SHAPE.h File Reference

This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints. More...

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Functions
int	vrna_sc_add_SHAPE_deigan (vrna_fold_compound_t *vc, const double *reactivities, double m, double b, unsigned int options)
	Add SHAPE reactivity data as soft constraints (Deigan et al. method) More...
int	vrna_sc_add_SHAPE_deigan_ali (vrna_fold_compound_t *vc, const char **shape_files, const int *shape_file_association, double m, double b, unsigned int options)
	Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan et al. method) More...
int	vrna_sc_add_SHAPE_zarringhalam (vrna_fold_compound_t *vc, const double *reactivities, double b, double default_value, const char *shape_conversion, unsigned int options)
	Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method) More...
int	vrna_sc_SHAPE_parse_method (const char *method_string, char *method, float *param_1, float *param_2)
	Parse a character string and extract the encoded SHAPE reactivity conversion method and possibly the parameters for conversion into pseudo free energies. More...
int	vrna_sc_SHAPE_to_pr (const char *shape_conversion, double *values, int length, double default_value)
	Convert SHAPE reactivity values to probabilities for being unpaired. More...

Detailed Description

This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints.

Function Documentation

int vrna_sc_SHAPE_parse_method	(	const char *	method_string,
		char *	method,
		float *	param_1,
		float *	param_2
	)

Parse a character string and extract the encoded SHAPE reactivity conversion method and possibly the parameters for conversion into pseudo free energies.

Parameters

method_string	The string that contains the encoded SHAPE reactivity conversion method
method	A pointer to the memory location where the method character will be stored
param_1	A pointer to the memory location where the first parameter of the corresponding method will be stored
param_2	A pointer to the memory location where the second parameter of the corresponding method will be stored

Returns

1 on successful extraction of the method, 0 on errors