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# H/2Dpfold.h

Go to the documentation of this file.

    00001 /*
    00002       minimum free energy
    00003       RNA secondary structure with
    00004       basepair distance d to reference structure prediction
    00005
    00006 */
    00007 #ifndef __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
    00008 #define __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
    00009
    00010 #include "data_structures.h"
    00011
    00012 #ifdef __GNUC__
    00013 #define DEPRECATED(func) func __attribute__ ((deprecated))
    00014 #else
    00015 #define DEPRECATED(func) func
    00016 #endif
    00017
    00039 TwoDpfold_vars  *get_TwoDpfold_variables( const char *seq,
    00040                                           const char *structure1,
    00041                                           char *structure2,
    00042                                           int circ);
    00043
    00056 TwoDpfold_vars  *get_TwoDpfold_variables_from_MFE(TwoDfold_vars *mfe_vars);
    00057
    00068 void            destroy_TwoDpfold_variables(TwoDpfold_vars *vars);
    00069
    00075 DEPRECATED(FLT_OR_DBL          **TwoDpfold(TwoDpfold_vars *our_variables,
    00076                                 int maxDistance1,
    00077                                 int maxDistance2));
    00078
    00084 DEPRECATED(FLT_OR_DBL          **TwoDpfold_circ(
    00085                                 TwoDpfold_vars *our_variables,
    00086                                 int maxDistance1,
    00087                                 int maxDistance2));
    00088
    00110 TwoDpfold_solution  *TwoDpfoldList( TwoDpfold_vars *vars,
    00111                                     int maxDistance1,
    00112                                     int maxDistance2);
    00113
    00131 char            *TwoDpfold_pbacktrack(TwoDpfold_vars *vars,
    00132                                       int d1,
    00133                                       int d2);
    00134
    00154 char            *TwoDpfold_pbacktrack5( TwoDpfold_vars *vars,
    00155                                           int d1,
    00156                                           int d2,
    00157                                           unsigned int length);
    00158
    00159 #endif