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RNAlib-2.2.5
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Collaboration diagram for Parsing, Converting, and Comparing - Functions to Manipulate Secondary Structures:Files | |
| file | RNAstruct.h |
| Parsing and Coarse Graining of Structures. | |
| file | structure_utils.h |
| Various utility- and helper-functions for secondary structure parsing, converting, etc. | |
Data Structures | |
| struct | vrna_hx_s |
Functions | |
| char * | b2HIT (const char *structure) |
| Converts the full structure from bracket notation to the HIT notation including root. More... | |
| char * | b2C (const char *structure) |
| Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers. More... | |
| char * | b2Shapiro (const char *structure) |
| Converts the full structure from bracket notation to the weighted coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers. More... | |
| char * | add_root (const char *structure) |
| Adds a root to an un-rooted tree in any except bracket notation. More... | |
| char * | expand_Shapiro (const char *coarse) |
| Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C(). More... | |
| char * | expand_Full (const char *structure) |
| Convert the full structure from bracket notation to the expanded notation including root. More... | |
| char * | unexpand_Full (const char *ffull) |
| Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers 'U' 'P' and 'R'. More... | |
| char * | unweight (const char *wcoarse) |
| Strip weights from any weighted tree. More... | |
| void | unexpand_aligned_F (char *align[2]) |
| Converts two aligned structures in expanded notation. More... | |
| void | parse_structure (const char *structure) |
| Collects a statistic of structure elements of the full structure in bracket notation. More... | |
| char * | vrna_db_pack (const char *struc) |
| Pack secondary secondary structure, 5:1 compression using base 3 encoding. More... | |
| char * | vrna_db_unpack (const char *packed) |
| Unpack secondary structure previously packed with vrna_db_pack() More... | |
| short * | vrna_ptable (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_ptable_copy (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 * | vrna_pt_snoop_get (const char *structure) |
| Create a pair table of a secondary structure (snoop version) More... | |
| int * | vrna_loopidx_from_ptable (const short *pt) |
| Get a loop index representation of a structure. | |
| char * | vrna_db_from_ptable (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... | |
| unsigned int * | vrna_refBPcnt_matrix (const 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... | |
| char * | vrna_db_from_probs (const FLT_OR_DBL *pr, unsigned int length) |
| Create a dot-bracket like structure string from base pair probability matrix. | |
| char | vrna_bpp_symbol (const float *x) |
| Get a pseudo dot bracket notation for a given probability information. | |
| char * | vrna_db_from_bp_stack (vrna_bp_stack_t *bp, unsigned int length) |
| Create a dot-backet/parenthesis structure from backtracking stack. More... | |
| vrna_plist_t * | vrna_plist (const char *struc, float pr) |
| Create a vrna_plist_t from a dot-bracket string. More... | |
| char * | vrna_db_from_plist (vrna_plist_t *pairs, unsigned int n) |
| Convert a list of base pairs into dot-bracket notation. More... | |
| void | assign_plist_from_db (vrna_plist_t **pl, const char *struc, float pr) |
| Create a vrna_plist_t from a dot-bracket string. More... | |
| char * | pack_structure (const char *struc) |
| Pack secondary secondary structure, 5:1 compression using base 3 encoding. More... | |
| char * | unpack_structure (const char *packed) |
| Unpack secondary structure previously packed with pack_structure() More... | |
| short * | make_pair_table (const char *structure) |
| Create a pair table of a secondary structure. More... | |
| short * | copy_pair_table (const short *pt) |
| Get an exact copy of a pair table. More... | |
| short * | alimake_pair_table (const char *structure) |
| short * | make_pair_table_snoop (const char *structure) |
| int | bp_distance (const char *str1, const char *str2) |
| Compute the "base pair" distance between two secondary structures s1 and s2. More... | |
| unsigned int * | make_referenceBP_array (short *reference_pt, unsigned int turn) |
| Make a reference base pair count matrix. More... | |
| unsigned int * | compute_BPdifferences (short *pt1, short *pt2, unsigned int turn) |
| Make a reference base pair distance matrix. More... | |
| void | parenthesis_structure (char *structure, vrna_bp_stack_t *bp, int length) |
| Create a dot-backet/parenthesis structure from backtracking stack. More... | |
| void | parenthesis_zuker (char *structure, vrna_bp_stack_t *bp, int length) |
| Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c. 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. More... | |
| char | bppm_symbol (const float *x) |
| Get a pseudo dot bracket notation for a given probability information. More... | |
Variables | |
| int | loop_size [STRUC] |
| contains a list of all loop sizes. loop_size[0] contains the number of external bases. | |
| int | helix_size [STRUC] |
| contains a list of all stack sizes. | |
| int | loop_degree [STRUC] |
| contains the corresponding list of loop degrees. | |
| int | loops |
| contains the number of loops ( and therefore of stacks ). | |
| int | unpaired |
| contains the number of unpaired bases. | |
| int | pairs |
| contains the number of base pairs in the last parsed structure. | |
| struct vrna_hx_s |
| char* b2HIT | ( | const char * | structure | ) |
#include <ViennaRNA/RNAstruct.h>
Converts the full structure from bracket notation to the HIT notation including root.
| structure |
| char* b2C | ( | const char * | structure | ) |
#include <ViennaRNA/RNAstruct.h>
Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers.
| structure |
| char* b2Shapiro | ( | const char * | structure | ) |
#include <ViennaRNA/RNAstruct.h>
Converts the full structure from bracket notation to the weighted coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers.
| structure |
| char* add_root | ( | const char * | structure | ) |
#include <ViennaRNA/RNAstruct.h>
Adds a root to an un-rooted tree in any except bracket notation.
| structure |
| char* expand_Shapiro | ( | const char * | coarse | ) |
#include <ViennaRNA/RNAstruct.h>
Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C().
| coarse |
| char* expand_Full | ( | const char * | structure | ) |
#include <ViennaRNA/RNAstruct.h>
Convert the full structure from bracket notation to the expanded notation including root.
| structure |
| char* unexpand_Full | ( | const char * | ffull | ) |
#include <ViennaRNA/RNAstruct.h>
Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers 'U' 'P' and 'R'.
| ffull |
| char* unweight | ( | const char * | wcoarse | ) |
| void unexpand_aligned_F | ( | char * | align[2] | ) |
#include <ViennaRNA/RNAstruct.h>
Converts two aligned structures in expanded notation.
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.
| align |
| void parse_structure | ( | const char * | structure | ) |
#include <ViennaRNA/RNAstruct.h>
Collects a statistic of structure elements of the full structure in bracket notation.
The function writes to the following global variables: loop_size, loop_degree, helix_size, loops, pairs, unpaired
| structure |
| char* vrna_db_pack | ( | const char * | struc | ) |
#include <ViennaRNA/structure_utils.h>
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_db_unpack | ( | const char * | packed | ) |
#include <ViennaRNA/structure_utils.h>
Unpack secondary structure previously packed with vrna_db_pack()
Translate a compressed binary string produced by vrna_db_pack() back into the familiar dot-bracket notation.
| packed | The binary encoded packed secondary structure |
| short* vrna_ptable | ( | const char * | structure | ) |
#include <ViennaRNA/structure_utils.h>
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 | ) |
#include <ViennaRNA/structure_utils.h>
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_ptable() this function also recognizes the base pairs denoted by '[' and ']' brackets.
| structure | The secondary structure in (extended) dot-bracket notation |
| short* vrna_ptable_copy | ( | const short * | pt | ) |
#include <ViennaRNA/structure_utils.h>
Get an exact copy of a pair table.
| pt | The pair table to be copied |
| short* vrna_pt_snoop_get | ( | const char * | structure | ) |
#include <ViennaRNA/structure_utils.h>
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.
| char* vrna_db_from_ptable | ( | short * | pt | ) |
#include <ViennaRNA/structure_utils.h>
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 | ||
| ) |
#include <ViennaRNA/structure_utils.h>
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 | ||
| ) |
#include <ViennaRNA/structure_utils.h>
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 | ||
| ) |
#include <ViennaRNA/structure_utils.h>
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!!!
| char* vrna_db_from_bp_stack | ( | vrna_bp_stack_t * | bp, |
| unsigned int | length | ||
| ) |
#include <ViennaRNA/structure_utils.h>
Create a dot-backet/parenthesis structure from backtracking stack.
This function is capable to create dot-bracket structures from suboptimal structure prediction sensu M. Zuker
| bp | Base pair stack containing the traced base pairs |
| length | The length of the structure |
| vrna_plist_t* vrna_plist | ( | const char * | struc, |
| float | pr | ||
| ) |
#include <ViennaRNA/structure_utils.h>
Create a vrna_plist_t 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 |
| char* vrna_db_from_plist | ( | vrna_plist_t * | pairs, |
| unsigned int | n | ||
| ) |
#include <ViennaRNA/structure_utils.h>
Convert a list of base pairs into dot-bracket notation.
| pairs | A vrna_plist_t containing the pairs to be included in the dot-bracket string |
| n | The length of the structure (number of nucleotides) |
| void assign_plist_from_db | ( | vrna_plist_t ** | pl, |
| const char * | struc, | ||
| float | pr | ||
| ) |
#include <ViennaRNA/structure_utils.h>
Create a vrna_plist_t 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 vrna_plist_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 | ) |
#include <ViennaRNA/structure_utils.h>
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* unpack_structure | ( | const char * | packed | ) |
#include <ViennaRNA/structure_utils.h>
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* make_pair_table | ( | const char * | structure | ) |
#include <ViennaRNA/structure_utils.h>
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* copy_pair_table | ( | const short * | pt | ) |
#include <ViennaRNA/structure_utils.h>
Get an exact copy of a pair table.
| pt | The pair table to be copied |
| short* alimake_pair_table | ( | const char * | structure | ) |
#include <ViennaRNA/structure_utils.h>
Pair table for snoop align
| short* make_pair_table_snoop | ( | const char * | structure | ) |
#include <ViennaRNA/structure_utils.h>
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.
| int bp_distance | ( | const char * | str1, |
| const char * | str2 | ||
| ) |
#include <ViennaRNA/structure_utils.h>
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* make_referenceBP_array | ( | short * | reference_pt, |
| unsigned int | turn | ||
| ) |
#include <ViennaRNA/structure_utils.h>
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* compute_BPdifferences | ( | short * | pt1, |
| short * | pt2, | ||
| unsigned int | turn | ||
| ) |
#include <ViennaRNA/structure_utils.h>
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, |
| vrna_bp_stack_t * | bp, | ||
| int | length | ||
| ) |
#include <ViennaRNA/structure_utils.h>
Create a dot-backet/parenthesis structure from backtracking stack.
| void parenthesis_zuker | ( | char * | structure, |
| vrna_bp_stack_t * | bp, | ||
| int | length | ||
| ) |
#include <ViennaRNA/structure_utils.h>
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.
| void bppm_to_structure | ( | char * | structure, |
| FLT_OR_DBL * | pr, | ||
| unsigned int | length | ||
| ) |
#include <ViennaRNA/structure_utils.h>
Create a dot-bracket like structure string from base pair probability matrix.
| char bppm_symbol | ( | const float * | x | ) |
#include <ViennaRNA/structure_utils.h>
Get a pseudo dot bracket notation for a given probability information.