Oligowalk_object Class Reference

Oligowalk_object Class. More...

#include <Oligowalk_object.h>

Inheritance diagram for Oligowalk_object:

RNA Thermodynamics

List of all members.

Public Member Functions

 Oligowalk_object (const char sequence[])
 Constructor - user provides a sequence as a c string.
 Oligowalk_object (const char filename[], const int type)
 Constructor - user provides a filename for existing file as a c string.
 Oligowalk_object (const bool IsRNA=true)
 Default Constructor - user provides nothing.
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.
char * GetErrorMessage (const int error)
 ~Oligowalk_object ()
 This is the destructor.

Private Member Functions

void CommonConstructor ()

Private Attributes

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

Detailed Description

Oligowalk_object Class.

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

Constructor & Destructor Documentation

Oligowalk_object::Oligowalk_object ( const char  sequence[]  ) 

Constructor - user provides a sequence as a c string.

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

Parameters:
sequence is a NULL terminated c string.

Oligowalk_object::Oligowalk_object ( const char  filename[],
const int  type 
)

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

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

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

Oligowalk_object::Oligowalk_object ( const bool  IsRNA = true  ) 

Default Constructor - user provides nothing.

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

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

Oligowalk_object::~Oligowalk_object (  ) 

This is the destructor.

Member Function Documentation

void Oligowalk_object::CommonConstructor (  )  [private]

double Oligowalk_object::GetBreakTargetDG ( const int  index  ) 

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

Parameters:
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.

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.

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.

Reimplemented from RNA.

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.

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.

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.

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.

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.

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.

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

int Oligowalk_object::length [private]

int ** Oligowalk_object::numofsubstructures [private]

siPREFILTER* Oligowalk_object::prefilter [private]

int** Oligowalk_object::table [private]

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