RNAlib-2.2.0-RC2
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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...
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_t * | vrna_params_get (vrna_md_t *md) |
Get a data structure containing prescaled free energy parameters. More... | |
vrna_param_t * | vrna_params_copy (vrna_param_t *par) |
Get a copy of the provided free energy parameters. More... | |
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. More... | |
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) More... | |
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) More... | |
vrna_exp_param_t * | get_scaled_pf_parameters (void) |
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. More... | |
vrna_exp_param_t * | get_boltzmann_factor_copy (vrna_exp_param_t *parameters) |
Get a copy of already precomputed Boltzmann factors. More... | |
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) More... | |
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. More... | |
vrna_param_t * | scale_parameters (void) |
Get precomputed energy contributions for all the known loop types. More... | |
vrna_param_t * | get_scaled_parameters (double temperature, vrna_md_t md) |
Get precomputed energy contributions for all the known loop types. More... | |
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.
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.
md | A pointer to the model details to store inside the structure (Maybe NULL) |
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.
par | The free energy parameters that are to be copied (Maybe NULL) |
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.
where 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.
md | A pointer to the model details to store inside the structure (Maybe NULL) |
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.
n_seq | The number of sequences in the alignment |
md | A pointer to the model details to store inside the structure (Maybe NULL) |
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.
par | The free energy parameters that are to be copied (Maybe NULL) |
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
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
temperature | The temperature in degrees Celcius used for (re-)scaling the energy contributions |
betaScale | A scaling value that is used as a multiplication factor for the absolute temperature of the system |
md | The model details to be used |
pf_scale | The scaling factor for the Boltzmann factors |
vrna_exp_param_t* get_boltzmann_factor_copy | ( | vrna_exp_param_t * | parameters | ) |
Get a copy of already precomputed Boltzmann factors.
parameters | The input data structure that shall be copied |
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)
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.
vrna_param_t* scale_parameters | ( | void | ) |
Get precomputed energy contributions for all the known loop types.
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
temperature | The temperature in degrees Celcius |
md | The model details |