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+MFE calculations and energy evaluations for single RNA sequences. +More...
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+ 
Include dependency graph for fold.h:
+ Include dependency graph for fold.h:
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Go to the source code of this file.
++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. | |
| float | fold (const char *sequence, char *structure) |
| Compute minimum free energy and an appropriate secondary structure of an RNA sequence. | |
| float | circfold (const char *sequence, char *structure) |
| Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence. | |
| 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. | |
| 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. | |
| float | energy_of_circ_structure (const char *string, const char *structure, int verbosity_level) |
| Calculate the free energy of an already folded circular RNA. | |
| 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. | |
| 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. | |
| 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. | |
| +void | free_arrays (void) |
| Free arrays for mfe folding. | |
| void | parenthesis_structure (char *structure, bondT *bp, int length) |
| Create a dot-backet/parenthesis structure from backtracking stack. | |
| 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. | |
| +void | update_fold_params (void) |
| Recalculate energy parameters. | |
| 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) | |
| 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) | |
| int | loop_energy (short *ptable, short *s, short *s1, int i) |
| Calculate energy of a loop. | |
| void | assign_plist_from_db (plist **pl, const char *struc, float pr) |
| Create a plist from a dot-bracket string. | |
| 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 | |
| +int | uniq_ML |
| do ML decomposition uniquely (for subopt) | |
| +int | cut_point |
| set to first pos of second seq for cofolding | |
| +int | eos_debug |
| verbose info from energy_of_struct | |
Detailed Description
+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...
+Function Documentation
+ +
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+
| void parenthesis_structure | +( | +char * | +structure, | +
| + | + | bondT * | +bp, | +
| + | + | int | +length | +
| + | ) | ++ |
+
+
+Create a dot-backet/parenthesis structure from backtracking stack.
+- Note:
- This function is threadsafe
+
+
+
+
+
+
| 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.
+- Note:
- This function is threadsafe
+
+
+
+
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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)
+If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
+- See also:
- make_pair_table(), energy_of_move()
- Parameters:
-
+
+
+string RNA sequence structure secondary structure in dot-bracket notation m1 first coordinate of base pair m2 second coordinate of base pair
+
- Returns:
- energy change of the move in kcal/mol
+
+
+
+
+
+
| 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)
+If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
+- See also:
- make_pair_table(), energy_of_move()
- Parameters:
-
+
+
+pt the pair table of the secondary structure s encoded RNA sequence s1 encoded RNA sequence m1 first coordinate of base pair m2 second coordinate of base pair
+
- Returns:
- energy change of the move in 10cal/mol
+
+
+
+
+
+
| int loop_energy | +( | +short * | +ptable, | +
| + | + | short * | +s, | +
| + | + | short * | +s1, | +
| + | + | int | +i | +
| + | ) | ++ |
+
+
+Calculate energy of a loop.
+- Parameters:
-
+
+
+ptable the pair table of the secondary structure s encoded RNA sequence s1 encoded RNA sequence i position of covering base pair
+
- Returns:
- free energy of the loop in 10cal/mol
+
+
+
+
+
+
| void assign_plist_from_db | +( | +plist ** | +pl, | +
| + | + | const char * | +struc, | +
| + | + | float | +pr | +
| + | ) | ++ |
+
+
+Create a plist from a dot-bracket string.
+The dot-bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.
+The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries
+This function is threadsafe
+- Parameters:
-
+
+
+pl A pointer to the plist that is to be created struc The secondary structure in dot-bracket notation pr The probability for each base pair
+
+
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+
+
+
| int LoopEnergy | +( | +int | +n1, | +
| + | + | int | +n2, | +
| + | + | int | +type, | +
| + | + | int | +type_2, | +
| + | + | int | +si1, | +
| + | + | int | +sj1, | +
| + | + | int | +sp1, | +
| + | + | int | +sq1 | +
| + | ) | ++ |
+
+- Deprecated:
- {This function is deprecated and will be removed soon. Use E_IntLoop() instead!}
+
+
+
+
+
+
| int HairpinE | +( | +int | +size, | +
| + | + | int | +type, | +
| + | + | int | +si1, | +
| + | + | int | +sj1, | +
| + | + | const char * | +string | +
| + | ) | ++ |
+
+- Deprecated:
- {This function is deprecated and will be removed soon. Use E_Hairpin() instead!}
+
+
+
+
+
+
| void initialize_fold | +( | +int | +length | ) | ++ |
+
+Allocate arrays for folding
+
- Deprecated:
- {This function is deprecated and will be removed soon!}
+
+
+
+
+
+
| float energy_of_struct | +( | +const char * | +string, | +
| + | + | const char * | +structure | +
| + | ) | ++ |
+
+Calculate the free energy of an already folded RNA
+- Note:
- This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
+
- Deprecated:
- This function is deprecated and should not be used in future programs! Use energy_of_structure() instead!
- Parameters:
-
+
+
+string RNA sequence structure secondary structure in dot-bracket notation
+
- Returns:
- the free energy of the input structure given the input sequence in kcal/mol
+
+
+
+
+
+
| int energy_of_struct_pt | +( | +const char * | +string, | +
| + | + | short * | +ptable, | +
| + | + | short * | +s, | +
| + | + | short * | +s1 | +
| + | ) | ++ |
+
+Calculate the free energy of an already folded RNA
+- Note:
- This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
+
- Deprecated:
- This function is deprecated and should not be used in future programs! Use energy_of_structure_pt() instead!
- See also:
- make_pair_table(), energy_of_structure()
- Parameters:
-
+
+
+string RNA sequence ptable the pair table of the secondary structure s encoded RNA sequence s1 encoded RNA sequence
+
- Returns:
- the free energy of the input structure given the input sequence in 10kcal/mol
+
+
+
+
+
| float energy_of_circ_struct | +( | +const char * | +string, | +
| + | + | const char * | +structure | +
| + | ) | ++ |
+
+Calculate the free energy of an already folded circular RNA
+- Note:
- This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
+
- Deprecated:
- This function is deprecated and should not be used in future programs Use energy_of_circ_structure() instead!
- Parameters:
-
+
+
+string RNA sequence structure secondary structure in dot-bracket notation
+
- Returns:
- the free energy of the input structure given the input sequence in kcal/mol
