RNAlib-2.2.0c
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This module provides interfaces that deal with the most basic data structures used in structure predicting and energy evaluating function of the RNAlib. More...
Data Structures | |
struct | vrna_mx_mfeT |
struct | vrna_mx_pfT |
struct | vrna_fold_compound |
Macros | |
#define | VRNA_VC_TYPE_SINGLE 1 |
fold_compound_type Single Sequence | |
#define | VRNA_VC_TYPE_ALIGNMENT 2 |
fold_compound_type Sequence Alignment | |
#define | VRNA_OPTION_MFE 1 |
Option flag to specify requirement of Minimum Free Energy (MFE) DP matrices and corresponding set of energy parameters. More... | |
#define | VRNA_OPTION_PF 2 |
Option flag to specify requirement of Partition Function (PF) DP matrices and corresponding set of Boltzmann factors. More... | |
#define | VRNA_OPTION_EVAL_ONLY 8 |
Option flag to specify that neither MFE, nor PF DP matrices are required. More... | |
Functions | |
vrna_fold_compound * | vrna_get_fold_compound (const char *sequence, model_detailsT *md_p, unsigned int options) |
Retrieve a vrna_fold_compound data structure for single sequences and hybridizing sequences. More... | |
vrna_fold_compound * | vrna_get_fold_compound_ali (const char **sequences, model_detailsT *md_p, unsigned int options) |
Retrieve a vrna_fold_compound data structure for sequence alignments. More... | |
void | vrna_free_fold_compound (vrna_fold_compound *vc) |
Free memory occupied by a vrna_fold_compound. More... | |
void | vrna_free_mfe_matrices (vrna_fold_compound *vc) |
Free memory occupied by the Minimum Free Energy (MFE) Dynamic Programming (DP) matrices. More... | |
void | vrna_free_pf_matrices (vrna_fold_compound *vc) |
Free memory occupied by the Partition Function (PF) Dynamic Programming (DP) matrices. More... | |
This module provides interfaces that deal with the most basic data structures used in structure predicting and energy evaluating function of the RNAlib.
Throughout the RNAlib, a data structure, the vrna_fold_compound, is used to group information and data that is required for structure prediction and energy evaluation. Here, you'll find interface functions to create, modify, and delete vrna_fold_compound data structures.
#define VRNA_OPTION_MFE 1 |
Option flag to specify requirement of Minimum Free Energy (MFE) DP matrices and corresponding set of energy parameters.
#define VRNA_OPTION_PF 2 |
Option flag to specify requirement of Partition Function (PF) DP matrices and corresponding set of Boltzmann factors.
#define VRNA_OPTION_EVAL_ONLY 8 |
Option flag to specify that neither MFE, nor PF DP matrices are required.
Use this flag in conjuntion with VRNA_OPTION_MFE, and VRNA_OPTION_PF to save memory for a vrna_fold_compound obtained from vrna_get_fold_compound(), or vrna_get_fold_compound_ali() in cases where only energy evaluation but no structure prediction is required.
vrna_fold_compound* vrna_get_fold_compound | ( | const char * | sequence, |
model_detailsT * | md_p, | ||
unsigned int | options | ||
) |
Retrieve a vrna_fold_compound data structure for single sequences and hybridizing sequences.
This function provides an easy interface to obtain a prefilled vrna_fold_compound by passing a single sequence, or two contatenated sequences as input. For the latter, sequences need to be seperated by an '&' character like this:
char *sequence = "GGGG&CCCC";
The optional parameter 'md_p' can be used to specify the model details for computations on the #vrna_fold_compounds content. The third parameter 'options' is used to specify the DP matrix requirements and the corresponding set of energy parameters. Use the macros:
to specify the required type of computations that will be performed with the vrna_fold_compound.
sequence | A single sequence, or two concatenated sequences seperated by an '&' character |
md_p | An optional set of model details |
options | The options for DP matrices memory allocation |
vrna_fold_compound* vrna_get_fold_compound_ali | ( | const char ** | sequences, |
model_detailsT * | md_p, | ||
unsigned int | options | ||
) |
Retrieve a vrna_fold_compound data structure for sequence alignments.
This function provides an easy interface to obtain a prefilled vrna_fold_compound by passing an alignment of sequences.
The optional parameter 'md_p' can be used to specify the model details for computations on the #vrna_fold_compounds content. The third parameter 'options' is used to specify the DP matrix requirements and the corresponding set of energy parameters. Use the macros:
to specify the required type of computations that will be performed with the vrna_fold_compound.
sequences | A sequence alignment including 'gap' characters |
md_p | An optional set of model details |
options | The options for DP matrices memory allocation |
void vrna_free_fold_compound | ( | vrna_fold_compound * | vc | ) |
Free memory occupied by a vrna_fold_compound.
vc | The vrna_fold_compound that is to be erased from memory |
void vrna_free_mfe_matrices | ( | vrna_fold_compound * | vc | ) |
Free memory occupied by the Minimum Free Energy (MFE) Dynamic Programming (DP) matrices.
vc | The vrna_fold_compound storing the MFE DP matrices that are to be erased from memory |
void vrna_free_pf_matrices | ( | vrna_fold_compound * | vc | ) |
Free memory occupied by the Partition Function (PF) Dynamic Programming (DP) matrices.
vc | The vrna_fold_compound storing the PF DP matrices that are to be erased from memory |