Deprecated Interface for Free Energy Evaluation
Using the functions below is discouraged as they have been marked deprecated and will be removed from the library in the (near) future!
Defines
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ON_SAME_STRAND(I, J, C)
- #include <ViennaRNA/loops/internal.h>
Functions
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float energy_of_structure(const char *string, const char *structure, int verbosity_level)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA using global model detail settings.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
- Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_struct_par() for a completely threadsafe implementation.
- Parameters:
string – RNA sequence
structure – secondary structure in dot-bracket notation
verbosity_level – a flag to turn verbose output on/off
- Returns:
the free energy of the input structure given the input sequence in kcal/mol
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float energy_of_struct_par(const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
- Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
- Parameters:
string – RNA sequence in uppercase letters
structure – Secondary structure in dot-bracket notation
parameters – A data structure containing the prescaled energy contributions and the model details.
verbosity_level – A flag to turn verbose output on/off
- Returns:
The free energy of the input structure given the input sequence in kcal/mol
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float energy_of_circ_structure(const char *string, const char *structure, int verbosity_level)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
- Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_circ_struct_par() for a completely threadsafe implementation.
- Parameters:
string – RNA sequence
structure – Secondary structure in dot-bracket notation
verbosity_level – A flag to turn verbose output on/off
- Returns:
The free energy of the input structure given the input sequence in kcal/mol
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float energy_of_circ_struct_par(const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
- Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
- Parameters:
string – RNA sequence
structure – Secondary structure in dot-bracket notation
parameters – A data structure containing the prescaled energy contributions and the model details.
verbosity_level – A flag to turn verbose output on/off
- Returns:
The free energy of the input structure given the input sequence in kcal/mol
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float energy_of_gquad_structure(const char *string, const char *structure, int verbosity_level)
- #include <ViennaRNA/eval.h>
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float energy_of_gquad_struct_par(const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
- #include <ViennaRNA/eval.h>
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int energy_of_structure_pt(const char *string, short *ptable, short *s, short *s1, int verbosity_level)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
- Deprecated:
Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!
See also
Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_struct_pt_par() for a completely threadsafe implementation.
- Parameters:
string – RNA sequence
ptable – the pair table of the secondary structure
s – encoded RNA sequence
s1 – encoded RNA sequence
verbosity_level – a flag to turn verbose output on/off
- Returns:
the free energy of the input structure given the input sequence in 10kcal/mol
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int energy_of_struct_pt_par(const char *string, short *ptable, short *s, short *s1, vrna_param_t *parameters, int verbosity_level)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
- Deprecated:
Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!
See also
- Parameters:
string – RNA sequence in uppercase letters
ptable – The pair table of the secondary structure
s – Encoded RNA sequence
s1 – Encoded RNA sequence
parameters – A data structure containing the prescaled energy contributions and the model details.
verbosity_level – A flag to turn verbose output on/off
- Returns:
The free energy of the input structure given the input sequence in 10kcal/mol
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float energy_of_move(const char *string, const char *structure, int m1, int m2)
- #include <ViennaRNA/eval.h>
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).
- Deprecated:
Use vrna_eval_move() instead!
See also
- 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
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int energy_of_move_pt(short *pt, short *s, short *s1, int m1, int m2)
- #include <ViennaRNA/eval.h>
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).
- Deprecated:
Use vrna_eval_move_pt() instead!
See also
- 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
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int loop_energy(short *ptable, short *s, short *s1, int i)
- #include <ViennaRNA/eval.h>
Calculate energy of a loop.
- Deprecated:
Use vrna_eval_loop_pt() instead!
See also
- 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
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float energy_of_struct(const char *string, const char *structure)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA
- Deprecated:
This function is deprecated and should not be used in future programs! Use energy_of_structure() instead!
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…
- 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
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int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA
- Deprecated:
This function is deprecated and should not be used in future programs! Use energy_of_structure_pt() instead!
See also
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…
- 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)
- #include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA
- Deprecated:
This function is deprecated and should not be used in future programs Use energy_of_circ_structure() instead!
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…
- 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
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int E_Stem(int type, int si1, int sj1, int extLoop, vrna_param_t *P)
- #include <ViennaRNA/loops/external.h>
Compute the energy contribution of a stem branching off a loop-region.
This function computes the energy contribution of a stem that branches off a loop region. This can be the case in multiloops, when a stem branching off increases the degree of the loop but also immediately interior base pairs of an exterior loop contribute free energy. To switch the behavior of the function according to the evaluation of a multiloop- or exterior-loop-stem, you pass the flag ‘extLoop’. The returned energy contribution consists of a TerminalAU penalty if the pair type is greater than 2, dangling end contributions of mismatching nucleotides adjacent to the stem if only one of the si1, sj1 parameters is greater than 0 and mismatch energies if both mismatching nucleotides are positive values. Thus, to avoid incorporating dangling end or mismatch energies just pass a negative number, e.g. -1 to the mismatch argument.
This is an illustration of how the energy contribution is assembled:
Here, (X,Y) is the base pair that closes the stem that branches off a loop region. The nucleotides si1 and sj1 are the 5’- and 3’- mismatches, respectively. If the base pair type of (X,Y) is greater than 2 (i.e. an A-U or G-U pair, the TerminalAU penalty will be included in the energy contribution returned. If si1 and sj1 are both nonnegative numbers, mismatch energies will also be included. If one of si1 or sj1 is a negative value, only 5’ or 3’ dangling end contributions are taken into account. To prohibit any of these mismatch contributions to be incorporated, just pass a negative number to both, si1 and sj1. In case the argument extLoop is 0, the returned energy contribution also includes the internal-loop-penalty of a multiloop stem with closing pair type.
- Deprecated:
Please use one of the functions vrna_E_ext_stem() and E_MLstem() instead! Use the former for cases where
extLoop!= 0 and the latter otherwise.
See also
E_MLstem(), _ExtLoop()
Note
This function is threadsafe
- Parameters:
type – The pair type of the first base pair un the stem
si1 – The 5’-mismatching nucleotide
sj1 – The 3’-mismatching nucleotide
extLoop – A flag that indicates whether the contribution reflects the one of an exterior loop or not
P – The data structure containing scaled energy parameters
- Returns:
The Free energy of the branch off the loop in dcal/mol
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int E_ExtLoop(int type, int si1, int sj1, vrna_param_t *P)
- #include <ViennaRNA/loops/external.h>
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FLT_OR_DBL exp_E_ExtLoop(int type, int si1, int sj1, vrna_exp_param_t *P)
- #include <ViennaRNA/loops/external.h>
This is the partition function variant of E_ExtLoop()
- Deprecated:
Use vrna_exp_E_ext_stem() instead!
See also
E_ExtLoop()
- Returns:
The Boltzmann weighted energy contribution of the introduced exterior-loop stem
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FLT_OR_DBL exp_E_Stem(int type, int si1, int sj1, int extLoop, vrna_exp_param_t *P)
- #include <ViennaRNA/loops/external.h>
Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region
This is the partition function variant of E_Stem()
See also
Note
This function is threadsafe
- Returns:
The Boltzmann weighted energy contribution of the branch off the loop
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static int E_IntLoop(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, vrna_param_t *P)
- #include <ViennaRNA/loops/internal.h>
Compute the Energy of an interior-loop
This function computes the free energy \(\Delta G\) of an interior-loop with the following structure: This general structure depicts an interior-loop that is closed by the base pair (X,Y). The enclosed base pair is (V,U) which leaves the unpaired bases a_1-a_n and b_1-b_n that constitute the loop. In this example, the length of the interior-loop is \((n+m)\)
where n or m may be 0 resulting in a bulge-loop or base pair stack. The mismatching nucleotides for the closing pair (X,Y) are:
5’-mismatch: a_1
3’-mismatch: b_m
and for the enclosed base pair (V,U):
5’-mismatch: b_1
3’-mismatch: a_n
See also
Note
Base pairs are always denoted in 5’->3’ direction. Thus the enclosed base pair must be ‘turned arround’ when evaluating the free energy of the interior-loop
This function is threadsafe
- Parameters:
n1 – The size of the ‘left’-loop (number of unpaired nucleotides)
n2 – The size of the ‘right’-loop (number of unpaired nucleotides)
type – The pair type of the base pair closing the interior loop
type_2 – The pair type of the enclosed base pair
si1 – The 5’-mismatching nucleotide of the closing pair
sj1 – The 3’-mismatching nucleotide of the closing pair
sp1 – The 3’-mismatching nucleotide of the enclosed pair
sq1 – The 5’-mismatching nucleotide of the enclosed pair
P – The datastructure containing scaled energy parameters
- Returns:
The Free energy of the Interior-loop in dcal/mol
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static FLT_OR_DBL exp_E_IntLoop(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, vrna_exp_param_t *P)
- #include <ViennaRNA/loops/internal.h>
Compute Boltzmann weight of interior loop
multiply by scale[u1+u2+2] for scaling
See also
get_scaled_pf_parameters(), vrna_exp_param_t, E_IntLoop()
Note
This function is threadsafe
- Parameters:
u1 – The size of the ‘left’-loop (number of unpaired nucleotides)
u2 – The size of the ‘right’-loop (number of unpaired nucleotides)
type – The pair type of the base pair closing the interior loop
type2 – The pair type of the enclosed base pair
si1 – The 5’-mismatching nucleotide of the closing pair
sj1 – The 3’-mismatching nucleotide of the closing pair
sp1 – The 3’-mismatching nucleotide of the enclosed pair
sq1 – The 5’-mismatching nucleotide of the enclosed pair
P – The datastructure containing scaled Boltzmann weights of the energy parameters
- Returns:
The Boltzmann weight of the Interior-loop
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static int E_IntLoop_Co(int type, int type_2, int i, int j, int p, int q, int cutpoint, short si1, short sj1, short sp1, short sq1, int dangles, vrna_param_t *P)
- #include <ViennaRNA/loops/internal.h>
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static int ubf_eval_int_loop(int i, int j, int p, int q, int i1, int j1, int p1, int q1, short si, short sj, short sp, short sq, unsigned char type, unsigned char type_2, int *rtype, int ij, int cp, vrna_param_t *P, vrna_sc_t *sc)
- #include <ViennaRNA/loops/internal.h>
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static int ubf_eval_int_loop2(int i, int j, int p, int q, int i1, int j1, int p1, int q1, short si, short sj, short sp, short sq, unsigned char type, unsigned char type_2, int *rtype, int ij, unsigned int *sn, unsigned int *ss, vrna_param_t *P, vrna_sc_t *sc)
- #include <ViennaRNA/loops/internal.h>
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static int ubf_eval_ext_int_loop(int i, int j, int p, int q, int i1, int j1, int p1, int q1, short si, short sj, short sp, short sq, unsigned char type, unsigned char type_2, int length, vrna_param_t *P, vrna_sc_t *sc)
- #include <ViennaRNA/loops/internal.h>
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static int E_MLstem(int type, int si1, int sj1, vrna_param_t *P)
- #include <ViennaRNA/loops/multibranch.h>
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static FLT_OR_DBL exp_E_MLstem(int type, int si1, int sj1, vrna_exp_param_t *P)
- #include <ViennaRNA/loops/multibranch.h>
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ON_SAME_STRAND(I, J, C)