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- RNAlib-2.1.2
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- Main Page -
- Related Pages + + +
- Note:
- This function is threadsafe
- Note:
- This function is threadsafe
- Note:
- This function is threadsafe
- Note:
- This function is threadsafe
- See also:
- make_pair_table(), energy_of_move()
- Parameters:
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string RNA sequence structure secondary structure in dot-bracket notation m1 first coordinate of base pair m2 second coordinate of base pair - See also:
- make_pair_table(), energy_of_move()
- Parameters:
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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
- Returns:
- energy change of the move in kcal/mol
-int energy_of_move_pt ( -short * -pt, +short * +pt, - short * -s, +short * +s, - short * -s1, +short * +s1, - int -m1, +int +m1, - int -m2 +int +m2 ) -+ ++-Calculate energy of a move (closing or opening of a base pair)
+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:
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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 - See also:
- make_pair_table(), energy_of_move()
- Parameters:
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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
- Returns:
- energy change of the move in 10cal/mol
-int loop_energy ( -short * -ptable, +short * +ptable, - short * -s, +short * +s, - short * -s1, +short * +s1, - int -i +int +i ) -+ ++Calculate energy of a loop.
-- Parameters:
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ptable the pair table of the secondary structure s encoded RNA sequence s1 encoded RNA sequence i position of covering base pair - Parameters:
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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
- Returns:
- free energy of the loop in 10cal/mol
-void assign_plist_from_db ( -plist ** -pl, +plist ** +pl, - const char * -struc, +const char * +struc, - float -pr +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
+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:
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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 - Parameters:
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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
- +
-int LoopEnergy ( -int -n1, +int +n1, - int -n2, +int +n2, - int -type, +int +type, - int -type_2, +int +type_2, - int -si1, +int +si1, - int -sj1, +int +sj1, - int -sp1, +int +sp1, - int -sq1 +int +sq1 ) -+ ++- Deprecated:
- {This function is deprecated and will be removed soon. Use E_IntLoop() instead!}
- +
-int HairpinE ( -int -size, +int +size, - int -type, +int +type, - int -si1, +int +si1, - int -sj1, +int +sj1, - const char * -string +const char * +string ) -+ ++- Deprecated:
- {This function is deprecated and will be removed soon. Use E_Hairpin() instead!}
- +
-void initialize_fold ( -int -length ) +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 * +string, - const char * -structure +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...
+- 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:
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string RNA sequence structure secondary structure in dot-bracket notation - Parameters:
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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
- Returns:
- the free energy of the input structure given the input sequence in kcal/mol
-int energy_of_struct_pt ( -const char * -string, +const char * +string, - short * -ptable, +short * +ptable, - short * -s, +short * +s, - short * -s1 +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...
+- 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:
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string RNA sequence ptable the pair table of the secondary structure s encoded RNA sequence s1 encoded RNA sequence - See also:
- make_pair_table(), energy_of_structure()
- Parameters:
-
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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
- 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 * +string, - const char * -structure +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...
+- 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:
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string RNA sequence structure secondary structure in dot-bracket notation - Parameters:
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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
- Returns:
- the free energy of the input structure given the input sequence in kcal/mol
-+-
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- Generated on Wed Jul 24 2013 13:38:58 for RNAlib-2.1.2 by
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1.8.1.1
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Generated on 11 Apr 2017 for RNAlib-2.1.2 by + + 1.6.1
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/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h File Reference
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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+More...
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+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 | ||||||
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.
+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
- +Function Documentation
+| void parenthesis_structure | ( | -char * | -structure, | +char * | +structure, | |
| - | bondT * | -bp, | +bondT * | +bp, | ||
| - | int | -length | +int | +length | ||
| ) | -+ |
+
+Create a dot-backet/parenthesis structure from backtracking stack.
-| void parenthesis_zuker | ( | -char * | -structure, | +char * | +structure, | |
| - | bondT * | -bp, | +bondT * | +bp, | ||
| - | int | -length | +int | +length | ||
| ) | -+ |
+
+Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.
-| float energy_of_move | ( | -const char * | -string, | +const char * | +string, | |
| - | const char * | -structure, | +const char * | +structure, | ||
| - | int | -m1, | +int | +m1, | ||
| - | int | -m2 | +int | +m2 | ||
| ) | -+ |
+
+
-
Calculate energy of a move (closing or opening of a base pair)
+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).
-