unstructured_domains.h

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#ifndef VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
#define VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H

typedef struct vrna_unstructured_domain_s vrna_ud_t;

typedef struct vrna_unstructured_domain_motif_s vrna_ud_motif_t;

#include <ViennaRNA/datastructures/basic.h>
#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/utils/structures.h>

typedef int (vrna_callback_ud_energy)(vrna_fold_compound_t  *vc,
                                      int                   i,
                                      int                   j,
                                      unsigned int          loop_type,
                                      void                  *data);

typedef FLT_OR_DBL (vrna_callback_ud_exp_energy)(vrna_fold_compound_t *vc,
                                                 int                  i,
                                                 int                  j,
                                                 unsigned int         loop_type,
                                                 void                 *data);

typedef void (vrna_callback_ud_production)(vrna_fold_compound_t *vc,
                                           void                 *data);

typedef void (vrna_callback_ud_exp_production)(vrna_fold_compound_t *vc,
                                               void                 *data);


typedef void (vrna_callback_ud_probs_add)(vrna_fold_compound_t  *vc,
                                          int                   i,
                                          int                   j,
                                          unsigned int          loop_type,
                                          FLT_OR_DBL            exp_energy,
                                          void                  *data);

typedef FLT_OR_DBL (vrna_callback_ud_probs_get)(vrna_fold_compound_t  *vc,
                                                int                   i,
                                                int                   j,
                                                unsigned int          loop_type,
                                                int                   motif,
                                                void                  *data);


#define VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP    1U

#define VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP     2U

#define VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP    4U

#define VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP     8U

#define VRNA_UNSTRUCTURED_DOMAIN_MOTIF       16U

#define VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS   (VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | \
                                              VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | \
                                              VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | \
                                              VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP)

struct vrna_unstructured_domain_s {
  /*
   **********************************
   * Keep track of all motifs added
   **********************************
   */
  int           uniq_motif_count;                   
  unsigned int  *uniq_motif_size;                   
  int           motif_count;                        
  char          **motif;                            
  char          **motif_name;                       
  unsigned int  *motif_size;                        
  double        *motif_en;                          
  unsigned int  *motif_type;                        
  /*
   **********************************
   * Grammar extension for ligand
   * binding
   **********************************
   */
  vrna_callback_ud_production     *prod_cb;       
  vrna_callback_ud_exp_production *exp_prod_cb;   
  vrna_callback_ud_energy         *energy_cb;     
  vrna_callback_ud_exp_energy     *exp_energy_cb; 
  void                            *data;          
  vrna_callback_free_auxdata      *free_data;     
  vrna_callback_ud_probs_add      *probs_add;     
  vrna_callback_ud_probs_get      *probs_get;     
};


struct vrna_unstructured_domain_motif_s {
  int start;
  int number;
};


vrna_ud_motif_t *
vrna_ud_motifs_centroid(vrna_fold_compound_t  *fc,
                        const char            *structure);


vrna_ud_motif_t *
vrna_ud_motifs_MEA(vrna_fold_compound_t *fc,
                   const char           *structure,
                   vrna_ep_t            *probability_list);


vrna_ud_motif_t *
vrna_ud_motifs_MFE(vrna_fold_compound_t *fc,
                   const char           *structure);


void  vrna_ud_add_motif(vrna_fold_compound_t  *vc,
                        const char            *motif,
                        double                motif_en,
                        const char            *motif_name,
                        unsigned int          loop_type);


int *vrna_ud_get_motif_size_at(vrna_fold_compound_t *vc,
                               int                  i,
                               unsigned int         loop_type);


int *
vrna_ud_get_motifs_at(vrna_fold_compound_t  *vc,
                      int                   i,
                      unsigned int          loop_type);


vrna_ud_motif_t *
vrna_ud_detect_motifs(vrna_fold_compound_t  *vc,
                      const char            *structure);


void  vrna_ud_remove(vrna_fold_compound_t *vc);


void  vrna_ud_set_data(vrna_fold_compound_t       *vc,
                       void                       *data,
                       vrna_callback_free_auxdata *free_cb);


void vrna_ud_set_prod_rule_cb(vrna_fold_compound_t        *vc,
                              vrna_callback_ud_production *pre_cb,
                              vrna_callback_ud_energy     *e_cb);


void  vrna_ud_set_exp_prod_rule_cb(vrna_fold_compound_t             *vc,
                                   vrna_callback_ud_exp_production  *pre_cb,
                                   vrna_callback_ud_exp_energy      *exp_e_cb);


void  vrna_ud_set_prob_cb(vrna_fold_compound_t        *vc,
                          vrna_callback_ud_probs_add  *setter,
                          vrna_callback_ud_probs_get  *getter);


#endif