Functions |
float | fold_par (const char *sequence, char *structure, paramT *parameters, int is_constrained, int is_circular) |
| Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
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float | fold (const char *sequence, char *structure) |
| Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
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float | circfold (const char *sequence, char *structure) |
| Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.
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float | energy_of_structure (const char *string, const char *structure, int verbosity_level) |
| Calculate the free energy of an already folded RNA using global model detail settings.
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float | energy_of_struct_par (const char *string, const char *structure, paramT *parameters, int verbosity_level) |
| Calculate the free energy of an already folded RNA.
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float | energy_of_circ_structure (const char *string, const char *structure, int verbosity_level) |
| Calculate the free energy of an already folded circular RNA.
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float | energy_of_circ_struct_par (const char *string, const char *structure, paramT *parameters, int verbosity_level) |
| Calculate the free energy of an already folded circular RNA.
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int | energy_of_structure_pt (const char *string, short *ptable, short *s, short *s1, int verbosity_level) |
| Calculate the free energy of an already folded RNA.
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int | energy_of_struct_pt_par (const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level) |
| Calculate the free energy of an already folded RNA.
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void | free_arrays (void) |
| Free arrays for mfe folding.
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void | parenthesis_structure (char *structure, bondT *bp, int length) |
| Create a dot-backet/parenthesis structure from backtracking stack.
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void | parenthesis_zuker (char *structure, bondT *bp, int length) |
| Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.
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void | update_fold_params (void) |
| Recalculate energy parameters.
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float | energy_of_move (const char *string, const char *structure, int m1, int m2) |
| Calculate energy of a move (closing or opening of a base pair).
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int | energy_of_move_pt (short *pt, short *s, short *s1, int m1, int m2) |
| Calculate energy of a move (closing or opening of a base pair).
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int | loop_energy (short *ptable, short *s, short *s1, int i) |
| Calculate energy of a loop.
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void | assign_plist_from_db (plist **pl, const char *struc, float pr) |
| Create a plist from a dot-bracket string.
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int | LoopEnergy (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1) |
int | HairpinE (int size, int type, int si1, int sj1, const char *string) |
void | initialize_fold (int length) |
float | energy_of_struct (const char *string, const char *structure) |
int | energy_of_struct_pt (const char *string, short *ptable, short *s, short *s1) |
float | energy_of_circ_struct (const char *string, const char *structure) |
Variables |
int | logML |
| if nonzero use logarithmic ML energy in energy_of_struct
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int | uniq_ML |
| do ML decomposition uniquely (for subopt)
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int | cut_point |
| set to first pos of second seq for cofolding
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int | eos_debug |
| verbose info from energy_of_struct
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MFE calculations and energy evaluations for single RNA sequences.
This file includes (almost) all function declarations within the RNAlib that are related to MFE folding...