RNAlib-2.2.0-RC2
Energy Parameter Sets and Boltzmann Factors

All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s). More...

+ Collaboration diagram for Energy Parameter Sets and Boltzmann Factors:

Modules

 Reading/Writing Energy Parameter Sets from/to File
 Read and Write energy parameter sets from and to text files.
 

Files

file  params.h
 

Data Structures

struct  vrna_param_t
 The datastructure that contains temperature scaled energy parameters. More...
 
struct  vrna_exp_param_t
 The datastructure that contains temperature scaled Boltzmann weights of the energy parameters. More...
 

Functions

vrna_param_tvrna_params_get (vrna_md_t *md)
 Get a data structure containing prescaled free energy parameters. More...
 
vrna_param_tvrna_params_copy (vrna_param_t *par)
 Get a copy of the provided free energy parameters. More...
 
vrna_exp_param_tvrna_exp_params_get (vrna_md_t *md)
 Get a data structure containing prescaled free energy parameters already transformed to Boltzmann factors. More...
 
vrna_exp_param_tvrna_exp_params_ali_get (unsigned int n_seq, vrna_md_t *md)
 Get a data structure containing prescaled free energy parameters already transformed to Boltzmann factors (alifold version) More...
 
vrna_exp_param_tvrna_exp_params_copy (vrna_exp_param_t *par)
 Get a copy of the provided free energy parameters (provided as Boltzmann factors) More...
 
vrna_exp_param_tget_scaled_pf_parameters (void)
 
vrna_exp_param_tget_boltzmann_factors (double temperature, double betaScale, vrna_md_t md, double pf_scale)
 Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. More...
 
vrna_exp_param_tget_boltzmann_factor_copy (vrna_exp_param_t *parameters)
 Get a copy of already precomputed Boltzmann factors. More...
 
vrna_exp_param_tget_scaled_alipf_parameters (unsigned int n_seq)
 Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) More...
 
vrna_exp_param_tget_boltzmann_factors_ali (unsigned int n_seq, double temperature, double betaScale, vrna_md_t md, double pf_scale)
 Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. More...
 
vrna_param_tscale_parameters (void)
 Get precomputed energy contributions for all the known loop types. More...
 
vrna_param_tget_scaled_parameters (double temperature, vrna_md_t md)
 Get precomputed energy contributions for all the known loop types. More...
 

Detailed Description

All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s).

This module covers all relevant functions for precalculation of the energy parameters necessary for the folding routines provided by RNAlib. Furthermore, the energy parameter set in the RNAlib can be easily exchanged by a user-defined one. It is also possible to write the current energy parameter set into a text file.

Function Documentation

vrna_param_t* vrna_params_get ( vrna_md_t md)

Get a data structure containing prescaled free energy parameters.

If a NULL pointer is passed for the model details parameter, the default model parameters are stored within the requested vrna_param_t structure.

See also
vrna_md_t, vrna_md_set_default(), vrna_exp_params_get()
Parameters
mdA pointer to the model details to store inside the structure (Maybe NULL)
Returns
A pointer to the memory location where the requested parameters are stored
vrna_param_t* vrna_params_copy ( vrna_param_t par)

Get a copy of the provided free energy parameters.

If NULL is passed as parameter, a default set of energy parameters is created and returned.

See also
vrna_params_get(), vrna_param_t
Parameters
parThe free energy parameters that are to be copied (Maybe NULL)
Returns
A copy or a default set of the (provided) parameters
vrna_exp_param_t* vrna_exp_params_get ( vrna_md_t md)

Get a data structure containing prescaled free energy parameters already transformed to Boltzmann factors.

This function returns a data structure that contains all necessary precomputed energy contributions for each type of loop.

In contrast to vrna_params_get(), the free energies within this data structure are stored as their Boltzmann factors, i.e.

$ exp(-E / kT) $

where $ E $ is the free energy.

If a NULL pointer is passed for the model details parameter, the default model parameters are stored within the requested vrna_exp_param_t structure.

See also
vrna_md_t, vrna_md_set_default(), vrna_params_get(), vrna_rescale_pf_params()
Parameters
mdA pointer to the model details to store inside the structure (Maybe NULL)
Returns
A pointer to the memory location where the requested parameters are stored
vrna_exp_param_t* vrna_exp_params_ali_get ( unsigned int  n_seq,
vrna_md_t md 
)

Get a data structure containing prescaled free energy parameters already transformed to Boltzmann factors (alifold version)

If a NULL pointer is passed for the model details parameter, the default model parameters are stored within the requested vrna_exp_param_t structure.

See also
vrna_md_t, vrna_md_set_default(), vrna_exp_params_get(), vrna_params_get()
Parameters
n_seqThe number of sequences in the alignment
mdA pointer to the model details to store inside the structure (Maybe NULL)
Returns
A pointer to the memory location where the requested parameters are stored
vrna_exp_param_t* vrna_exp_params_copy ( vrna_exp_param_t par)

Get a copy of the provided free energy parameters (provided as Boltzmann factors)

If NULL is passed as parameter, a default set of energy parameters is created and returned.

See also
vrna_exp_params_get(), vrna_exp_param_t
Parameters
parThe free energy parameters that are to be copied (Maybe NULL)
Returns
A copy or a default set of the (provided) parameters
vrna_exp_param_t* get_scaled_pf_parameters ( void  )

get a datastructure of type vrna_exp_param_t which contains the Boltzmann weights of several energy parameters scaled according to the current temperature

Deprecated:
Use vrna_exp_params_get() instead!
Returns
The datastructure containing Boltzmann weights for use in partition function calculations
vrna_exp_param_t* get_boltzmann_factors ( double  temperature,
double  betaScale,
vrna_md_t  md,
double  pf_scale 
)

Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature.

This function returns a data structure that contains all necessary precalculated Boltzmann factors for each loop type contribution.
In contrast to get_scaled_pf_parameters(), this function enables setting of independent temperatures for both, the individual energy contributions as well as the thermodynamic temperature used in $ exp(-\Delta G / kT) $

Deprecated:
Use vrna_exp_params_get() instead!
See also
get_scaled_pf_parameters(), get_boltzmann_factor_copy()
Parameters
temperatureThe temperature in degrees Celcius used for (re-)scaling the energy contributions
betaScaleA scaling value that is used as a multiplication factor for the absolute temperature of the system
mdThe model details to be used
pf_scaleThe scaling factor for the Boltzmann factors
Returns
A set of precomputed Boltzmann factors
vrna_exp_param_t* get_boltzmann_factor_copy ( vrna_exp_param_t parameters)

Get a copy of already precomputed Boltzmann factors.

Deprecated:
Use vrna_exp_params_copy() instead!
See also
get_boltzmann_factors(), get_scaled_pf_parameters()
Parameters
parametersThe input data structure that shall be copied
Returns
A copy of the provided Boltzmann factor dataset
vrna_exp_param_t* get_scaled_alipf_parameters ( unsigned int  n_seq)

Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant)

Deprecated:
Use vrna_exp_params_ali_get() instead!
vrna_exp_param_t* get_boltzmann_factors_ali ( unsigned int  n_seq,
double  temperature,
double  betaScale,
vrna_md_t  md,
double  pf_scale 
)

Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature.

Deprecated:
Use vrna_exp_params_ali_get() instead!
vrna_param_t* scale_parameters ( void  )

Get precomputed energy contributions for all the known loop types.

Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See get_scaled_parameters() for a completely threadsafe implementation.
Deprecated:
Use vrna_params_get() instead!
Returns
A set of precomputed energy contributions
vrna_param_t* get_scaled_parameters ( double  temperature,
vrna_md_t  md 
)

Get precomputed energy contributions for all the known loop types.

Call this function to retrieve precomputed energy contributions, i.e. scaled according to the temperature passed. Furthermore, this function assumes a data structure that contains the model details as well, such that subsequent folding recursions are able to retrieve the correct model settings

Deprecated:
Use vrna_params_get() instead!
See also
vrna_md_t, set_model_details()
Parameters
temperatureThe temperature in degrees Celcius
mdThe model details
Returns
precomputed energy contributions and model settings