#include <Oligowalk_object.h>

Inheritance diagram for Oligowalk_object:

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...

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, bool allow_isolated=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, bool allowisolated=false, int maxinter=30)
	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, const char filename[]="")
	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 ()

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

DynProgArray< PFPRECISION > *	wlc

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() [1/3]

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

sequence is a NULL terminated c string.

◆ Oligowalk_object() [2/3]

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

filename	is null terminated c string.
type	is an integer that indicates the file type.

◆ Oligowalk_object() [3/3]

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

IsRNA is a bool where true=RNA and false=DNA.

◆ ~Oligowalk_object()

Oligowalk_object::~Oligowalk_object ( )

This is the destructor.

Member Function Documentation

◆ CommonConstructor()

void Oligowalk_object::CommonConstructor ( )

private

◆ GetBreakTargetDG()

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

index is 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.

◆ GetDuplexDG()

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

index is 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.

◆ GetErrorMessage()

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

error is 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.

◆ GetOligoOligoDG()

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

index is 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.

◆ GetOligoSelfDG()

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

index is 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.

◆ GetOverallDG()

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

index is 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.

◆ GetTm()

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

index is 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.

◆ OligoScreen()

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

infilename	is a c-string that indicates the filename to be read.
outfilename	is 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.

◆ Oligowalk()

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_length	is an int that gives the length of the oligonucleotides.
isDNA	is a bool that indicates the oligonucleotide chemistry, where true = DNA and false = RNA.
option	is 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_concentration	is a double that indicates the oligonucleotide concentration in M.
usesub	is an int that indicates whether suboptimal structures are to be used, where 0 = none and 3 = use heuristic method.
start	is an int that indicates the starting location of the walk.
stop	is 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.

◆ WriteReport()

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

outputfilename	is a c-string that provides a filename to which the report will be written.
oligo_length	is an int that gives the length of the oligonucleotides.
isDNA	is a bool that indicates the oligonucleotide chemistry, where true = DNA and false = RNA.
option	is 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_concentration	is a double that indicates the oligonucleotide concentration in M.
usesub	is an int that indicates whether suboptimal structures are to be used, where 0 = none and 3 = use heuristic method.
start	is an int that indicates the starting location of the walk.
stop	is 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

◆ length

int Oligowalk_object::length

private

◆ numofsubstructures

int ** Oligowalk_object::numofsubstructures

private

◆ prefilter

siPREFILTER* Oligowalk_object::prefilter

private

◆ table

int** Oligowalk_object::table

private

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

RNA_class/Oligowalk_object.h
RNA_class/Oligowalk_object.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Oligowalk_object() [1/3]

◆ Oligowalk_object() [2/3]

◆ Oligowalk_object() [3/3]

◆ ~Oligowalk_object()

Member Function Documentation

◆ CommonConstructor()

◆ GetBreakTargetDG()

◆ GetDuplexDG()

◆ GetErrorMessage()

◆ GetOligoOligoDG()

◆ GetOligoSelfDG()

◆ GetOverallDG()

◆ GetTm()

◆ OligoScreen()

◆ Oligowalk()

◆ WriteReport()

Member Data Documentation

◆ length

◆ numofsubstructures

◆ prefilter

◆ table