HybridRNA Class Reference

HybridRNA Class. More...

#include <HybridRNA.h>

Inheritance diagram for HybridRNA:

RNA Thermodynamics

List of all members.

Public Member Functions

 HybridRNA (const char sequence1[], const char sequence2[], const bool IsRNA=true)
 Constructors.
 HybridRNA (const char filename1[], const int type1, const char filename2[], const int type2, const bool IsRNA=true)
int AccessFold (const double gamma=0.4, const float percent=50, const int maximumstructures=20, const int window=0, const int maxinternalloopsize=30)
int FoldBimolecular (const float percent=10, const int maximumstructures=20, const int window=0, const char savefile[]="", const int maxinternalloopsize=30)
 Predict the lowest free energy secondary structure and generate suboptimal structures using a heuristic.
int FoldDuplex (const float percent=40, const int maximumstructures=10, const int window=0, const int maxinternalloopsize=30)
 Predict the lowest free energy secondary structure for two strands that cannot form intramolecular pairs and generate suboptimal structures using a heuristic.
int PartitionFunctionBimolecular (const char savefile[]="")
 Predict the bimolecular partition function for a sequence (with no intramolecular pairs).
RNA * GetRNA1 ()
RNA * GetRNA2 ()
int GetErrorCode ()
 Return an error code, where a return of zero is no error.
char * GetErrorMessage (const int error)
 Return error messages based on code from GetErrorCode and other error codes.
bool GetForbidIntramolecular ()
 Get whether intramolecular pairs are allowed.
void SetForbidIntramolecular (const bool forbid)
 Set whether intramolecular pairs are allowed.
void SetProgress (TProgressDialog &Progress)
void StopProgress ()
 ~HybridRNA ()

Private Member Functions

void commonconstructor ()
void SetupBimolecular ()

Private Attributes

bool forbidunimolecular
TwoRNA * sequences

Detailed Description

HybridRNA Class.

The HybridRNA class provides an entry point for all the bimolecular structure prediction routines of RNAstructure. The class is inherited from the RNA class and contains an instance of TwoRNA, which itself contains two instances to the class RNA.

Constructor & Destructor Documentation

HybridRNA::HybridRNA ( const char  sequence1[],
const char  sequence2[],
const bool  IsRNA = true 
)

Constructors.

The two constuctors are available to reach the TwoRNA constructors, from which this class is built. Please see the TwoRNA constructor entries for documentation.

HybridRNA::HybridRNA ( const char  filename1[],
const int  type1,
const char  filename2[],
const int  type2,
const bool  IsRNA = true 
)

HybridRNA::~HybridRNA (  ) 

Member Function Documentation

int HybridRNA::AccessFold ( const double  gamma = 0.4,
const float  percent = 50,
const int  maximumstructures = 20,
const int  window = 0,
const int  maxinternalloopsize = 30 
)

Predict the lowest free energy secondary structure for two interacting strands and generate suboptimal structures. Thuis method does not allow intramolecular pairs. It considers accessibility with a heuristic that uses tge partition function. If the temperature has not been specified using the RNA base class 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:
gamma is a scaling factor that weights accessibility. The defaults is 0.4
percent is the maximum % difference in free energy in suboptimal structures from the lowest free energy structure. The default is 50.
maximumstructures is the maximum number of suboptimal structures to generate. The fefault 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 0.
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.
Returns:
An int that indicates an error code (0 = no error, 5 = error reading thermodynamic parameter files, 14 = traceback error).

void HybridRNA::commonconstructor (  )  [private]

int HybridRNA::FoldBimolecular ( const float  percent = 10,
const int  maximumstructures = 20,
const int  window = 0,
const char  savefile[] = "",
const int  maxinternalloopsize = 30 
)

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 the RNA base class 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 10.
maximumstructures is the maximum number of suboptimal structures to generate. The defaults 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 0.
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.
Returns:
An int that indicates an error code (0 = no error, 5 = error reading thermodynamic parameter files, 14 = traceback error).

int HybridRNA::FoldDuplex ( const float  percent = 40,
const int  maximumstructures = 10,
const int  window = 0,
const int  maxinternalloopsize = 30 
)

Predict the lowest free energy secondary structure for two strands that cannot form intramolecular pairs and generate suboptimal structures using a heuristic.

This function predicts the lowest free energy bimolecular structure and suboptimal structures. This function does not allow any folding constraints. 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 40.
maximumstructures is the maximum number of suboptimal structures to generate. The default is 10.
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 0.
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.
Returns:
An int that indicates an error code (0 = no error, 5 = error reading thermodynamic parameter files, 14 = traceback error).

int HybridRNA::GetErrorCode (  ) 

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.

Reimplemented from RNA.

char * HybridRNA::GetErrorMessage ( const int  error  ) 

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

0 = no error <100 = Error to be fetched from RNA base class. 100-999 = Error associated with bimolecular folding, to be handled here. >=1000 = Errors for underlying sequence, get message from TwoRNA base class.

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.

Reimplemented from RNA.

bool HybridRNA::GetForbidIntramolecular (  ) 

Get whether intramolecular pairs are allowed.

Returns:
A bool that indicates whether intramolecular pairs are forbidden (true = forbidden, false = not).

RNA * HybridRNA::GetRNA1 (  ) 

Access the underlying RNA class from an instance of TwoRNA. This is provided for use with two sequence methods. Generally, there is no need for end users to use this function.

Returns:
A pointer to the underlying RNA class for sequence 1.

RNA * HybridRNA::GetRNA2 (  ) 

Access the underlying RNA class from an instance of TwoRNA. This is provided for use with two sequence methods. Generally, there is no need for end users to use this function.

Returns:
A pointer to the underlying RNA class for sequence 2.

int HybridRNA::PartitionFunctionBimolecular ( const char  savefile[] = ""  ) 

Predict the bimolecular partition function for a sequence (with no intramolecular pairs).

This function must be called to predict base pair probabilities, perform stochastic traceback, or for maximizing expected accuracy. This predicts the partition function without intramolecular pairs. 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:
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.
Returns:
An int that indicates an error code (0 = no error, 5 = error reading thermodynamic parameter files).

void HybridRNA::SetForbidIntramolecular ( const bool  forbid  ) 

Set whether intramolecular pairs are allowed.

If true is passed to this function, intramolecular pairs will be forbidden in FoldBimolecular.

Parameters:
forbid is a bool that indicates whether intramolecular pairs are forbid.

void HybridRNA::SetProgress ( TProgressDialog &  Progress  ) 

Provide a TProgressDialog for following calculation progress. A TProgressDialog class has a public function void update(int percent) that indicates the progress of a long calculation.

Parameters:
Progress is a TProgressDialog class.

Reimplemented from RNA.

void HybridRNA::SetupBimolecular (  )  [private]

void HybridRNA::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.

Reimplemented from RNA.

Member Data Documentation

bool HybridRNA::forbidunimolecular [private]

TwoRNA* HybridRNA::sequences [private]

The documentation for this class was generated from the following files:
Generated on Wed Sep 2 14:36:50 2015 for RNAstructure Classes by  doxygen 1.5.7.1