concentrations.h File Reference

Concentration computations for RNA-RNA interactions. More...

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Data Structures
struct	vrna_dimer_conc_s
	Data structure for concentration dependency computations. More...

Functions
vrna_dimer_conc_t *	get_concentrations (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)
	Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. More...
typedef struct vrna_dimer_conc_s	vrna_dimer_conc_t
	Typename for the data structure that stores the dimer concentrations, vrna_dimer_conc_s, as required by vrna_pf_dimer_concentration()
typedef struct vrna_dimer_conc_s	ConcEnt
	Backward compatibility typedef for vrna_dimer_conc_s.
vrna_dimer_conc_t *	vrna_pf_dimer_concentrations (double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const vrna_exp_param_t *exp_params)
	Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. More...

Detailed Description

Concentration computations for RNA-RNA interactions.

Function Documentation

vrna_dimer_conc_t* get_concentrations	(	double	FEAB,
		double	FEAA,
		double	FEBB,
		double	FEA,
		double	FEB,
		double *	startconc
	)

Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers.

This function takes an array 'startconc' of input concentrations with alternating entries for the initial concentrations of molecules A and B (terminated by two zeroes), then computes the resulting equilibrium concentrations from the free energies for the dimers. Dimer free energies should be the dimer-only free energies, i.e. the FcAB entries from the vrna_dimer_pf_t struct.

Deprecated:

{ Use vrna_pf_dimer_concentrations() instead!}

Parameters

FEAB	Free energy of AB dimer (FcAB entry)
FEAA	Free energy of AA dimer (FcAB entry)
FEBB	Free energy of BB dimer (FcAB entry)
FEA	Free energy of monomer A
FEB	Free energy of monomer B
startconc	List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0]

Returns

vrna_dimer_conc_t array containing the equilibrium energies and start concentrations