H/params.h File Reference

Several functions to obtain (pre)scaled energy parameter data containers. More...

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Functions
paramT *	scale_parameters (void)
	Get precomputed energy contributions for all the known loop types.
paramT *	get_scaled_parameters (double temperature, model_detailsT md)
	Get precomputed energy contributions for all the known loop types.
pf_paramT *	get_scaled_pf_parameters (void)
	get a datastructure of type pf_paramT which contains the Boltzmann weights of several energy parameters scaled according to the current temperature
pf_paramT *	get_boltzmann_factors (double temperature, double betaScale, model_detailsT md, double pf_scale)
	Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature.
pf_paramT *	get_boltzmann_factor_copy (pf_paramT *parameters)
	Get a copy of already precomputed Boltzmann factors.
pf_paramT *	get_scaled_alipf_parameters (unsigned int n_seq)
	Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant).
pf_paramT *	get_boltzmann_factors_ali (unsigned int n_seq, double temperature, double betaScale, model_detailsT md, double pf_scale)
	Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature.

Detailed Description

Several functions to obtain (pre)scaled energy parameter data containers.

Function Documentation

paramT* 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.

Returns:: A set of precomputed energy contributions

paramT* get_scaled_parameters	(	double	temperature,
		model_detailsT	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

See also:: model_detailsT, set_model_details()

Parameters:

	temperature	The temperature in degrees Celcius
	md	The model details

Returns:: precomputed energy contributions and model settings

pf_paramT* get_scaled_pf_parameters ( void )

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

Returns:: The datastructure containing Boltzmann weights for use in partition function calculations

pf_paramT* get_boltzmann_factors	(	double	temperature,
		double	betaScale,
		model_detailsT	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 $exp(-\Delta G / kT)$

See also:: get_scaled_pf_parameters(), get_boltzmann_factor_copy()

Parameters:

	dangle_model	The dangle model to be used (possible values: 0 or 2)
	temperature	The temperature in degC used for (re-)scaling the energy contributions
	alpha	A scaling value that is used as a multiplication factor for the absolute temperature of the system

Returns:: A set of precomputed Boltzmann factors

pf_paramT* get_boltzmann_factor_copy ( pf_paramT * parameters )

Get a copy of already precomputed Boltzmann factors.

See also:: get_boltzmann_factors(), get_scaled_pf_parameters()

Parameters:

parameters

The input data structure that shall be copied

Returns:: A copy of the provided Boltzmann factor dataset

pf_paramT* get_scaled_alipf_parameters ( unsigned int n_seq )

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

pf_paramT* get_boltzmann_factors_ali	(	unsigned int	n_seq,
		double	temperature,
		double	betaScale,
		model_detailsT	md,
		double	pf_scale
	)

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

H/params.h File Reference

Functions

Detailed Description

Function Documentation