RNA Class Reference

#include <RNA.h>

Inheritance diagram for RNA:

Public Member Functions
	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...
double	ExteriorLoopCorrection (const int structurenumber, const bool UseSimpleMBLoopRules, int min_index, int max_index)
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, double threshold=0)
	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, double threshold=0)
	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[], const bool bynt=false)
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...
void	SetConstraints (vector< int > ss)
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, const int start=0, const int end=0)
	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
std::string	GetSequence (size_t start, size_t length=std::string::npos) const
bool	GetBackboneType () const
	Get the backbone type. More...
double	GetVprimeQ (const int i, const int j)
double	GetW (const int i, const int j)
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 ()

Static Public Member Functions
static const char *	GetErrorMessage (const int error)
	Return error messages based on code from GetErrorCode and other error codes. More...

Protected Member Functions
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
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
DynProgArray< PFPRECISION > *	wlc
PFPRECISION	Q
Protected Attributes inherited from Thermodynamics
datatable *	data
datatable *	enthalpy
bool	copied
double	nominal_temperature
string	nominal_alphabetName
bool	skipThermoTables

Private Attributes
structure *	ct
bool	partitionfunctionallocated
bool	energyallocated
DynProgArray< integersize > *	ew2
DynProgArray< integersize > *	ewmb2
integersize *	ew5
integersize *	ew3
int	vmin
DynProgArray< integersize > *	ev
DynProgArray< integersize > *	ew
DynProgArray< integersize > *	ewmb
bool *	lfce
bool *	mod
forceclass *	fce
coordinates *	structurecoordinates
bool	drawallocated
string	lastErrorDetails

Additional Inherited Members
Public Attributes inherited from Thermodynamics
bool	isrna

Constructor & Destructor Documentation

RNA() [1/5]

RNA::RNA	(	const char	sequence[],
		const bool	IsRNA = true
	)

Constructor - user provides a sequence as a c string.

Input sequence should contain A,C,G,T,U,a,c,g,t,u,x,X. The sequence is case-sensitive. Lower case letters are marked as unpaired. T=t=u=U. If IsRNA is true, the backbone is RNA, so U is assumed. If IsRNA is false, the backbone is DNA, so T is assumed. x=X= nucleotide that neither stacks nor pairs. Unknown nucs result in an error. 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

sequence	is a NULL terminated c string.
IsRNA	is a bool that indicates whether this sequence is RNA or DNA. true=RNA. false=DNA. Default is true.

RNA() [2/5]

RNA::RNA	(	const char	filepathOrSequence[],
		const RNAInputType	fileType,
		const char *const	alphabetName,
		const bool	allowUnknownBases = false,
		const bool	skipThermoTables = false
	)

Constructor - user provides a filename for existing file as a c string. The existing file, specified by filename, can either be a ct file, a sequence, or an RNAstructure save file. 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 that the contructor needs to be explicitly told, via IsRNA, what the backbone is because files do not store this information. Note also that save files explicitly store the thermodynamic parameters, therefore changing the backbone type as compared to the original calculation will not change structure predictions.

Parameters

filepathOrSequence	is null terminated c string that can be either a path to a CT, SEQ, FASTA, PFS, SAV, or DBN file or a full RNA sequence (whitepsace allowed)
fileType	is an RNAInputType (e.g FILE_CT, FILE_SEQ etc) that indicates what type of file filepathOrSequence refers to. If filepathOrSequence is an in-place sequence, fileType should be SEQUENCE_STRING.
alphabetName	is a c-string that specifies the alphabet name (e.g. "rna", "dna", etc)
allowUnknownBases	boolean that determines the handling of unknown bases (i.e. those not defined in the alphabet) If allowUnknownBases is true, they will be interpreted as bases that neither pair nor stack. Otherwise they will result in an error.
skipThermoTables	If true, only the alphabet specification will be loaded, not the full thermodynamic energy tables. The default is false – i.e. load all tables. This should only be set to true in programs that never make use of energies – i.e. ct2dot etc.

RNA() [3/5]

RNA::RNA	(	const char	filepathOrSequence[],
		const RNAInputType	fileType,
		const Thermodynamics *	copyThermo
	)

Constructor - user provides a filename for existing file as a c string. Construct an RNA from either a sequence or file. Copy the Thermodynamics info and datatable from another Thermodynamics instance.

Parameters

filepathOrSequence	is null terminated c string that can be either a path to a CT, SEQ, FASTA, PFS, SAV, or DBN file or a full RNA sequence (whitepsace allowed)
fileType	is an RNAInputType (e.g FILE_CT, FILE_SEQ etc) that indicates what type of file filepathOrSequence refers to. If filepathOrSequence is an in-place sequence, fileType should be SEQUENCE_STRING.
copyThermo	A pointer to an existing Thermodynamics from which to copy the datatables.

RNA() [4/5]

RNA::RNA	(	const char	filename[],
		const RNAInputType	fileType,
		const bool	IsRNA = true
	)

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

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: 1 => .ct file, 2 => .seq file, 3 => partition function save (.pfs) file, 4 => folding save file (.sav), 5 => DotBracket (DBN) file 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 that the contructor needs to be explicitly told, via IsRNA, what the backbone is because files do not store this information. 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

filename	is null terminated c string.
fileType	is an integer that indicates the file type.
IsRNA	is a bool that indicates whether this sequence is RNA or DNA. true=RNA. false=DNA. Default is true.

RNA() [5/5]

RNA::RNA

(

const bool

IsRNA = true

)

Default Constructor - user provides nothing. This basic constructor is provided for bimolecular folding and should not generally need to be accessed by end users of the RNA class.

Parameters

IsRNA

is a bool that indicates whether this sequence is RNA or DNA. true=RNA. false=DNA. Default is true.

~RNA()

RNA::~RNA

(

)

Destructor.

The destructor automatically cleans up all allocated memory for predicted or specified structures.

Member Function Documentation

AddComment()

int RNA::AddComment	(	const char	comment[],
		const int	structurenumber = 1
	)

Add a comment associated with a structure.

This comment will appear in a written .ct file. The comment is appended to any existing comments, like titles read from .seq files. This function is especially useful if the constructor is used in which a character array is provided with the sequence. In that case, there is no sequence title read. The function returns 0 in the case of no errors, or 3 if the structurenumber is invalid. An error message can be retrieved using GetErrorMessage() called with the errorcode.

Parameters

comment	is a character array that contains a null terminated c-string with the comment to be registered.
structurenumber	is an integer that specifies to which structure the comment should be added.

Returns

An integer that contains an error code, where 0 is no error and non-zero is an error.

BreakPseudoknot()

int RNA::BreakPseudoknot	(	const bool	minimum_energy = true,
		const int	structurenumber = 0,
		const bool	useFastMethod = true
	)

Break any pseudoknots that might be in a structure.

This function uses the method of Smit et al. to break pseudoknots by running a dynamic programming algorithm that cannot predict pseudoknots while only allowing the pairs that already exist in the structure. When minimum_energy = true (the default), this function predicts the lowest free energy structure that has no pseudoknots. Note that when minimum_energy = true, this function might additionally break pairs that are not pseudoknotted if the pairs increase the folding free energy change or are forbidden (as in an isolated pair). Also note that when minum_energy=true, this function uses the GenerateAllSuboptimalStructures methodology behind the scenes, so large internal loops in the input would lead to a loss of pairs. When minumum_energy is set to false, this function maximizes the number of base pairs in the pseudoknot free structure. Return 0 if no error and non-zero errors can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

minimum_energy	is a bool thgat indicates where the structure should be minimum in free energy (true) or maximize pairs (false).
structurenumber	is an int that indicates a specific structure for which to break pseudoknots (indexed from 1). The default value, 0, indicates that all structures should have pseudoknots broken.
useFastMethod	If true (default) a fast method that is energy and sequence agnostic will be used to find pseudoknots. This method should be identical in results to MEAFill, but much faster. However, if minimum_energy is also true, AllTrace will be used instead of the fast method (i.e. this parameter will be ignored).

Returns

an int that provides an error code. 0 = no error.

CalculateFreeEnergy()

double RNA::CalculateFreeEnergy	(	const int	structurenumber = 1,
		const bool	UseSimpleMBLoopRules = false
	)

Return the predicted Gibb's free energy change for structure # structurenumber, defaulted to 1.

Free energies are in kcal/mol. The first time this is called, if no other free energy calculation has been performed and the folding temperature has not been specifed, thermodynamic parameter files (.dat) files will be read from disk. The parameter files should be located in the directory specified by environment variable $DATAPATH, or the pwd. 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(). GetErrorCode() will return 0 when there is no error and other codes can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

structurenumber	is an integer that refers to the index of the structure for which to calculate the folding free energy change. This defaults to 1.
UseSimpleMBLoopRules	is a bool that indicates what energy rules to use. The default, false, uses the complete nearest neighbor model for multibranch loops. When true is passed, the energy model is instead a simplified model that is the one used by the dynamic programming algorithms.

Returns

A double which is the folding free energy change in kcal/mol.

ContainsPseudoknot()

bool RNA::ContainsPseudoknot

(

const int

structurenumber

)

Report if there are any pseudoknots in a structure.

This method checks for any "crossing pairs," i.e. i-j and i'-j' s.t. i < i' < j < jp. If there is at least one crossing pair set, then there is a pseudoknot and the function returns true. This function generates internal error codes that can be accessed by GetErrorCode() after the constructor is called: 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters

structurenumber

is an int that indicates the structure number to check. Note that indexing of structures starts with structure #1.

Returns

A bool that indicates whether there is a pseudoknot.

CopyThermo()

void RNA::CopyThermo

(

Thermodynamics &

copy

)

Copy thermodynamic parameters from an instance of an RNA class.

This is generally not needed because functions automatically populate the parameters from disk. It is helpful, however, in constructors of derived classes. Normally the Thermodyanamic(Thermodynamic* copy) constructor should be used instead. Reason: Since the extended alphabet, the datatable is loaded in the RNA class constructor, so copying the datatable must also happen in the constructor to avoid reading a (possibly different) datatable first.

DetermineDrawingCoordinates()

int RNA::DetermineDrawingCoordinates	(	const int	height,
		const int	width,
		const int	structurenumber = 1
	)

Determine the coordinates for drawing a secondary structure.

This function determines drawing coordinates for all nucleotides in structure number structurenumber. User must specify the height and width of a character (use the largest of nucleotides). The coordinates are in an abstract palette; the user must determine the minimum and maximum coordinate in both the x and y direction. The actual coordinates are fetched using GetNucleotideXCoordinate(int i) and GetNucleotideYCoordinate(int i). This function returns are error code, where 0=no error and other messages can be resolved to a c string using GetErrorMessage. The structure to be drawn must be free of pseudoknots.

Parameters

height	is an integer that refers to the height of a nucleotide.
width	is an integer that refers to the width of a nucleotide, where the largest nucleotide should be provided or a non-proportional font should be used.
structurenumber	is an integer that refers to the structure to be drawn.

Returns

An int that provides an error code, 0 = no error and other errors can be resolved to a c string using GetErrorMessage.

EnsureStructureCapcacity()

void RNA::EnsureStructureCapcacity

(

const int

minimumStructures

)

Ensure that at a minumum number of structures have been created.

ExteriorLoopCorrection()

double RNA::ExteriorLoopCorrection	(	const int	structurenumber,
		const bool	UseSimpleMBLoopRules,
		int	min_index,
		int	max_index
	)

FileReader()

int RNA::FileReader ( const char  filename[], const RNAInputType  fileType  )

protected

FoldSingleStrand()

int RNA::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.

This function predicts the lowest free energy structure and suboptimal structures. If the temperature has not been specified using SetTemperature and no free energies have been calculated, the thermodynamic parameters have not been read and therefore they will be read by this function call. The parameter files should be located in the directory specified by the environment variable $DATAPATH of the pwd. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

percent	is the maximum % difference in free energy in suboptimal structures from the lowest free energy structure. The default is 20.
maximumstructures	is the maximum number of suboptimal structures to generate. The default is 20.
window	is a parameter that specifies how different the suboptimal structures should be from each other (0=no restriction and larger integers require structures to be more different). The defaults is 5, but this should be customized based on sequence length.
savefile	is c string containing a file path and name for a savefile (.sav)that can be used to generate energy dot plots and to refold the secondary structure using different suboptimal structure parameters. The default is "", which results in no save file written.
maxinternalloopsize	is the maximum number of unpaired nucleotides in bulge and internal loops. This is used to accelerate the prediction speed. The default is 30.
mfeonly	is a bool that indicates whether only the minimum free energy structure will be generated. This saves half the calculation time, but no save file can be generated. Default is false.

Returns

An int that indicates an error code (0 = no error, 5 = error reading thermodynamic parameter files, 14 = traceback error).

ForceDoubleStranded()

int RNA::ForceDoubleStranded

(

const int

i

)

Force a nucleotide to be double stranded (base paired).

This function indicates a nucleotide that is double stranded (paired). In subsequent structure prediction, this nucleotide will be double stranded. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

i	is the index of the paired nucleotide.

Returns

An integer that indicates an error code (0 = no error, 4 = nucleotide out of range, 8 = too many restraints specified, 9 = same nucleotide in conflicting restraint).

ForceFMNCleavage()

int RNA::ForceFMNCleavage

(

const int

i

)

Indicate a nucleotide that is accessible to FMN cleavage (a U in GU pair).

In subsequent structure prediction, this nucleotide will be in a GU pair. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

i	is the index of the FMN-cleaved nucleotide.

Returns

An integer that indicates an error code (0 = no error, 4 = nucleotide out of range, 8 = too many restraints specified, 9 = same nucleotide in conflicting restraint, 11 = nucleotide not U).

ForceMaximumPairingDistance()

int RNA::ForceMaximumPairingDistance

(

const int

distance

)

Force a maximum distance between apired nucleotides.

In a subsequent structure prediction, there will be no pairs allowed between nucleotides more distant than distance, i.e. |j-i| < distance for i to pair to j. The function returns and error code; 0==no error, 12== too long or too short distance.

Parameters

distance

is the maximum pairing distance.

Returns

An integer that indicates an error code (0 = no error, 12 = too short).

ForceModification()

int RNA::ForceModification

(

const int

i

)

Force modification for a nucleotide.

This function indicates a nucleotide that is accessible to chemical modification. In subsequent structure prediction, this nucleotide will be single stranded, at the end of a helix, or in or adjacent to a GU pair. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

i	is the index of the nucleotide accessible to chemical modification.

Returns

An integer that indicates an error code (0 = no error, 4 = nucleotide out of range, 8 = too many restraints specified).

ForcePair()

int RNA::ForcePair	(	const int	i,
		const int	j
	)

Force a pair between two nucleotides.

This function forces a pair between two nucleotides in subsequent structure predictions. When multiple pairs are specified, the pairs must not force a pseudoknot. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

i	is the index of one nucleotide in the pair.
j	is the index of the second nucleotide in the pair.

Returns

An integer that indicates an error code (0 = no error, 4 = nucleotide out of range, 6 = pseudoknot formation, 7 = non-canonical pair, 8 = too many restraints specified, 9 = same nucleotide in conflicting restraint).

ForceProhibitPair()

int RNA::ForceProhibitPair	(	const int	i,
		const int	j
	)

Prohibit a pair between two nucleotides.

This function prevents a pair between two nucleotides in subsequent structure predictions. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

i	is the index of one nucleotide in the pair.
j	is the index of the second nucleotide in the pair.

Returns

An integer that indicates an error code (0 = no error, 4 = nucleotide out of range, 8 = too many restraints specified, 9 = nucleotide in conflicting restraint).

ForceSingleStranded()

int RNA::ForceSingleStranded

(

const int

i

)

Force a nucleotide to be single stranded.

This function indicates a nucleotide that is single stranded. In subsequent structure prediction, this nucleotide will be single stranded. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

i	is the index of the nucleotide that is single stranded.

Returns

An integer that indicates an error code (0 = no error, 4 = nucleotide out of range, 8 = too many restraints specified, 9 = same nucleotide in conflicting restraint).

GenerateAllSuboptimalStructures()

int RNA::GenerateAllSuboptimalStructures	(	const float	percent = 5,
		const double	deltaG = 0.6
	)

Predict the lowest free energy secondary structure and generate all suboptimal structures.

This function predicts the lowest free energy structure and suboptimal structures. If the temperature has not been specified using SetTemperature and no free energies have been calculated, the thermodynamic parameters have not been read and therefore they will be read by this function call. The parameter files should be located in the directory specified by the environment variable $DATAPATH of the pwd. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString(). Two controls are available for limiting the number of structures, the maximum % difference in energy (percent) and the maximum absolute change in energy (deltaG). The smaller of the two will be used as the limit.

Parameters

percent	is the maximum % difference in free energy in suboptimal structures from the lowest free energy structure. The default is 5.
deltaG	is the maximum difference in free energy change above the lowest free energy structure (in kcal/mol). The defaults is 0.6 kcal/mol.

Returns

An int that indicates an error code (0 = no error, non-zero = error).

GetBackboneType()

bool RNA::GetBackboneType

(

)

const

Get the backbone type.

This function returns whether the backbone is RNA or DNA. Note that backbone type is set when calling the constructor.

Returns

A bool that indicates the backbone (true = RNA, false = DNA).

GetCommentString()

std::string RNA::GetCommentString

(

const int

structurenumber = 1

)

Provide the comment from the ct file as a string.

This function provides the comment from the CT file for a structure as a string. This function generates internal error codes that can be accessed by GetErrorCode() after the function is called: 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters

structurenumber

is the structure for which the comment is to be provided.

Returns

A string that provides the comment.

GetEnsembleDefect()

double RNA::GetEnsembleDefect	(	const int	structurenumber = 1,
		const int	start = 0,
		const int	end = 0
	)

Get the ensemble defect of a secondary structure.

Returns the ensemble defect as determined by the partition function.

Parameters

structurenumber	is an integer indicating the predicted structure number.
start	is the start nucleotide (1-indexed) for a local calculation. end is the end nucleotide for a local calculation.

Returns

A double that is the ensemble defect. To get the Normalized Ensemble Defect, this number must be divided by the Sequence Length.

GetEnsembleEnergy()

double RNA::GetEnsembleEnergy

(

)

Get the ensemble folding free energy change.

Returns the ensemble folding free energy change as determined by the partition function. This is a handy way of getting the size of the partition function Q, which itself is too large to fit in a double for all but the shortest sequences. The ensemble folding free energy change = -RT ln (Q). Function requires that the partition function data be present either because PartitionFunction() has been called or the constructor that reads a partition function save was used. This function generates internal error codes that can be accessed by GetErrorCode() after the constructor is called: 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage.

Returns

A double that is the ensemble folding free energy change in kcal/mol.

GetErrorCode()

int RNA::GetErrorCode

(

)

const

Return an error code, where a return of zero is no error.

This function returns and error flag that is generated during construction by RNA(const char &filename, const int type, const bool IsRNA=true) or from CalculateFreeEnergy(). An error of zero is always no error. Other codes are errors and a c-string can be fetched for the error with GetErrorMessage().

Returns

An integer that provides the error code.

GetErrorDetails()

const string RNA::GetErrorDetails

(

)

const

Returns extended details about the last error. (e.g. error messages produced during file read operations that are otherwise lost.)

GetErrorMessage()

const char * RNA::GetErrorMessage ( const int  error )

static

Return error messages based on code from GetErrorCode and other error codes.

0 = no error 1 = input file not found 2 = error opening file 3 = structure number out of range 4 = nucleotide number out of range 5 = error reading thermodynamic parameters 6 = pseudoknot formation 7 = non-canonical pair 8 = too many restraints specified 9 = same nucleotide in conflicting restraint 10 = no structures to write 11 = nucleotide not a U (caused by ForceFMNCleavage() 12 = distance too short 13 = error reading constraint file 14 = traceback error 15 = no partition function data present 16 = incorrect save file version used 17 = cannot be performed without having read a save file (.sav) 18 = threshold is too low to be valid 19 = drawing coordinates have not been determined 20 = no sequence has been read 21 = over 1 probability error on stochastic traceback 22 = programming error, unrecognized input to constructor 23 = no structures present 24 = too few iterations 25 = index (for drawing) is not a multiple of 10

Parameters

error

is the integer error code provided by GetErrorCode() or from other functions that return integer error codes.

Returns

A pointer to a c string that provides an error message.

GetErrorMessageString()

string RNA::GetErrorMessageString

(

const int

error

)

const

Return error messages based on code from GetErrorCode and other error codes.

Although RNA generally uses c strings, this function returns a string that is suitable for interfacing with JAVA, etc. See the error list in the GetErrorMessage() entry.

Parameters

error

is the integer error code provided by GetErrorCode() or from other functions that return integer error codes.

Returns

A string that provides an error message.

GetForcedDoubleStranded()

int RNA::GetForcedDoubleStranded

(

const int

constraintnumber

)

Return a nucleotide that is forced double stranded.

This function returns a nucleotide that is constrainted to be paired. Constraints are numbered from zero to GetNumberofForcedDoubleStranded()-1.

Parameters

constraintnumber

is the index to the constraint number.

Returns

An integer that is the nucleotide index. If the constraintnumber is for a constraint that does not exist, zero is returned.

GetForcedFMNCleavage()

int RNA::GetForcedFMNCleavage

(

const int

constraintnumber

)

Return a nucleotide that is accessible to FMN cleavage.

This function returns a nucleotide that is constrainted to be accessible to FMN cleavage (a U in a GU pair). Constraints are numbered from zero to GetNumberofForcedFMNCleavages()-1.

Parameters

constraintnumber

is the index to the constraint number.

Returns

An integer that is the nucleotide index. If the constraintnumber is for a constraint that does not exist, zero is returned.

GetForcedModification()

int RNA::GetForcedModification

(

const int

constraintnumber

)

Return a nucleotide that is accessible to modification.

This function returns a nucleotide that is constrainted to be accessible to chemical modification. Constraints are numbered from zero to GetNumberofModifications()-1.

Parameters

constraintnumber

is the index to the constraint number.

Returns

An integer that is the nucleotide index. If the constraintnumber is for a constraint that does not exist, zero is returned.

GetForcedPair()

int RNA::GetForcedPair	(	const int	constraintnumber,
		const bool	fiveprime
	)

Return a nucleotide in a forced pair.

This function returns either the five prime or three prime nucleotide in a forced pair constraint, depending on the value of fiveprime. Constraints are numbered from zero to GetNumberofForcedPairs()-1.

Parameters

constraintnumber	is the index to the constraint number.
fiveprime	determines if the nucleotide is the five prime or the three prime nucleotide in the constraint. true = five prime nucleotide.

Returns

An integer that is the nucleotide index. If the constraintnumber is for a constraint that does not exist, zero is returned.

GetForcedProhibitedPair()

int RNA::GetForcedProhibitedPair	(	const int	constraintnumber,
		const bool	fiveprime
	)

Return a nucleotide in a prohibited pair.

This function returns either the five prime or three prime nucleotide in a prohibited pair constraint, depending on the value of fiveprime. Constraints are numbered from zero to GetNumberofForcedProhibited()-1.

Parameters

constraintnumber	is the index to the constraint number.
fiveprime	determines if the nucleotide is the five prime or the three prime nucleotide in the constraint. true = five prime nucleotide.

Returns

An integer that is the nucleotide index. If the constraintnumber is for a constraint that does not exist, zero is returned.

GetForcedSingleStranded()

int RNA::GetForcedSingleStranded

(

const int

constraintnumber

)

Return a nucleotide that is forced single stranded.

This function returns a nucleotide that is constrainted to be single stranded. Constraints are numbered from zero to GetNumberofForcedSingleStranded()-1.

Parameters

constraintnumber

is the index to the constraint number.

Returns

An integer that is the nucleotide index. If the constraintnumber is for a constraint that does not exist, zero is returned.

GetFreeEnergy()

double RNA::GetFreeEnergy

(

const int

structurenumber

)

Get the folding free energy change for a predicted structure.

Returns the folding free energy change of structure i as determined by a previous folding calculation. Function requires that the structure be predicted by a structure prediction method. This function generates internal error codes that can be accessed by GetErrorCode() after the constructor is called: 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters

structurenumber

is an integer indicating the predicted structure number.

Returns

A double that is the folding free energy change in kcal/mol.

GetFullErrorMessage()

string RNA::GetFullErrorMessage

(

)

const

If there was an error, this returns the error message, along with error details (if any). if there was no error (i.e. GetErrorCode() returns 0 and GetErrorDetails() returns NULL), this function returns an empty string ("");

GetLabelXCoordinate()

int RNA::GetLabelXCoordinate

(

const int

i

)

Get the X coordinate for placing the nucleotide index label specified by i.

This function gets the X coordinate for placing the nucleotide index label specified by i. The user needs to have determined the coordinates for a complete structure using DetermineDrawingCoordinates prior to making this call. This function generates internal error codes that can be accessed by GetErrorCode(): 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage. Zero is returned in case of error, but note that zero is also a valid coordinate. One additiona caveat: Labels that are placed at 0,0 are lables that would have overlapped nucleotides. These labels should not be drawn.

Parameters

i	is an integer refering to the label to be drawn. This needs to be a multiple of 10.

Returns

An int that gives the X coordinate.

GetLabelYCoordinate()

int RNA::GetLabelYCoordinate

(

const int

i

)

Get the Y coordinate for placing the nucleotide index label specified by i.

This function gets the Y coordinate for placing the nucleotide index label specified by i. The user needs to have determined the coordinates for a complete structure using DetermineDrawingCoordinates prior to making this call. This function generates internal error codes that can be accessed by GetErrorCode(): 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage. Zero is returned in case of error, but note that zero is also a valid coordinate. One additiona caveat: Labels that are placed at 0,0 are lables that would have overlapped nucleotides. These labels should not be drawn.

Parameters

i	is an integer refering to the label to be drawn. This needs to be a multiple of 10.

Returns

An int that gives the Y coordinate.

GetMaximumPairingDistance()

int RNA::GetMaximumPairingDistance

(

)

Return the maximum pairing distance.

return An integer that indicates the maximum distance allowed between paired nucleotides, where -1 indicates that the maximum distance is not set.

GetNucleotide()

char RNA::GetNucleotide

(

const int

i

)

param An integer specifying the nucleotide index (starting at 1 and ending at GetSequenceLength()). This function generates internal error codes that can be accessed by GetErrorCode(): 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage. Note that nucleotides are numbered starting at an index of 1. return The char representing the nucleotide at index i or '-' if an error occured.

GetNucleotideXCoordinate()

int RNA::GetNucleotideXCoordinate

(

const int

i

)

Get the X coordinate for nucleotide i for drawing a structure.

This function gets the X coordinate for placing the nucleotide specified by i. The user needs to have determined the coordinates for a complete structure using DetermineDrawingCoordinates prior to making this call. This function generates internal error codes that can be accessed by GetErrorCode(): 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage. Zero is returned in case of error, but note that zero is also a valid coordinate.

Parameters

i	is an integer refering to the nucleotide to be drawn.

Returns

An int that gives the X coordinate.

GetNucleotideYCoordinate()

int RNA::GetNucleotideYCoordinate

(

const int

i

)

Get the Y coordinate for nucleotide i for drawing a structure.

This function gets the Y coordinate for placing the nucleotide specified by i. The user needs to have determined the coordinates for a complete structure using DetermineDrawingCoordinates prior to making this call. This function generates internal error codes that can be accessed by GetErrorCode(): 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage. Zero is returned in case of error, but note that zero is also a valid coordinate.

Parameters

i	is an integer refering to the nucleotide to be drawn.

Returns

An int that gives the Y coordinate.

GetNumberOfForcedDoubleStranded()

int RNA::GetNumberOfForcedDoubleStranded

(

)

Return the number of nucletides forced to be paired.

Returns

An integer that indicates the number of nucleotides that are forced pair.

GetNumberOfForcedFMNCleavages()

int RNA::GetNumberOfForcedFMNCleavages

(

)

Return the number of nucleotides accessible to FMN cleavage.

Returns

An integer that indicates the number of FMN cleavage nucleotides (Us in GU pairs).

GetNumberOfForcedModifications()

int RNA::GetNumberOfForcedModifications

(

)

Return the number of nucleotides accessible to chemical modification.

Returns

An integer that indicates the number of modified nucleotides.

GetNumberOfForcedPairs()

int RNA::GetNumberOfForcedPairs

(

)

Return the number of forced base pairs.

Returns

An integer that indicates the number of forced pairs.

GetNumberOfForcedProhibitedPairs()

int RNA::GetNumberOfForcedProhibitedPairs

(

)

Return the number of prohibited base pairs.

Returns

An integer that indicates the number of pairs that are prohibited.

GetNumberOfForcedSingleStranded()

int RNA::GetNumberOfForcedSingleStranded

(

)

Return the number of nucleotides that are not allowed to pair.

Returns

An integer that indicates the number of nucleotides not allowed to pair.

GetPair()

int RNA::GetPair	(	const int	i,
		const int	structurenumber = 1
	)

Get the nucleotide to which the specified nucleotide is paired.

Returns the pairing partner of the ith nucleotide in structure number structurenumber. Zero means the nucleotide is unpaired. This function generates internal error codes that can be accessed by GetErrorCode() after the constructor is called: 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters

i	is an int that indicates the nucleotide to which the pairing partner is being queried.
structurenumber	is an int that indicates the structure number, where the default is 1.

Returns

An int that indicates the other nucleotide in pair, where 0 is no paired.

GetPairEnergy()

double RNA::GetPairEnergy	(	const int	i,
		const int	j
	)

Get the lowest folding free energy possible for a structure containing pair i-j.

Returns a folding free energy change in kcal/mol for use in energy dot plots. This function requires that the RNA constructor be called with a save file (.sav) name. (That is, for historical resaons, this cannot be called after FoldSingleStrand without writing the data to disk.) This function generates internal error codes that can be accessed by GetErrorCode() after the constructor is called: 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage. param i and j are ints that provide indexes the 5' and 3' nucleotides, respectively, in a pair. return A double that is the folding free energy change in kcal/mol.

GetPairProbabilities()

int RNA::GetPairProbabilities	(	double *	arr,
		const int	size
	)

Fills an array with all basepair probabilities Function requires that the partition function data be present either because PartitionFunction() has been called or the constructor that reads a partition function save was used. This function generates internal error codes that can be accessed by GetErrorCode(): 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters

arr	A pointer to an array of doubles to receive the probabilities. The array should be allocated to hold (N-1)*N/2 elments, where N is the sequence length. The array will be filled with probabilities in upper-triangular format: e.g. for N=5 the array would be: P(1:2) P(1:3) P(1:4) P(1:5) P(2:3) P(2:4) P(2:5) P(3:4) P(3:5) P(4:5) (i.e. 5*4/2 = 10 elements)
size	The size of the array of doubles. If this is less than the required size, the array will not be modified and the function will return the required array size.

Returns

The total size required to hold the array of probabilities. This is equal to (N-1)*N/2 elments, where N is the sequence length. The function returns a negative number if an error occurred. Call GetErrorMessage(-returnValue) to get a textual description of the error.

GetPairProbability()

double RNA::GetPairProbability	(	const int	i,
		const int	j
	)

Get a base pair probability.

Returns the base pair probability for the pair between i and j. Function requires that the partition function data be present either because PartitionFunction() has been called or the constructor that reads a partition function save was used. This function generates internal error codes that can be accessed by GetErrorCode(): 0 = no error, nonzero = error. The errorcode can be resolved to a c string using GetErrorMessage.

Parameters

i	provides the 5' nucleotide in a pair.
j	provides the 3' nucleotides in a pair.

Returns

A double that is the base pair probability. If i and j cannot pair, 0.0 is returned. If an error occurs, 0.0 is returned.

GetProgress()

ProgressHandler * RNA::GetProgress

(

)

Return the current pointer to an instance of a class derived from ProgressHandler (such as TProgressDialog for text-mode programs or a simple ProgressHandler for GUI progams or scripts) This is used during inheritance to provide access to the underlying TProgressDialog.

GetSequence() [1/2]

const char * RNA::GetSequence

(

)

const

Returns

The full nucleotide sequence.

GetSequence() [2/2]

std::string RNA::GetSequence	(	size_t	start,
		size_t	length = std::string::npos
	)		const

Returns

A segment of the nucleotide sequence.

GetSequenceLength()

int RNA::GetSequenceLength

(

)

const

Get the total length of the sequence.

Returns

An integer that specifies the total length of the sequence.

GetStructure()

structure * RNA::GetStructure

(

)

Access the underlying structure class. This is provided for use with two sequence methods. Generally, there is no need for end users to use this function because the RNA class provides an convenient wrapper for accessing the information in an RNA class.

Returns

A pointer to structure.

GetStructureNumber()

int RNA::GetStructureNumber

(

)

const

Get the total number of specified or predicted structures.

Returns

An integer specify the total number of structures.

GetVprimeQ()

double RNA::GetVprimeQ	(	const int	i,
		const int	j
	)

GetW()

double RNA::GetW	(	const int	i,
		const int	j
	)

init()

void RNA::init ( const char *  sequenceOrFileName, const RNAInputType  fileType, const bool  allowUnknownBases = false, const bool  skipThermoTables = false  )

protected

MaximizeExpectedAccuracy()

int RNA::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.

This function predicts structures composed of probable base pairs and single-srtranded nucleotide, weighted by gamma. The score for a structure is = gamma * 2 * (sum of pairing probabilities for pairs) + (sum of unpairing probabilities for single stranded nucleotides). This function requires partition function data from either a previous partition function calculations or from having read a partition function save file during construction of the class. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

maxPercent	is the maximum percent difference is score in generating suboptimal structures. The default is 20.
maxStructures	is the maximum number of suboptimal structures to generate. The default is 20.
window	is the window parameter, where a higher value generates suboptimal structures that are more different from each other. The default is 1.
gamma	is the weight given to base pairs

Returns

An int that indicates an error code (0 = no error, non-zero = error).

PartitionFunction()

int RNA::PartitionFunction	(	const char	savefile[] = "",
		double	temperature = -10.0,
		bool	disablecoax = false,
		bool	restoreSHAPE = true
	)

Predict the partition function for a sequence.

This function must be called to predict base pair probabilities, perform stochastic traceback, or for maximizing expected accuracy. If the temperature has not been specified using SetTemperature and no free energies have been calculated, the thermodynamic parameters have not been read and therefore they will be read by this function call. The parameter files should be located in the directory specified by the environment variable $DATAPATH of the pwd. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString(). Note that the parameter temperature is used when calculating equilibrium constants, but does not change the temperature at which the free energies are determined. SetTemperature, from the underlying base class Thermodynamics, should be used to change the temperature for most calculations. This parameter should generally not be used. The default is -10.0 and values below zero cause this parameter to be ignored (the correct default behavior). Note also that if SetTemperature is not used, the temperature defaults to 310.15 K (37 deg. C), which is the desired behavior for most purposes.

Parameters

savefile	is a c string that contains the path and filename for creating a save file. This defaults to "", which indicates no file is to be written.
temperature	is a double that indicates a pseudo-temperature for calculating equilibrium constants from free energies at fixed temperature previously specified.
restoreSHAPE	Whether SHAPE data should be restored after this call. The default is true. PartitionFunction converts SHAPE pseudo-energies into equillibrium constants, overwriting the GetStructure()->SHAPE array. If restoreSHAPE is true, the original values will be restored before the function returns. Otherwise the equillibrium constants will remain in the GetStructure()->SHAPE array.

Returns

An int that indicates an error code (0 = no error, 5 = error reading thermodynamic parameter files).

PredictProbablePairs()

int RNA::PredictProbablePairs

(

const float

probability = 0

)

Predict structures containing highly probable pairs.

This function predicts structures composed of probable base pairs. This function requires partition function data from either a previous partition function calculations or from having read a partition function save file during construction of the class. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

probability

is the pairing probability threshold, where pairs will be predicted if they have a higher probability. Note that a value of less than 0.5 (50%), will cause an error. The default value of zero will trigger the creation of 8 structures, with thresholds of >=0.99, >=0.97, >=0.95, >=0.90, >=0.80, >=0.70, >=0.60, >0.50.

Returns

An int that indicates an error code (0 = no error, non-zero = error).

ProbKnot()

int RNA::ProbKnot	(	int	iterations = 1,
		int	MinHelixLength = 1,
		double	threshold = 0
	)

Predict maximum expected accuracy structures that contain pseudoknots from either a sequence or a partition function save file.

This function uses base pair probabilities to predict structures that contains pseudoknots. This function requires partition function data from either a previous partition function calculations or from having read a partition function save file during construction of the class. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

iterations	is the number of iterations of pair selection that are performed. The default and recommended value is 1.
MinHelixLength	is the shortest helix that is allowed. If this is set >1, a post-processing step is performed to remove short helices. Default = 1, i.e. no post-processing.
threshold	is the required minimum probability for a pair. Only include pairs with a higher probability. Default = 0, i.e. include all pairs.

Returns

An int that indicates an error code (0 = no error, non-zero = error).

ProbKnotFromSample()

int RNA::ProbKnotFromSample	(	int	iterations = 1,
		int	MinHelixLength = 1,
		double	threshold = 0
	)

Predict maximum expected accuracy structures that contain pseudoknots from a file containing ensemble of structures.

This function uses base pair probabilities to predict structures that contains pseudoknots. This function requires a file with ensemble of structures. This function processes the file to calculate pair probabilities. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

iterations	is the number of iterations of pair selection that are performed. The default and recommended value is 1.
MinHelixLength	is the shortest helix that is allowed. If this is set >1, a post-processing step is performed to remove short helices. Default = 1, i.e. no post-processing.
threshold	is the required minimum probability for a pair. Only include pairs with a higher probability. Default = 0, i.e. include all pairs.

Returns

An int that indicates an error code (0 = no error, non-zero = error).

ReadConstraints()

int RNA::ReadConstraints

(

const char

filename[]

)

Read a set of folding constraints to disk in a plain text file.

The file format for constraints is that generated by the WriteConstraints() function. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString(). Note that calling ReadConstraints() will erase previously defined constraints (except for SHAPE pseudoenergy restraints).

Parameters

filename

is a c string that is the file name to be read.

Returns

An integer that indicates an error code (0 = no error, 1 = file not found, 13 = error reading constraint file).

ReadDMS()

int RNA::ReadDMS	(	const char	filename[],
		const bool	bynt = false
	)

Read DMS data to constrain structure prediction on subsequent structure predictions.

Parameters

filename

is a c string that indicates a file that contains DMS data.

Returns

Returns an integer that indicates an error code (0 = no error, 1 = input file not found).

ReadDSO()

int RNA::ReadDSO

(

const char

filename[]

)

Read double strand offset data from disk.

The double strand offset is data that is used to constrain structure prediction on subsequent structure predictions. This is a free energy in kcal/mol that is added to a specific nucleotide that is double stranded. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

filename

is a c string that indicates a file that contains data, in a raw format with nucleotide index and offset (one set per line).

Returns

An integer that indicates an error code (0 = no error, 1 = input file not found).

ReadExperimentalPairBonus()

int RNA::ReadExperimentalPairBonus	(	const char	filename[],
		double const	experimentalOffset,
		double const	experimentalScaling
	)

Read experimental pair bonuses from disk.

This is a quantity that results in a bonus added to a specific pair, once per stack, so that pairs in the middle of a helix get the bonus twice and those at the end of a helix get the bonus once. The bonus is in the form of experimentalScaling*value + experimentalOffset. The data is formatted using a simple square matrix of values and no headers. The format requires that there be N^2 entries for a sequence of N nucleotides.

Parameters

filename	is a c string that indicates a file that contains data.
experimentalOffset	is a double that is added to each value.
experimentalScaling	is a double by which each value is multiplied.

Returns

An integer that indicates an error code (0 = no error, 1 = input file not found).

ReadSHAPE() [1/2]

int RNA::ReadSHAPE	(	const char	filename[],
		const double	slope,
		const double	intercept,
		RestraintType	modifier = RESTRAINT_SHAPE,
		const bool	IsPseudoEnergy = true
	)

Read SHAPE data from disk.

The SHAPE data is used to constrain structure prediction on subsequent structure predictions. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString(). Pseudo folding free energy change parameters should be in units of kcal/mol.

Parameters

filename	is a c string that indicates a file that contains SHAPE data.
IsPseudoEnergy	indicates whether this is the pseudo folding free energy constraint (the preferred method). This defaults to true.
slope	is the slope when IsPseudoEnergy=true and is a threshold above which nucleotides are forced single stranded otherwise.
intercept	is the intercept when IsPseudoEnergy=true and is a threshold above which a nucleotide is considered chemically modified otherwise.
modifier	is the type of chemical modification probe that was used (currently accepted values are SHAPE, diffSHAPE, DMS, and CMCT). Defaults to SHAPE.

Returns

An integer that indicates an error code (0 = no error, 1 = input file not found).

ReadSHAPE() [2/2]

int RNA::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.

The SHAPE data is used to constrain structure prediction on subsequent structure predictions. This version of the overloaded function includes a single-stranded pseudo free energy change. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString(). Pseudo folding free energy change parameters should be in units of kcal/mol.

Parameters

filename	is a c string that indicates a file that contains SHAPE data.
dsSlope	is the double-stranded slope.
dsIntercept	is the double-stranded intercept.
modifier	is the type of chemical modification probe that was used (currently accepted values are SHAPE, DMS, and CMCT). Defaults to SHAPE.
ssSlope	is the single-stranded slope.
ssIntercept	is the single-stranded intercept.

Returns

An integer that indicates an error code (0 = no error, 1 = input file not found).

ReadSSO()

int RNA::ReadSSO

(

const char

filename[]

)

Read single strand offset data from disk.

The single strand offset is data that is used to constrain structure prediction on subsequent structure predictions. This is a free energy in kcal/mol that is added to a specific nucleotide that is single stranded. The function returns 0 with no error and a non-zero otherwise that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

filename

is a c string that indicates a file that contains data, in a raw format with nucleotide index and offset (one set per line).

Returns

An integer that indicates an error code (0 = no error, 1 = input file not found).

ReFoldSingleStrand()

int RNA::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.

This function predicts the lowest free energy structure and suboptimal structure after a save file (.sav) was specified to the constructor. The step of predicting structures from the save file is rapid, so this is laregely a method to quickly generate a different set of suboptimal structures. Refolding can only be performed if the RNA constructor was called with a save file name. (That is, you cannot call this after calling fold single strand, without loading the data from disk with a new instance of RNA. This is for historical reasons.) In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

percent	is the maximum % difference in free energy in suboptimal structures from the lowest free energy structure. The default is 20.
maximumstructures	is the maximum number of suboptimal structures to generate. The default is 20.
window	is a parameter that specifies how different the suboptimal structures should be from each other (0=no restriction and larger integers require structures to be more different). The default is 5.

Returns

An int that indicates an error code (0 = no error, 5 = error reading thermodynamic parameter files, 14 = traceback error).

RemoveBasePair()

int RNA::RemoveBasePair	(	const int	i,
		const int	structurenumber = 1
	)

Remove a specified pair in a specified structure.

Break the pair between i and i's pairing partner Return 0 if there is no error. Return 3 if structurenumber out of range. Return 4 if nucleotide number out of range.

Parameters

i	is the index of a nucleotide in a pair that will be broken.
structurenumber	is an integer specifying the structure from which to remove the pairs.

Returns

An integer that indicates an error code that can be parsed by GetErrorMessage() or GetErrorMessageString(), 0 = no error.

RemoveConstraints()

void RNA::RemoveConstraints

(

)

Remove all folding constraints.

This function strips all previously assigned folding constraints. Note that this function does not delete SHAPE constraints or pseudo free energies.

RemovePairs()

int RNA::RemovePairs	(	const int	structurenumber = 1,
		bool	removeIfLastStructure = true
	)

Remove all the current base pairs in a specified structure.

Return 0 if there is no error. Return 3 if there are no structures or if structurenumber is out of range.

Parameters

structurenumber	is an integer specifying the structure from which to remove the pairs.
removeIfLastStructure	If true and this is the last structure in the group, it will be removed. (default: true)

Returns

An integer that indicates an error code that can be parsed by GetErrorMessage() or GetErrorMessageString(), 0 = no error.

ResetError()

void RNA::ResetError

(

)

Reset the RNA's internal error code to 0 This should be invoked after the error condition is handled

Rsample()

int 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
	)

Rsample function calculates partition function with the pseudo-dg restraints from Rsample algorithm. It calls partition function twice.

Parameters

experimentalRestraints	is a 0-based vector of experimental restraints (such as SHAPE or DMS).
refdata	are 3 vectors read by RsampleData calss that contain paired-end, paired-middle and unpaired reference reactivities.
savefile	is a c string that contains the path and filename for creating a save file. This defaults to "", which indicates no file is to be written.
cparam	is the C parameter that Rsample algorith uses. Default value is 0.5.
offset	is the Offset parameter that Rsample algorith uses. Default value is 1.1.
numsamples	is the number of samples to get from stochastic sampling routine called inside Rsample function. Default is 10,000.

Returns

An int that indicates an error code (0 = no error).

SetConstraints()

void RNA::SetConstraints

(

vector< int >

ss

)

SetErrorDetails()

void RNA::SetErrorDetails

(

const string &

details

)

Set extended details about the last error. (e.g. error messages produced during file read operations that are otherwise lost.)

SetExtrinsic()

int RNA::SetExtrinsic	(	int	i,
		int	j,
		double	k
	)

Add extrinsic restraints for partition function calculations.

This function multiplies the equilibrium constant for structures including the i-j basepair by k. This applies only to partition functions and to stochastic traceback. If k>1, then the i-j pair is favored and if k<1, the i-j pair is disfavored. k should always be >= 0. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

i	is the index of a nucleotide in the i-j pair.
j	is the index of the other nucleotide in the i-j pair.
k	is an equilibrium constant that is >= 0.

Returns

An integer that indicates an error code (0 = no error, >0 indicates an error).

SetProgress()

void RNA::SetProgress

(

ProgressHandler &

Progress

)

Provide a reference to an instance of a class derived from ProgressHandler (such as TProgressDialog for text-mode programs or a simple ProgressHandler for GUI progams or scripts) A ProgressHandler class has a public function void update(int percent) that indicates the progress of a long calculation.

Parameters

Progress

is an instance of a ProgressHandler, TProgressDialog, or PartialProgress etc.

SetSequenceLabel()

void RNA::SetSequenceLabel

(

const string &

label

)

Set the name of the sequence. (This must be called before structure prediction for it to affect the resulting structures.)

SpecifyPair()

int RNA::SpecifyPair	(	const int	i,
		const int	j,
		const int	structurenumber = 1
	)

Specify a base pair between nucleotides i and j.

The base pair is in structure number structurenumber, which is assumed to be structure 1. Return 0 if there is no problem, otherwise return an error code: error = 3 -> structurenumber out of range. error = 4 -> nucleotide number out of range. A c string or string description of the error are available using GetErrorMessage() or GetErrorMessageString(). Note!: Sequences with the 5' end = nucleotide 1. Note!: Structures start at structure 1.

Parameters

i	is an integer for the position of the first nucleotide in the pair.
j	in an integer for the position of the second nucleotide in the pair.
structurenumber	is the structure that has the pair. This defaults to 1.

Returns

An integer that indicates an error code that can be parsed by GetErrorMessage() or GetErrorMessageString(), 0 = no error.

Stochastic()

int RNA::Stochastic	(	const int	structures = 1000,
		const int	seed = 1
	)

Sample structures from the Boltzman ensemable.

This function requires partition function data from either a previous partition function calculations or from having read a partition function save file during construction of the class. In case of error, the function returns a non-zero that can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

structures	is the number of structures to be sampled. The default is 1000.
seed	is an integer that seeds the random number generator that is required for sampling, which defaults to 1.

Returns

An int that indicates an error code (0 = no error, non-zero = error).

StopProgress()

void RNA::StopProgress

(

)

Provide a means to stop using a TProgressDialog. StopProgress tells the RNA class to no longer follow progress. This should be called if the TProgressDialog is deleted, so that this class does not make reference to it.

WriteConstraints()

int RNA::WriteConstraints

(

const char

filename[]

)

Write the current set of folding constraints to disk in a plain text file.

This function does not write SHAPE pseudo energies.

Parameters

filename

is a c string that is the file name to be written.

Returns

An integer that indicates an error code (0 = no error). Currently, this function does not generate errors, but the return is provided to add error handling in the future.

WriteCt()

int RNA::WriteCt	(	const char	filename[],
		bool	append = false,
		CTCommentProvider &	commentProvider = CTComments::Energy
	)		const

Write a ct file of the structures.

Return 0 if no error and non-zero errors can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

filename	is a NULL terminated c string that specifies the name of the ct file to be written.
append	is a bool that indiactes whether the ct data should be appended to an existing file. If true, data will be appended if the file exists, or a new file will be created if the file does not exist. If false (the default), any existing file is overwritten.
commentProvider	a reference to an object that returns application-defined comments for each structure in a CT file. (e.g. "ENERGY = ..." ) This parameter allows a program to customize when comments are written and how they appear. For example many programs write "ENERGY = ..." but only when GetEnergy() != 0. However, a program like MaxExpect might write "SCORE = ..." (even if GetEnergy() returns zero). Similarly, Design might want to add comments like "NED = 0.02" which would require a different source of information than GetEnergy() – or at the very least, different formatting/precision. To provide custom comments, pass an in an object derived from CTCommentProvider that has overridden the getComment function. To disable comments, pass in CTComments::None. The default is CTComments::Energy, which provides legacy "ENERGY = ..." comments.

Returns

An integer that provides an error code. 0 = no error. Use GetErrorMessage to get a textual description of the error.

WriteDotBracket()

int RNA::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.

Return 0 if no error and non-zero errors can be parsed by GetErrorMessage() or GetErrorMessageString().

Parameters

filename

is a NULL terminated c string that specified the name of the file to be written.

Returns

An integer that provides an error code. 0 = no error.

WriteThermodynamicDetails()

int RNA::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.

Free energies are in kcal/mol. The first time this is called, if no other free energy calculation has been performed and the folding temperature has not been specifed, thermodynamic parameter files (.dat) files will be read from disk. The parameter files should be located in the directory specified by environment variable $DATAPATH, or the pwd. In case of error, the function returns a non-zero.

Parameters

filename	is a c-string that provides the name of the output file to be written. If filename==NULL, free energies will be calculated, but no file will be written.
UseSimpleMBLoopRules	is a bool that indicates what energy rules to use. The default, false, uses the complete nearest neighbor model for multibranch loops. When true is passed, the energy model is instead a simplified model that is the one used by the dynamic programming algorithms.

Returns

An int that indicates whether an error occurred (0 = no error; 5 = error reading parameter files).

Member Data Documentation

ct

structure* RNA::ct

private

drawallocated

bool RNA::drawallocated

private

energyallocated

bool RNA::energyallocated

private

ErrorCode

int RNA::ErrorCode

protected

ev

DynProgArray<integersize>* RNA::ev

private

ew

DynProgArray<integersize> * RNA::ew

private

ew2

DynProgArray<integersize>* RNA::ew2

private

ew3

integersize * RNA::ew3

private

ew5

integersize* RNA::ew5

private

ewmb

DynProgArray<integersize> * RNA::ewmb

private

ewmb2

DynProgArray<integersize> * RNA::ewmb2

private

fce

forceclass* RNA::fce

private

lastErrorDetails

string RNA::lastErrorDetails

private

lfce

bool* RNA::lfce

private

mod

bool * RNA::mod

private

partitionfunctionallocated

bool RNA::partitionfunctionallocated

private

pfdata

pfdatatable* RNA::pfdata

protected

progress

ProgressHandler* RNA::progress

protected

Q

PFPRECISION RNA::Q

protected

structurecoordinates

coordinates* RNA::structurecoordinates

private

v

DynProgArray<PFPRECISION> * RNA::v

protected

vmin

int RNA::vmin

private

w

DynProgArray<PFPRECISION>* RNA::w

protected

w3

PFPRECISION * RNA::w3

protected

w5

PFPRECISION* RNA::w5

protected

wca

PFPRECISION ** RNA::wca

protected

wcoax

DynProgArray<PFPRECISION> * RNA::wcoax

protected

wl

DynProgArray<PFPRECISION> * RNA::wl

protected

wlc

DynProgArray<PFPRECISION> * RNA::wlc

protected

wmb

DynProgArray<PFPRECISION> * RNA::wmb

protected

wmbl

DynProgArray<PFPRECISION> * RNA::wmbl

protected

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

• RNA_class/RNA.h
• RNA_class/RNA.cpp