ProbScan Class Reference

#include <ProbScan.h>

Inheritance diagram for ProbScan:

Public Member Functions
	ProbScan (std::string sequence, bool isRNA=true)
	Constructor - user provides a sequence as a c string. More...
	ProbScan (const char filename[], bool from_sequence_file, bool isRNA=true)
	Constructor - user provides a filename for existing file as a c string. More...
double	probability_of_hairpin (int i, int j)
	Returns probability of a hairpin closed at a specific position. More...
double	probability_of_stemloop (int i, int j, int ip, int jp)
std::vector< hairpin_t >	probability_of_all_hairpins (int min, int max, double threshold)
	Calculates the probabilities of all possible hairpins in this sequence. More...
double	probability_of_internal_loop (int i, int j, int k, int l)
	Returns probability of an internal loop or bulge loop closed at a specific position. More...
std::vector< internal_loop_t >	probability_of_all_internal_loops (double threshold, std::string mode=std::string("both"))
	Calculates the probabilities of all possible internal loops and/or bulge loops in this sequence. More...
double	probability_of_stack (int i, int j)
double	probability_of_helix (const int i, const int j, const int how_many_stacks)
	Calculates probability of an helix at a specific position. More...
std::vector< basestack_t >	probability_of_all_helices (double threshold, int length)
	Calculates the probabilities of all possible helices in this sequence of a specific length. More...
double	probability_of_multibranch_loop (const multibranch_loop_t &mb)
	Calculates probability of a multibranch loop at a specific position. 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)
	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 ()

Private Member Functions
PFPRECISION	equilibrium_constant_for_multibranch_loop (const multibranch_loop_t &)
std::vector< mb_element >	construct_mb_element_array (const multibranch_loop_t &)

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

Constructor & Destructor Documentation

ProbScan() [1/2]

ProbScan::ProbScan	(	std::string	sequence,
		bool	isRNA = true
	)

Constructor - user provides a sequence as a c string.

The partition function will be calculated. If the sequence is long, this may take some time. Input sequence should contain A,C,G,T,U,a,c,g,t,u,x,X. Capitalization makes no difference. 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. 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 containing the nucleotide sequence.
isRNA	is a bool that indicates whether this sequence is RNA or DNA. true=RNA. false=DNA. Default is true.

ProbScan() [2/2]

ProbScan::ProbScan	(	const char	filename[],
		bool	from_sequence_file,
		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: type = 1 => .ct file, type = 2 => .seq file, type = 3 => partition function save (.pfs) file, type = 4 => folding save file (.sav). If the input file is ont a partition function save file, the partition function will be calculated. If the sequence is long, this may take some time. 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 containing the path to the input file.
from_sequence_file	is a bool which tells the constructor whether we are initializing from a sequence file, in which case the partition function must be calculated
isRNA	is a bool that indicates whether this sequence is RNA or DNA. true=RNA. false=DNA. Default is true.

Member Function Documentation

construct_mb_element_array()

vector< mb_element > ProbScan::construct_mb_element_array ( const multibranch_loop_t &  mb )

private

equilibrium_constant_for_multibranch_loop()

PFPRECISION ProbScan::equilibrium_constant_for_multibranch_loop ( const multibranch_loop_t &  mb )

private

probability_of_all_hairpins()

vector< hairpin_t > ProbScan::probability_of_all_hairpins	(	int	min,
		int	max,
		double	threshold
	)

Calculates the probabilities of all possible hairpins in this sequence.

Parameters

min	The minimum size of a hairpin
max	The maximum size of a hairpin
threshold	The minimum probability for candidate hairpins

Returns

A vector of hairpin objects, containing the positions of the hairpins and their probabilities

probability_of_all_helices()

std::vector< basestack_t > ProbScan::probability_of_all_helices	(	double	threshold,
		int	length
	)

Calculates the probabilities of all possible helices in this sequence of a specific length.

Parameters

threshold	the minimum probability of candidate helices
length	the number of base pair stacks to search for

Returns

A vector of helix objects, containing the positions of the helices and their probabilities

probability_of_all_internal_loops()

vector< internal_loop_t > ProbScan::probability_of_all_internal_loops	(	double	threshold,
		std::string	mode = std::string("both")
	)

Calculates the probabilities of all possible internal loops and/or bulge loops in this sequence.

Parameters

threshold	the minimum probability of candidate loops
mode	a string which indicates what type of loops should be searched for. Allowed values are "internal", "bulge", and "both"

Returns

A vector of internal loop objects, containing the positions of the loops and their probabilities

probability_of_hairpin()

double ProbScan::probability_of_hairpin	(	int	i,
		int	j
	)

Returns probability of a hairpin closed at a specific position.

Parameters

i	The 5' nucleotide closing the hairpin
j	The 3' nucleotide closing the hairpin

Returns

A double containing the probability of the hairpin

probability_of_helix()

double ProbScan::probability_of_helix	(	const int	i,
		const int	j,
		const int	how_many_stacks
	)

Calculates probability of an helix at a specific position.

Parameters

i	The 5' nucleotide closing the helix on the exterior
j	The 3' nucleotide closing the helix on the exterior
how_many_stacks	The number of base pair STACKS in the helix (this is the number of pairs minus 1)

Returns

A double containing the probability of the helix

probability_of_internal_loop()

double ProbScan::probability_of_internal_loop	(	int	i,
		int	j,
		int	k,
		int	l
	)

Returns probability of an internal loop or bulge loop closed at a specific position.

Parameters

i	The 5' nucleotide closing the loop on the exterior
j	The 3' nucleotide closing the loop on the exterior
k	The 5' nucleotide closing the loop on the interior
l	The 3' nucleotide closing the loop on the interior

Returns

A double containing the probability of the internal loop

probability_of_multibranch_loop()

double ProbScan::probability_of_multibranch_loop

(

const multibranch_loop_t &

mb

)

Calculates probability of a multibranch loop at a specific position.

Parameters

mb	A multibranch loop object, containing a vector of pairs describing the multibranch loop. These can be created with the multibranch_loop function. See the text interface for the ProbScan program for an example of usage.

Returns

A double containing the probability of the multibranch loop

probability_of_stack()

double ProbScan::probability_of_stack	(	int	i,
		int	j
	)

Calculates probability of a base pair stack closed at a specific position Note that this is a special case of probability_of_helix where the size is set to 1

Parameters

i	The 5' nucleotide closing the stack
j	The 3' nucleotide closing the stack

Returns

A double containing the probability of the stack

probability_of_stemloop()

double ProbScan::probability_of_stemloop	(	int	i,
		int	j,
		int	ip,
		int	jp
	)

Parameters

i	The 5' nucleotide closing the hairpin
j	The 3' nucleotide closing the hairpin
ip	The 5'-most nucleotide closing the stem
jp	The 3'-most nucleotide closing the stem

Returns

A double containing the probability of the hairpin stem-loop

---

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

• RNA_class/ProbScan.h
• RNA_class/ProbScan.cpp