// typedefs typedef struct vrna_hx_s vrna_hx_t typedef struct vrna_elem_prob_s vrna_ep_t // structs struct vrna_elem_prob_s struct vrna_hx_s // global variables int loop_size[STRUC] int helix_size[STRUC] int loop_degree[STRUC] int loops int unpaired int pairs // global functions char* b2HIT (const char* structure) char* b2C (const char* structure) char* b2Shapiro (const char* structure) char* add_root (const char* structure) char* expand_Shapiro (const char* coarse) char* expand_Full (const char* structure) char* unexpand_Full (const char* ffull) char* unweight (const char* wcoarse) void unexpand_aligned_F (char* align [2]) void parse_structure (const char* structure) char* vrna_db_pack (const char* struc) char* vrna_db_unpack (const char* packed) short* vrna_ptable (const char* structure) short* vrna_ptable_from_string ( const char* string, unsigned int options ) short* vrna_pt_pk_get (const char* structure) short* vrna_ptable_copy (const short* pt) short* vrna_pt_ali_get (const char* structure) short* vrna_pt_snoop_get (const char* structure) int* vrna_loopidx_from_ptable (const short* pt) void vrna_db_flatten ( char* structure, unsigned int options ) void vrna_db_flatten_to ( char* string, const char target [3], unsigned int options ) char* vrna_db_from_ptable (short* pt) char* vrna_db_from_WUSS (const char* wuss) int vrna_bp_distance ( const char* str1, const char* str2 ) unsigned int* vrna_refBPcnt_matrix ( const short* reference_pt, unsigned int turn ) unsigned int* vrna_refBPdist_matrix ( const short* pt1, const short* pt2, unsigned int turn ) char* vrna_db_from_probs ( const FLT_OR_DBL* pr, unsigned int length ) char vrna_bpp_symbol (const float* x) char* vrna_db_from_bp_stack ( vrna_bp_stack_t* bp, unsigned int length ) void vrna_letter_structure ( char* structure, vrna_bp_stack_t* bp, unsigned int length ) vrna_ep_t* vrna_plist ( const char* struc, float pr ) char* vrna_db_from_plist ( vrna_ep_t* pairs, unsigned int n ) char* vrna_db_to_element_string (const char* structure) vrna_hx_t* vrna_hx_from_ptable (short* pt) vrna_hx_t* vrna_hx_merge ( const vrna_hx_t* list, int maxdist ) void assign_plist_from_db ( vrna_ep_t** pl, const char* struc, float pr ) char* pack_structure (const char* struc) char* unpack_structure (const char* packed) short* make_pair_table (const char* structure) short* make_pair_table_pk (const char* structure) short* copy_pair_table (const short* pt) short* alimake_pair_table (const char* structure) short* make_pair_table_snoop (const char* structure) int* make_loop_index_pt (short* pt) int bp_distance ( const char* str1, const char* str2 ) unsigned int* make_referenceBP_array ( short* reference_pt, unsigned int turn ) unsigned int* compute_BPdifferences ( short* pt1, short* pt2, unsigned int turn ) void parenthesis_structure ( char* structure, vrna_bp_stack_t* bp, int length ) void parenthesis_zuker ( char* structure, vrna_bp_stack_t* bp, int length ) void letter_structure ( char* structure, vrna_bp_stack_t* bp, int length ) void bppm_to_structure ( char* structure, FLT_OR_DBL* pr, unsigned int length ) char bppm_symbol (const float* x) // macros #define STRUC #define VRNA_BRACKETS_ALPHA #define VRNA_BRACKETS_ANG #define VRNA_BRACKETS_CLY #define VRNA_BRACKETS_DEFAULT #define VRNA_BRACKETS_RND #define VRNA_BRACKETS_SQR #define VRNA_PLIST_TYPE_BASEPAIR #define VRNA_PLIST_TYPE_GQUAD #define VRNA_PLIST_TYPE_H_MOTIF #define VRNA_PLIST_TYPE_I_MOTIF #define VRNA_PLIST_TYPE_STACK #define VRNA_PLIST_TYPE_UD_MOTIF
typedef struct vrna_elem_prob_s vrna_ep_t
int loop_size [STRUC]
int helix_size [STRUC]
int loop_degree [STRUC]
int loops
int unpaired
int pairs
char* b2HIT (const char* structure)
Parameters:
structure |
Returns:
char* b2C (const char* structure)
Parameters:
structure |
Returns:
char* b2Shapiro (const char* structure)
Parameters:
structure |
Returns:
char* add_root (const char* structure)
Parameters:
structure |
Returns:
char* expand_Shapiro (const char* coarse)
Parameters:
coarse |
Returns:
char* expand_Full (const char* structure)
Parameters:
structure |
Returns:
char* unexpand_Full (const char* ffull)
Parameters:
ffull |
Returns:
char* unweight (const char* wcoarse)
Parameters:
wcoarse |
Returns:
void unexpand_aligned_F (char* align [2])
Takes two aligned structures as produced by tree_edit_distance() function back to bracket notation with ‘_’ as the gap character. The result overwrites the input.
Parameters:
align |
void parse_structure (const char* structure)
The function writes to the following global variables: loop_size , loop_degree , helix_size , loops , pairs , unpaired
Parameters:
structure |
Returns:
char* vrna_db_pack (const char* struc)
Returns a binary string encoding of the secondary structure using a 5:1 compression scheme. The string is NULL terminated and can therefore be used with standard string functions such as strcmp(). Useful for programs that need to keep many structures in memory.
Parameters:
struc | The secondary structure in dot-bracket notation |
Returns:
The binary encoded structure
See also:
char* vrna_db_unpack (const char* packed)
Translate a compressed binary string produced by vrna_db_pack() back into the familiar dot-bracket notation.
Parameters:
packed | The binary encoded packed secondary structure |
Returns:
The unpacked secondary structure in dot-bracket notation
See also:
short* vrna_ptable (const char* structure)
Returns a newly allocated table, such that table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure.
Parameters:
structure | The secondary structure in dot-bracket notation |
Returns:
A pointer to the created pair_table
See also:
short* vrna_ptable_from_string ( const char* string, unsigned int options )
This function takes an input string of a secondary structure annotation in Dot-Bracket Notation (a.k.a. Dot-Parenthesis Notation) or Extended Dot-Bracket Notation , and converts it into a pair table representation.
Parameters:
string | Secondary structure in Extended Dot-Bracket Notation |
options | A bitmask to specify which brackets are recognized during conversion to pair table |
Returns:
A pointer to a new pair table of the provided secondary structure
short* vrna_pt_pk_get (const char* structure)
Returns a newly allocated table, such that table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure.
In contrast to vrna_ptable() this function also recognizes the base pairs denoted by ‘[‘ and ‘]’ brackets.
Parameters:
structure | The secondary structure in (extended) dot-bracket notation |
Returns:
A pointer to the created pair_table
short* vrna_ptable_copy (const short* pt)
Parameters:
pt | The pair table to be copied |
Returns:
A pointer to the copy of ‘pt’
short* vrna_pt_ali_get (const char* structure)
short* vrna_pt_snoop_get (const char* structure)
int* vrna_loopidx_from_ptable (const short* pt)
void vrna_db_flatten ( char* structure, unsigned int options )
This function can be used to replace brackets of unusual types, such as angular brackets <> , to dot-bracket format. The options
parameter is used tpo specify which types of brackets will be replaced by round parenthesis () .
SWIG Wrapper Notes This function flattens an input structure string in-place! The second parameter is optional and defaults to VRNA_BRACKETS_DEFAULT .
An overloaded version of this function exists, where an additional second parameter can be passed to specify the target brackets, i.e. the type of matching pair characters all brackets will be flattened to. Therefore, in the scripting language interface this function is a replacement for vrna_db_flatten_to() .
Parameters:
structure | The structure string where brackets are flattened in-place |
options | A bitmask to specify which types of brackets should be flattened out |
void vrna_db_flatten_to ( char* string, const char target [3], unsigned int options )
This function can be used to replace brackets in a structure annotation string, such as square brackets [] , to another type of pair characters, e.g. angular brackets <> .
The target
array must contain a character for the ‘pair open’ annotation at position 0, and one for ‘pair close’ at position 1. T options
parameter is used to specify which types of brackets will be replaced by the new pairs.
SWIG Wrapper Notes This function is available as an overloaded version of vrna_db_flatten()
Parameters:
structure | The structure string where brackets are flattened in-place |
target | The new pair characters the string will be flattened to |
options | A bitmask to specify which types of brackets should be flattened out |
char* vrna_db_from_ptable (short* pt)
Parameters:
pt | The pair table to be copied |
Returns:
A char pointer to the dot-bracket string
char* vrna_db_from_WUSS (const char* wuss)
Parameters:
wuss | The input string in WUSS notation |
Returns:
A dot-bracket notation of the input secondary structure
Note
This function flattens all brackets, and treats pseudo-knots annotated by matching pairs of upper/lowercase letters as unpaired nucleotides
int vrna_bp_distance ( const char* str1, const char* str2 )
The sequences should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-pair close-pair as move-set
Parameters:
str1 | First structure in dot-bracket notation |
str2 | Second structure in dot-bracket notation |
Returns:
The base pair distance between str1 and str2
unsigned int* vrna_refBPcnt_matrix ( const short* reference_pt, unsigned int turn )
unsigned int* vrna_refBPdist_matrix ( const short* pt1, const short* pt2, unsigned int turn )
char* vrna_db_from_probs ( const FLT_OR_DBL* pr, unsigned int length )
char vrna_bpp_symbol (const float* x)
char* vrna_db_from_bp_stack ( vrna_bp_stack_t* bp, unsigned int length )
This function is capable to create dot-bracket structures from suboptimal structure prediction sensu M. Zuker
Parameters:
bp | Base pair stack containing the traced base pairs |
length | The length of the structure |
Returns:
The secondary structure in dot-bracket notation as provided in the input
vrna_ep_t* vrna_plist ( const char* struc, float pr )
The dot-bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.
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
Parameters:
struc | The secondary structure in dot-bracket notation |
pr | The probability for each base pair used in the plist |
Returns:
The plist array
char* vrna_db_from_plist ( vrna_ep_t* pairs, unsigned int n )
Parameters:
pairs | A vrna_ep_t containing the pairs to be included in the dot-bracket string |
n | The length of the structure (number of nucleotides) |
Returns:
The dot-bracket string containing the provided base pairs
See also:
void assign_plist_from_db ( vrna_ep_t** pl, const char* struc, float pr )
The dot-bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.
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
Deprecated Use vrna_plist() instead
Parameters:
pl | A pointer to the vrna_ep_t that is to be created |
struc | The secondary structure in dot-bracket notation |
pr | The probability for each base pair |
char* pack_structure (const char* struc)
Returns a binary string encoding of the secondary structure using a 5:1 compression scheme. The string is NULL terminated and can therefore be used with standard string functions such as strcmp(). Useful for programs that need to keep many structures in memory.
Deprecated Use vrna_db_pack() as a replacement
Parameters:
struc | The secondary structure in dot-bracket notation |
Returns:
The binary encoded structure
char* unpack_structure (const char* packed)
Translate a compressed binary string produced by pack_structure() back into the familiar dot-bracket notation.
Deprecated Use vrna_db_unpack() as a replacement
Parameters:
packed | The binary encoded packed secondary structure |
Returns:
The unpacked secondary structure in dot-bracket notation
short* make_pair_table (const char* structure)
Returns a newly allocated table, such that table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure.
Deprecated Use vrna_ptable() instead
Parameters:
structure | The secondary structure in dot-bracket notation |
Returns:
A pointer to the created pair_table
short* copy_pair_table (const short* pt)
Deprecated Use vrna_ptable_copy() instead
Parameters:
pt | The pair table to be copied |
Returns:
A pointer to the copy of ‘pt’
short* alimake_pair_table (const char* structure)
Pair table for snoop align
Deprecated Use vrna_pt_ali_get() instead!
short* make_pair_table_snoop (const char* structure)
int bp_distance ( const char* str1, const char* str2 )
The sequences should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-pair close-pair as move-set
Deprecated Use vrna_bp_distance instead
Parameters:
str1 | First structure in dot-bracket notation |
str2 | Second structure in dot-bracket notation |
Returns:
The base pair distance between str1 and str2
unsigned int* make_referenceBP_array ( short* reference_pt, unsigned int turn )
Get an upper triangular matrix containing the number of basepairs of a reference structure for each interval [i,j] with i<j. Access it via iindx!!!
Deprecated Use vrna_refBPcnt_matrix() instead
unsigned int* compute_BPdifferences ( short* pt1, short* pt2, unsigned int turn )
Get an upper triangular matrix containing the base pair distance of two reference structures for each interval [i,j] with i<j. Access it via iindx!!!
Deprecated Use vrna_refBPdist_matrix() instead
void parenthesis_structure ( char* structure, vrna_bp_stack_t* bp, int length )
Deprecated use vrna_parenthesis_structure() instead
Note
This function is threadsafe
void parenthesis_zuker ( char* structure, vrna_bp_stack_t* bp, int length )
Deprecated use vrna_parenthesis_zuker instead
Note
This function is threadsafe
void bppm_to_structure ( char* structure, FLT_OR_DBL* pr, unsigned int length )
char bppm_symbol (const float* x)
#define VRNA_BRACKETS_ALPHA
See also:
#define VRNA_BRACKETS_ANG
<>
See also:
vrna_ptable_from_string() , vrna_db_flatten() , vrna_db_flatten_to()
#define VRNA_BRACKETS_CLY
{}
See also:
vrna_ptable_from_string() , vrna_db_flatten() , vrna_db_flatten_to()
#define VRNA_BRACKETS_DEFAULT
See also:
vrna_ptable_from_string() , vrna_db_flatten() , vrna_db_flatten_to()
#define VRNA_BRACKETS_RND
()
See also:
vrna_ptable_from_string() , vrna_db_flatten() , vrna_db_flatten_to()
#define VRNA_BRACKETS_SQR
[]
See also:
vrna_ptable_from_string() , vrna_db_flatten() , vrna_db_flatten_to()