// global variables int st_back // global functions char* vrna_pbacktrack5 ( vrna_fold_compound_t* vc, int length ) char* vrna_pbacktrack (vrna_fold_compound_t* vc) char* pbacktrack (char* sequence) char* pbacktrack_circ (char* sequence)
int st_back
Set this variable to 1 prior to a call of pf_fold() to ensure that all matrices needed for stochastic backtracking are filled in the forward recursions
Deprecated set the uniq_ML flag in vrna_md_t before passing it to vrna_fold_compound() .
See also:
char* vrna_pbacktrack5 ( vrna_fold_compound_t* vc, int length )
SWIG Wrapper Notes This function is attached as overloaded method pbacktrack() to objects of type fold_compound
Parameters:
vc | The fold compound data structure |
length | The length of the subsequence to consider (starting with 5’ end) |
Returns:
A sampled secondary structure in dot-bracket notation (or NULL on error)
Pre-Condition
Unique multiloop decomposition has to be active upon creation of vc
with vrna_fold_compound() or similar. This can be done easily by passing vrna_fold_compound() a model details parameter with vrna_md_t.uniq_ML = 1.
vrna_pf() has to be called first to fill the partition function matrices
char* vrna_pbacktrack (vrna_fold_compound_t* vc)
SWIG Wrapper Notes This function is attached as overloaded method pbacktrack() to objects of type fold_compound that accepts an optional length
argument. Hence, it serves as a replacement for vrna_pbacktrack() .
Parameters:
vc | The fold compound data structure |
Returns:
A sampled secondary structure in dot-bracket notation (or NULL on error)
Note
This function is polymorphic. It accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE , and VRNA_FC_TYPE_COMPARATIVE .
The function will automagically detect cicular RNAs based on the model_details in exp_params as provided via the vrna_fold_compound_t
Pre-Condition
Unique multiloop decomposition has to be active upon creation of vc
with vrna_fold_compound() or similar. This can be done easily by passing vrna_fold_compound() a model details parameter with vrna_md_t.uniq_ML = 1.
vrna_pf() has to be called first to fill the partition function matrices
char* pbacktrack (char* sequence)
Parameters:
sequence | The RNA sequence |
Returns:
A sampled secondary structure in dot-bracket notation
Pre-Condition
st_back has to be set to 1 before calling pf_fold() or pf_fold_par()
pf_fold_par() or pf_fold() have to be called first to fill the partition function matrices
char* pbacktrack_circ (char* sequence)
This function does the same as pbacktrack() but assumes the RNA molecule to be circular
Deprecated Use vrna_pbacktrack() instead.
Parameters:
sequence | The RNA sequence |
Returns:
A sampled secondary structure in dot-bracket notation
Pre-Condition
st_back has to be set to 1 before calling pf_fold() or pf_fold_par()
pf_fold_par() or pf_circ_fold() have to be called first to fill the partition function matrices