Variations of the global partition function algorithm. More...
Variations of the global partition function algorithm.
We provide implementations of the global partition function algorithm for
Modules | |
Computing Partition Functions of a Distance Based Partitioning | |
Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures. | |
Predicting various thermodynamic properties | |
Compute various thermodynamic properties using the partition function. | |
Deprecated Interface for Global Partition Function Computation | |
Files | |
file | part_func.h |
Partition function implementations. | |
Data Structures | |
struct | vrna_dimer_pf_s |
Data structure returned by vrna_pf_dimer() More... | |
struct | vrna_multimer_pf_s |
Functions | |
vrna_ep_t * | vrna_plist_from_probs (vrna_fold_compound_t *vc, double cut_off) |
Create a vrna_ep_t from base pair probability matrix. More... | |
Basic global partition function interface | |
FLT_OR_DBL | vrna_pf (vrna_fold_compound_t *vc, char *structure) |
Compute the partition function ![]() | |
vrna_dimer_pf_t | vrna_pf_dimer (vrna_fold_compound_t *vc, char *structure) |
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More... | |
FLT_OR_DBL * | vrna_pf_substrands (vrna_fold_compound_t *fc, size_t complex_size) |
FLT_OR_DBL | vrna_pf_add (FLT_OR_DBL dG1, FLT_OR_DBL dG2, double kT) |
Simplified global partition function computation using sequence(s) or multiple sequence alignment(s) | |
float | vrna_pf_fold (const char *sequence, char *structure, vrna_ep_t **pl) |
Compute Partition function ![]() | |
float | vrna_pf_circfold (const char *sequence, char *structure, vrna_ep_t **pl) |
Compute Partition function ![]() | |
float | vrna_pf_alifold (const char **sequences, char *structure, vrna_ep_t **pl) |
Compute Partition function ![]() | |
float | vrna_pf_circalifold (const char **sequences, char *structure, vrna_ep_t **pl) |
Compute Partition function ![]() | |
vrna_dimer_pf_t | vrna_pf_co_fold (const char *seq, char *structure, vrna_ep_t **pl) |
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More... | |
struct vrna_dimer_pf_s |
Data structure returned by vrna_pf_dimer()
Data Fields | |
double | F0AB |
Null model without DuplexInit. | |
double | FAB |
all states with DuplexInit correction | |
double | FcAB |
true hybrid states only | |
double | FA |
monomer A | |
double | FB |
monomer B | |
struct vrna_multimer_pf_s |
float vrna_pf | ( | vrna_fold_compound_t * | vc, |
char * | structure | ||
) |
#include <ViennaRNA/part_func.h>
Compute the partition function for a given RNA sequence, or sequence alignment.
If structure is not a NULL pointer on input, it contains on return a string consisting of the letters " . , | { } ( ) " denoting bases that are essentially unpaired, weakly paired, strongly paired without preference, weakly upstream (downstream) paired, or strongly up- (down-)stream paired bases, respectively. If the model's compute_bpp is set to 0 base pairing probabilities will not be computed (saving CPU time), otherwise after calculations took place pr will contain the probability that bases i and j pair.
stdout
.[in,out] | vc | The fold compound data structure |
[in,out] | structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
vrna_dimer_pf_t vrna_pf_dimer | ( | vrna_fold_compound_t * | vc, |
char * | structure | ||
) |
#include <ViennaRNA/part_func.h>
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers.
This is the cofold partition function folding.
FA
, FB
, FAB
, F0AB
members of the output data structure in case of contradicting constraints or numerical over-/underflow. In the latter case, a corresponding warning will be issued to stdout
.vc | the fold compound data structure |
structure | Will hold the structure or constraints |
float vrna_pf_fold | ( | const char * | sequence, |
char * | structure, | ||
vrna_ep_t ** | pl | ||
) |
#include <ViennaRNA/part_func.h>
Compute Partition function (and base pair probabilities) for an RNA sequence using a comparative method.
This simplified interface to vrna_pf() computes the partition function and, if required, base pair probabilities for an RNA sequence using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing.
sequence | RNA sequence |
structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
pl | A pointer to a list of vrna_ep_t to store pairing probabilities (Maybe NULL) |
float vrna_pf_circfold | ( | const char * | sequence, |
char * | structure, | ||
vrna_ep_t ** | pl | ||
) |
#include <ViennaRNA/part_func.h>
Compute Partition function (and base pair probabilities) for a circular RNA sequences using a comparative method.
This simplified interface to vrna_pf() computes the partition function and, if required, base pair probabilities for a circular RNA sequence using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing.
Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [11] for further details.
sequence | A circular RNA sequence |
structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
pl | A pointer to a list of vrna_ep_t to store pairing probabilities (Maybe NULL) |
float vrna_pf_alifold | ( | const char ** | sequences, |
char * | structure, | ||
vrna_ep_t ** | pl | ||
) |
#include <ViennaRNA/part_func.h>
Compute Partition function (and base pair probabilities) for an RNA sequence alignment using a comparative method.
This simplified interface to vrna_pf() computes the partition function and, if required, base pair probabilities for an RNA sequence alignment using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing.
sequences | RNA sequence alignment |
structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
pl | A pointer to a list of vrna_ep_t to store pairing probabilities (Maybe NULL) |
float vrna_pf_circalifold | ( | const char ** | sequences, |
char * | structure, | ||
vrna_ep_t ** | pl | ||
) |
#include <ViennaRNA/part_func.h>
Compute Partition function (and base pair probabilities) for an alignment of circular RNA sequences using a comparative method.
This simplified interface to vrna_pf() computes the partition function and, if required, base pair probabilities for an RNA sequence alignment using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing.
Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [11] for further details.
sequences | Sequence alignment of circular RNAs |
structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
pl | A pointer to a list of vrna_ep_t to store pairing probabilities (Maybe NULL) |
vrna_ep_t * vrna_plist_from_probs | ( | vrna_fold_compound_t * | vc, |
double | cut_off | ||
) |
#include <ViennaRNA/utils/structures.h>
Create a vrna_ep_t from base pair probability matrix.
The probability matrix provided via the vrna_fold_compound_t is parsed and all pair probabilities above the given threshold are used to create an entry in the plist
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
[in] | vc | The fold compound |
[in] | cut_off | The cutoff value |
vrna_dimer_pf_t vrna_pf_co_fold | ( | const char * | seq, |
char * | structure, | ||
vrna_ep_t ** | pl | ||
) |
#include <ViennaRNA/part_func.h>
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers.
This simplified interface to vrna_pf_dimer() computes the partition function and, if required, base pair probabilities for an RNA-RNA interaction using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing.
seq | Two concatenated RNA sequences with a delimiting '&' in between |
structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
pl | A pointer to a list of vrna_ep_t to store pairing probabilities (Maybe NULL) |