RNAlib-2.2.0RC0
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Various utility- and helper-functions for secondary structure parsing, converting, etc. More...
Go to the source code of this file.
Functions | |
char * | vrna_pack_structure (const char *struc) |
Pack secondary secondary structure, 5:1 compression using base 3 encoding. More... | |
char * | pack_structure (const char *struc) |
Pack secondary secondary structure, 5:1 compression using base 3 encoding. More... | |
char * | vrna_unpack_structure (const char *packed) |
Unpack secondary structure previously packed with pack_structure() More... | |
char * | unpack_structure (const char *packed) |
Unpack secondary structure previously packed with pack_structure() More... | |
short * | vrna_pt_get (const char *structure) |
Create a pair table of a secondary structure. More... | |
short * | make_pair_table (const char *structure) |
Create a pair table of a secondary structure. More... | |
short * | vrna_pt_pk_get (const char *structure) |
Create a pair table of a secondary structure (pseudo-knot version) More... | |
short * | vrna_pt_copy (const short *pt) |
Get an exact copy of a pair table. More... | |
short * | copy_pair_table (const short *pt) |
Get an exact copy of a pair table. More... | |
short * | vrna_pt_ali_get (const char *structure) |
Create a pair table of a secondary structure (snoop align version) | |
short * | alimake_pair_table (const char *structure) |
short * | vrna_pt_snoop_get (const char *structure) |
Create a pair table of a secondary structure (snoop version) More... | |
short * | make_pair_table_snoop (const char *structure) |
int * | vrna_get_loop_index (const short *pt) |
Get a loop index representation of a structure. | |
char * | vrna_pt_to_db (short *pt) |
Convert a pair table into dot-parenthesis notation. More... | |
int | vrna_bp_distance (const char *str1, const char *str2) |
Compute the "base pair" distance between two secondary structures s1 and s2. More... | |
int | bp_distance (const char *str1, const char *str2) |
Compute the "base pair" distance between two secondary structures s1 and s2. More... | |
unsigned int * | vrna_refBPcnt_matrix (const short *reference_pt, unsigned int turn) |
Make a reference base pair count matrix. More... | |
unsigned int * | make_referenceBP_array (short *reference_pt, unsigned int turn) |
Make a reference base pair count matrix. More... | |
unsigned int * | vrna_refBPdist_matrix (const short *pt1, const short *pt2, unsigned int turn) |
Make a reference base pair distance matrix. More... | |
unsigned int * | compute_BPdifferences (short *pt1, short *pt2, unsigned int turn) |
Make a reference base pair distance matrix. More... | |
plist * | vrna_get_plist_from_pr (vrna_fold_compound *vc, double cut_off) |
Create a plist from base pair probability matrix. More... | |
void | assign_plist_from_pr (plist **pl, FLT_OR_DBL *probs, int length, double cutoff) |
Create a plist from a probability matrix. More... | |
void | bppm_to_structure (char *structure, FLT_OR_DBL *pr, unsigned int length) |
Create a dot-bracket like structure string from base pair probability matrix. | |
char | bppm_symbol (const float *x) |
Get a pseudo dot bracket notation for a given probability information. | |
void | vrna_parenthesis_structure (char *structure, bondT *bp, int length) |
Create a dot-backet/parenthesis structure from backtracking stack. | |
void | parenthesis_structure (char *structure, bondT *bp, int length) |
Create a dot-backet/parenthesis structure from backtracking stack. More... | |
void | vrna_parenthesis_zuker (char *structure, bondT *bp, int length) |
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c. More... | |
void | parenthesis_zuker (char *structure, bondT *bp, int length) |
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c. More... | |
plist * | vrna_get_plist_from_db (const char *struc, float pr) |
Create a plist from a dot-bracket string. More... | |
void | assign_plist_from_db (plist **pl, const char *struc, float pr) |
Create a plist from a dot-bracket string. More... | |
Various utility- and helper-functions for secondary structure parsing, converting, etc.
char* vrna_pack_structure | ( | const char * | struc | ) |
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
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.
struc | The secondary structure in dot-bracket notation |
char* pack_structure | ( | const char * | struc | ) |
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
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.
struc | The secondary structure in dot-bracket notation |
char* vrna_unpack_structure | ( | const char * | packed | ) |
Unpack secondary structure previously packed with pack_structure()
Translate a compressed binary string produced by pack_structure() back into the familiar dot-bracket notation.
packed | The binary encoded packed secondary structure |
char* unpack_structure | ( | const char * | packed | ) |
Unpack secondary structure previously packed with pack_structure()
Translate a compressed binary string produced by pack_structure() back into the familiar dot-bracket notation.
packed | The binary encoded packed secondary structure |
short* vrna_pt_get | ( | const char * | structure | ) |
Create a pair table of a secondary 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.
structure | The secondary structure in dot-bracket notation |
short* make_pair_table | ( | const char * | structure | ) |
Create a pair table of a secondary 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.
structure | The secondary structure in dot-bracket notation |
short* vrna_pt_pk_get | ( | const char * | structure | ) |
Create a pair table of a secondary structure (pseudo-knot version)
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_pt_get() this function also recognizes the base pairs denoted by '[' and ']' brackets.
structure | The secondary structure in (extended) dot-bracket notation |
short* vrna_pt_copy | ( | const short * | pt | ) |
Get an exact copy of a pair table.
pt | The pair table to be copied |
short* copy_pair_table | ( | const short * | pt | ) |
Get an exact copy of a pair table.
pt | The pair table to be copied |
short* alimake_pair_table | ( | const char * | structure | ) |
Pair table for snoop align
short* vrna_pt_snoop_get | ( | const char * | structure | ) |
Create a pair table of a secondary structure (snoop version)
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. The special pseudoknotted H/ACA-mRNA structure is taken into account.
short* make_pair_table_snoop | ( | 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. The special pseudoknotted H/ACA-mRNA structure is taken into account.
char* vrna_pt_to_db | ( | short * | pt | ) |
Convert a pair table into dot-parenthesis notation.
pt | The pair table to be copied |
int vrna_bp_distance | ( | const char * | str1, |
const char * | str2 | ||
) |
Compute the "base pair" distance between two secondary structures s1 and s2.
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
str1 | First structure in dot-bracket notation |
str2 | Second structure in dot-bracket notation |
int bp_distance | ( | const char * | str1, |
const char * | str2 | ||
) |
Compute the "base pair" distance between two secondary structures s1 and s2.
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
str1 | First structure in dot-bracket notation |
str2 | Second structure in dot-bracket notation |
unsigned int* vrna_refBPcnt_matrix | ( | const short * | reference_pt, |
unsigned int | turn | ||
) |
Make a reference base pair count matrix.
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!!!
unsigned int* make_referenceBP_array | ( | short * | reference_pt, |
unsigned int | turn | ||
) |
Make a reference base pair count matrix.
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!!!
unsigned int* vrna_refBPdist_matrix | ( | const short * | pt1, |
const short * | pt2, | ||
unsigned int | turn | ||
) |
Make a reference base pair distance matrix.
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!!!
unsigned int* compute_BPdifferences | ( | short * | pt1, |
short * | pt2, | ||
unsigned int | turn | ||
) |
Make a reference base pair distance matrix.
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!!!
void parenthesis_structure | ( | char * | structure, |
bondT * | bp, | ||
int | length | ||
) |
Create a dot-backet/parenthesis structure from backtracking stack.
void vrna_parenthesis_zuker | ( | char * | structure, |
bondT * | bp, | ||
int | length | ||
) |
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.
void parenthesis_zuker | ( | char * | structure, |
bondT * | bp, | ||
int | length | ||
) |
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.
plist* vrna_get_plist_from_db | ( | const char * | struc, |
float | pr | ||
) |
Create a plist from a dot-bracket string.
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
struc | The secondary structure in dot-bracket notation |
pr | The probability for each base pair used in the plist |
void assign_plist_from_db | ( | plist ** | pl, |
const char * | struc, | ||
float | pr | ||
) |
Create a plist from a dot-bracket string.
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
pl | A pointer to the plist that is to be created |
struc | The secondary structure in dot-bracket notation |
pr | The probability for each base pair |