary structure and generate all suboptimal structures. More...
 
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...
 
int PartitionFunction (const char savefile[]="", double temperature=-10.0, bool disablecoax=false, bool restoreSHAPE=true)
 Predict the partition function for a sequence. More...
 
int 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)
 
int PredictProbablePairs (const float probability=0)
 Predict structures containing highly probable pairs. More...
 
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...
 
int ProbKnotFromSample (int iterations=1, int MinHelixLength=1)
 Predict maximum expected accuracy structures that contain pseudoknots from a file containing ensemble of structures. More...
 
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...
 
int Stochastic (const int structures=1000, const int seed=1)
 Sample structures from the Boltzman ensemable. More...
 
int ForceDoubleStranded (const int i)
 Force a nucleotide to be double stranded (base paired). More...
 
int ForceFMNCleavage (const int i)
 Indicate a nucleotide that is accessible to FMN cleavage (a U in GU pair). More...
 
int ForceMaximumPairingDistance (const int distance)
 Force a maximum distance between apired nucleotides. More...
 
int ForceModification (const int i)
 Force modification for a nucleotide. More...
 
int ForcePair (const int i, const int j)
 Force a pair between two nucleotides. More...
 
int ForceProhibitPair (const int i, const int j)
 Prohibit a pair between two nucleotides. More...
 
int ForceSingleStranded (const int i)
 Force a nucleotide to be single stranded. More...
 
int GetForcedDoubleStranded (const int constraintnumber)
 Return a nucleotide that is forced double stranded. More...
 
int GetForcedFMNCleavage (const int constraintnumber)
 Return a nucleotide that is accessible to FMN cleavage. More...
 
int GetForcedModification (const int constraintnumber)
 Return a nucleotide that is accessible to modification. More...
 
int GetForcedPair (const int constraintnumber, const bool fiveprime)
 Return a nucleotide in a forced pair. More...
 
int GetForcedProhibitedPair (const int constraintnumber, const bool fiveprime)
 Return a nucleotide in a prohibited pair. More...
 
int GetForcedSingleStranded (const int constraintnumber)
 Return a nucleotide that is forced single stranded. More...
 
int GetMaximumPairingDistance ()
 Return the maximum pairing distance. More...
 
int GetNumberOfForcedDoubleStranded ()
 Return the number of nucletides forced to be paired. More...
 
int GetNumberOfForcedFMNCleavages ()
 Return the number of nucleotides accessible to FMN cleavage. More...
 
int GetNumberOfForcedModifications ()
 Return the number of nucleotides accessible to chemical modification. More...
 
int GetNumberOfForcedPairs ()
 Return the number of forced base pairs. More...
 
int GetNumberOfForcedProhibitedPairs ()
 Return the number of prohibited base pairs. More...
 
int GetNumberOfForcedSingleStranded ()
 Return the number of nucleotides that are not allowed to pair. More...
 
int ReadConstraints (const char filename[])
 Read a set of folding constraints to disk in a plain text file. More...
 
int ReadSHAPE (const char filename[], const double slope, const double intercept, RestraintType modifier=RESTRAINT_SHAPE, const bool IsPseudoEnergy=true)
 Read SHAPE data from disk. More...
 
int ReadSHAPE (const char filename[], const double dsSlope, const double dsIntercept, const double ssSlope, const double ssIntercept, RestraintType modifier=RESTRAINT_SHAPE)
 Read SHAPE data from disk including single-stranded SHAPE pseudo free energys. More...
 
int ReadDMS (const char filename[])
 
int ReadDSO (const char filename[])
 Read double strand offset data from disk. More...
 
int ReadSSO (const char filename[])
 Read single strand offset data from disk. More...
 
int ReadExperimentalPairBonus (const char filename[], double const experimentalOffset, double const experimentalScaling)
 Read experimental pair bonuses from disk. More...
 
void RemoveConstraints ()
 Remove all folding constraints. More...
 
int SetExtrinsic (int i, int j, double k)
 Add extrinsic restraints for partition function calculations. More...
 
int WriteConstraints (const char filename[])
 Write the current set of folding constraints to disk in a plain text file. More...
 
int AddComment (const char comment[], const int structurenumber=1)
 Add a comment associated with a structure. More...
 
int WriteCt (const char filename[], bool append=false, CTCommentProvider &commentProvider=CTComments::Energy) const
 Write a ct file of the structures. More...
 
int WriteDotBracket (const char filename[], const int structurenumber=-1, const DotBracketFormat format=DBN_FMT_MULTI_TITLE, CTCommentProvider &commentProvider=CTComments::Energy) const
 Write dot-bracket file of structures. More...
 
int BreakPseudoknot (const bool minimum_energy=true, const int structurenumber=0, const bool useFastMethod=true)
 Break any pseudoknots that might be in a structure. More...
 
bool ContainsPseudoknot (const int structurenumber)
 Report if there are any pseudoknots in a structure. More...
 
double GetEnsembleEnergy ()
 Get the ensemble folding free energy change. More...
 
double GetEnsembleDefect (const int structurenumber=1)
 Get the ensemble defect of a secondary structure. More...
 
double GetFreeEnergy (const int structurenumber)
 Get the folding free energy change for a predicted structure. More...
 
int GetPair (const int i, const int structurenumber=1)
 Get the nucleotide to which the specified nucleotide is paired. More...
 
double GetPairEnergy (const int i, const int j)
 Get the lowest folding free energy possible for a structure containing pair i-j. More...
 
double GetPairProbability (const int i, const int j)
 Get a base pair probability. More...
 
int GetPairProbabilities (double *arr, const int size)
 
int GetStructureNumber () const
 Get the total number of specified or predicted structures. More...
 
int DetermineDrawingCoordinates (const int height, const int width, const int structurenumber=1)
 Determine the coordinates for drawing a secondary structure. More...
 
std::string GetCommentString (const int structurenumber=1)
 Provide the comment from the ct file as a string. More...
 
int GetNucleotideXCoordinate (const int i)
 Get the X coordinate for nucleotide i for drawing a structure. More...
 
int GetNucleotideYCoordinate (const int i)
 Get the Y coordinate for nucleotide i for drawing a structure. More...
 
int GetLabelXCoordinate (const int i)
 Get the X coordinate for placing the nucleotide index label specified by i. More...
 
int GetLabelYCoordinate (const int i)
 Get the Y coordinate for placing the nucleotide index label specified by i. More...
 
char GetNucleotide (const int i)
 
int GetSequenceLength () const
 Get the total length of the sequence. More...
 
const char * GetSequence () const
 
bool GetBackboneType () const
 Get the backbone type. More...
 
structure * GetStructure ()
 
void SetProgress (ProgressHandler &Progress)
 
void StopProgress ()
 
ProgressHandler * GetProgress ()
 
 ~RNA ()
 Destructor. More...
 
void CopyThermo (Thermodynamics &copy)
 Copy thermodynamic parameters from an instance of an RNA class. More...
 
- Public Member Functions inherited from Thermodynamics
 Thermodynamics (const bool isRNA=true, const char *const alphabetName=NULL, const double temperature=310.15)
 
 Thermodynamics (const Thermodynamics &copyThermo)
 
int SetTemperature (double temperature)
 Set the temperature of folding in K. More...
 
double GetTemperature () const
 
string GetAlphabetName () const
 Get the name of the extended alphabet for which thermodynamic parameters should be loaded. More...
 
int ReadThermodynamic (const char *directory=NULL, const char *alphabet=NULL, const double temperature=-1.0)
 Function to read the thermodynamic parameters. More...
 
int ReloadDataTables (const double new_temperature=-1.0)
 
bool VerifyThermodynamic ()
 Force the datatables to be read if they haven't already. Return true if the tables were already loaded or if the attempt to (re)open them succeded. More...
 
datatable * GetDatatable ()
 
datatable * GetEnthalpyTable (const char *alphabet=NULL)
 
void ClearEnergies ()
 Clear the currently loaded energy datatable and release its resources. More...
 
void ClearEnthalpies ()
 Clear the currently loaded enthalpy datatable and release its resources. More...
 
bool GetEnergyRead () const
 Return whether this instance of Thermodynamics has the paremters populated (either from disk or from another Thermodynamics class). More...
 
bool IsAlphabetRead () const
 
 ~Thermodynamics ()
 

Private Member Functions

void CommonConstructor ()
 

Private Attributes

int ** table
 
int ** numofsubstructures
 
siPREFILTER * prefilter
 
int length
 

Additional Inherited Members

- Static Public Member Functions inherited from RNA
static const char * GetErrorMessage (const int error)
 Return error messages based on code from GetErrorCode and other error codes. More...
 
- Public Attributes inherited from Thermodynamics
bool isrna
 
- Protected Member Functions inherited from RNA
int FileReader (const char filename[], const RNAInputType fileType)
 
void init (const char *sequenceOrFileName, const RNAInputType fileType, const bool allowUnknownBases=false, const bool skipThermoTables=false)
 
- Protected Member Functions inherited from Thermodynamics
virtual void CopyThermo (const Thermodynamics &copy)
 Copy thermodynamic parameters from an instance of Thermodynamics class. More...
 
- Protected Attributes inherited from RNA
int ErrorCode
 
ProgressHandler * progress
 
PFPRECISION * w5
 
PFPRECISION * w3
 
PFPRECISION ** wca
 
pfdatatable * pfdata
 
DynProgArray< PFPRECISION > * w
 
DynProgArray< PFPRECISION > * v
 
DynProgArray< PFPRECISION > * wmb
 
DynProgArray< PFPRECISION > * wl
 
DynProgArray< PFPRECISION > * wmbl
 
DynProgArray< PFPRECISION > * wcoax
 
PFPRECISION Q
 
- Protected Attributes inherited from Thermodynamics
datatable * data
 
datatable * enthalpy
 
bool copied
 
double nominal_temperature
 
string nominal_alphabetName
 
bool skipThermoTables
 

Detailed Description

Oligowalk_object Class.

The Oligowalk_class inhereits from RNA and provides the OligoWalk functionality. Additionally, it provides OligoScreen.

Constructor & Destructor Documentation

Oligowalk_object::Oligowalk_object ( const char  sequence[])

Constructor - user provides a sequence as a c string.

This constructor simply calls the underlying RNA(const char sequence[], const bool IsRNA=true) constructor and sets IsRNA=true. Input sequence should contain A,C,G,T,U,a,c,g,t,u,x,X. Capitalization makes no difference. T=t=u=U. U is assumed by OligoWalk. x=X= nucleotide that neither stacks nor pairs. For now, any unknown nuc is considered 'X'. Note that sequences will subsequently be indexed starting at 1 (like a biologist), so that the 0th position in the sequence array will be nucleotide 1.

Parameters
sequenceis a NULL terminated c string.
Oligowalk_object::Oligowalk_object ( const char  filename[],
const int  type 
)

Constructor - user provides a filename for existing file as a c string.

This constructor simply calls the underlying RNA(const char filename[], const int type, const bool IsRNA=true) constructor and sets IsRNA=true. The existing file, specified by filename, can either be a ct file, a sequence, or an RNAstructure save file. Therefore, the user provides a flag for the file: type = 1 => .ct file, type = 2 => .seq file, type = 3 => partition function save (.pfs) file, type = 4 => folding save file (.sav). For OligoWalk calculations, types 1 and 2 are the relevant types. This constructor generates internal error codes that can be accessed by GetErrorCode() after the constructor is called. 0 = no error. The errorcode can be resolved to a c string using GetErrorMessage. Note also that save files explicitly store the thermodynamic parameters, therefore changing the backbone type as compaared to the original calculation will not change structure predictions.

Parameters
filenameis null terminated c string.
typeis an integer that indicates the file type.
Oligowalk_object::Oligowalk_object ( const bool  IsRNA = true)

Default Constructor - user provides nothing.

This constructor calls the underlying RNA(IsRNA=true) constructor. This basic constructor is provided for performing OligoScreen calculations, which do not need an input sequence. This constructor needs to be called with RNA=true for Oligos to be RNA and RNA=false for Oligos to be DNA.

Parameters
IsRNAis a bool where true=RNA and false=DNA.
Oligowalk_object::~Oligowalk_object ( )

This is the destructor.

Member Function Documentation

void Oligowalk_object::CommonConstructor ( )
private
double Oligowalk_object::GetBreakTargetDG ( const int  index)

Get the breaking target DG for a given nucleotide. This can only be called after performing a valid OligoWalk calculation. In case of error, the function returns a free energy change of zero. Note!: That a free energy change of zero is also a valid folding free energy change. Errors will also generate an internal error code, accessible with GetErrorCode().

Parameters
indexis an int that specifies the 5' end of an oligonucleotide binding site on the target.
Returns
A double that is the free energy change in kcal/mol.
double Oligowalk_object::GetDuplexDG ( const int  index)

Get the duplex DG for a given nucleotide. This can only be called after performing a valid OligoWalk calculation. In case of error, the function returns a free energy change of zero. Note!: That a free energy change of zero is also a valid folding free energy change. Errors will also generate an internal error code, accessible with GetErrorCode().

Parameters
indexis an int that specifies the 5' end of an oligonucleotide binding site on the target.
Returns
A double that is the free energy change in kcal/mol.
const char * Oligowalk_object::GetErrorMessage ( const int  error)

Return error messages based on code from GetErrorCode and other error codes. 100 = no OligoWalk data present 101 = OligoWalk has already been performed other codes are handled by the RNA base class function GetErrorMessage.

Parameters
erroris the integer error code provided by GetErrorCode()/
Returns
A pointer to a c string that provides an error message or from other functions that return integer error codes.
double Oligowalk_object::GetOligoOligoDG ( const int  index)

Get the bimolecular oligo-oligo DG for a given nucleotide. This can only be called after performing a valid OligoWalk calculation. In case of error, the function returns a free energy change of zero. Note!: That a free energy change of zero is also a valid folding free energy change. Errors will also generate an internal error code, accessible with GetErrorCode().

Parameters
indexis an int that specifies the 5' end of an oligonucleotide binding site on the target.
Returns
A double that is the free energy change in kcal/mol.
double Oligowalk_object::GetOligoSelfDG ( const int  index)

Get the oligo-self DG for a given nucleotide. This can only be called after performing a valid OligoWalk calculation. In case of error, the function returns a free energy change of zero. Note!: That a free energy change of zero is also a valid folding free energy change. Errors will also generate an internal error code, accessible with GetErrorCode().

Parameters
indexis an int that specifies the 5' end of an oligonucleotide binding site on the target.
Returns
A double that is the free energy change in kcal/mol.
double Oligowalk_object::GetOverallDG ( const int  index)

Get the overall DG for a given nucleotide. This can only be called after performing a valid OligoWalk calculation. In case of error, the function returns a free energy change of zero. Note!: That a free energy change of zero is also a valid folding free energy change. Errors will also generate an internal error code, accessible with GetErrorCode().

Parameters
indexis an int that specifies the 5' end of an oligonucleotide binding site on the target.
Returns
A double that is the free energy change in kcal/mol.
double Oligowalk_object::GetTm ( const int  index)

Get the Tm for a given nucleotide. This can only be called after performing a valid OligoWalk calculation. In case of error, the function returns a free energy change of zero. Note!: That a free energy change of zero is also a valid folding free energy change. Errors will also generate an internal error code, accessible with GetErrorCode().

Parameters
indexis an int that specifies the 5' end of an oligonucleotide binding site on the target.
Returns
A double that is the Tm in degrees C.
int Oligowalk_object::OligoScreen ( const char  infilename[],
const char  outfilename[] 
)

This function runs OligoScreen.

Read a list of oligonucleotides in infilename and output thermodynamic characteristics in outfilename. The backbone type is set when the constructor is called. Note that oligoscreen has no target sequence, so the default constructor OligoWalk(bool IsRNA) should be used.

Parameters
infilenameis a c-string that indicates the filename to be read.
outfilenameis a c-string that indicates the name of an output file to be written with report.
Returns
An int that indicates an error code that can be parsed by GetErrorMessage() or GetErrorMessageString(), 0 = no error.
int Oligowalk_object::Oligowalk ( const int  oligo_length,
const bool  isDNA,
const int  option,
const double  oligo_concentration,
const int  usesub,
const int  start,
const int  stop 
)

Perform an OligoWalk calculation. Note that this can only be performed once.

Parameters
oligo_lengthis an int that gives the length of the oligonucleotides.
isDNAis a bool that indicates the oligonucleotide chemistry, where true = DNA and false = RNA.
optionis an int that gives the calculation type, where option 1 = break local target structure to bind oligo, option 2 = refold target RNA after oligo binding, and option 3 = no target structure considered.
oligo_concentrationis a double that indicates the oligonucleotide concentration in M.
usesubis an int that indicates whether suboptimal structures are to be used, where 0 = none and 3 = use heuristic method.
startis an int that indicates the starting location of the walk.
stopis an int that indicates the ending location of the walk.
Returns
An integer that indicates an error code that can be parsed by GetErrorMessage() or GetErrorMessageString(), 0 = no error.
int Oligowalk_object::WriteReport ( const char  outputfilename[],
const int  oligo_length,
const bool  isDNA,
const int  option,
const double  oligo_concentration,
const int  usesub,
const int  start,
const int  stop 
)

Write a report for an OligoWalk calculation. This must be called after performing a valid OligoWalk calculation.

Parameters
outputfilenameis a c-string that provides a filename to which the report will be written.
oligo_lengthis an int that gives the length of the oligonucleotides.
isDNAis a bool that indicates the oligonucleotide chemistry, where true = DNA and false = RNA.
optionis an int that gives the calculation type, where option 1 = break local target structure to bind oligo, option 2 = refold target RNA after oligo binding, and option 3 = no target structure considered.
oligo_concentrationis a double that indicates the oligonucleotide concentration in M.
usesubis an int that indicates whether suboptimal structures are to be used, where 0 = none and 3 = use heuristic method.
startis an int that indicates the starting location of the walk.
stopis an int that indicates the ending location of the walk.
Returns
An integer that indicates an error code that can be parsed by GetErrorMessage() or GetErrorMessageString(), 0 = no error.

Member Data Documentation

int Oligowalk_object::length
private
int ** Oligowalk_object::numofsubstructures
private
siPREFILTER* Oligowalk_object::prefilter
private
int** Oligowalk_object::table
private

The documentation for this class was generated from the following files: