RNAlib-2.2.0-RC3
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This module covers all functions and variables related to the problem of incorporating secondary structure constraints into the folding recursions. More...
Modules | |
Hard Constraints | |
Soft Constraints | |
Macros | |
#define | VRNA_CONSTRAINT_DB_PIPE 1U |
Flag that is used to indicate the pipe '|' sign in pseudo dot-bracket notation of hard constraints. More... | |
#define | VRNA_CONSTRAINT_DB_DOT 2U |
dot '.' switch for structure constraints (no constraint at all) More... | |
#define | VRNA_CONSTRAINT_DB_X 4U |
'x' switch for structure constraint (base must not pair) More... | |
#define | VRNA_CONSTRAINT_DB_ANG_BRACK 8U |
angle brackets '<', '>' switch for structure constraint (paired downstream/upstream) More... | |
#define | VRNA_CONSTRAINT_DB_RND_BRACK 16U |
round brackets '(',')' switch for structure constraint (base i pairs base j) More... | |
#define | VRNA_CONSTRAINT_DB_INTRAMOL 2048U |
Flag that is used to indicate the character 'l' in pseudo dot-bracket notation of hard constraints. More... | |
#define | VRNA_CONSTRAINT_DB_INTERMOL 4096U |
Flag that is used to indicate the character 'e' in pseudo dot-bracket notation of hard constraints. More... | |
#define | VRNA_CONSTRAINT_DB_GQUAD 8192U |
'+' switch for structure constraint (base is involved in a gquad) More... | |
#define | VRNA_CONSTRAINT_DB_ENFORCE_BP 16384U |
Switch for dot-bracket structure constraint to enforce base pairs. More... | |
#define | VRNA_CONSTRAINT_ALL 128U |
placeholder for all constraining characters | |
#define | VRNA_CONSTRAINT_DB 256U |
Flag for vrna_add_constraints() to indicate that constraint is passed in pseudo dot-bracket notation. More... | |
#define | VRNA_CONSTRAINT_FILE 512U |
Flag for vrna_add_constraints() to indicate that constraints are present in a text file. More... | |
Functions | |
void | vrna_message_constraint_options (unsigned int option) |
Print a help message for pseudo dot-bracket structure constraint characters to stdout. (constraint support is specified by option parameter) More... | |
void | vrna_message_constraints_all (void) |
Print structure constraint characters to stdout (full constraint support) More... | |
void | vrna_add_constraints (vrna_fold_compound *vc, const char *constraint, unsigned int options) |
Add constraints to a vrna_fold_compound data structure. More... | |
This module covers all functions and variables related to the problem of incorporating secondary structure constraints into the folding recursions.
This module provides general functions that allow for an easy control of constrained secondary structure prediction and evaluation. Secondary Structure constraints can be subdivided into two groups:
While Hard-Constraints directly influence the production rules used in the folding recursions by allowing, disallowing, or enforcing certain decomposition steps, Soft-constraints on the other hand are used to change position specific contributions in the recursions by adding bonuses/penalties in form of pseudo free energies to certain loop configurations.
#define VRNA_CONSTRAINT_DB_PIPE 1U |
Flag that is used to indicate the pipe '|' sign in pseudo dot-bracket notation of hard constraints.
Use this definition to indicate the pipe sign '|' (paired with another base)
#define VRNA_CONSTRAINT_DB_DOT 2U |
dot '.' switch for structure constraints (no constraint at all)
#define VRNA_CONSTRAINT_DB_X 4U |
'x' switch for structure constraint (base must not pair)
#define VRNA_CONSTRAINT_DB_ANG_BRACK 8U |
angle brackets '<', '>' switch for structure constraint (paired downstream/upstream)
#define VRNA_CONSTRAINT_DB_RND_BRACK 16U |
round brackets '(',')' switch for structure constraint (base i pairs base j)
#define VRNA_CONSTRAINT_DB_INTRAMOL 2048U |
Flag that is used to indicate the character 'l' in pseudo dot-bracket notation of hard constraints.
Use this definition to indicate the usage of 'l' character (intramolecular pairs only)
#define VRNA_CONSTRAINT_DB_INTERMOL 4096U |
Flag that is used to indicate the character 'e' in pseudo dot-bracket notation of hard constraints.
Use this definition to indicate the usage of 'e' character (intermolecular pairs only)
#define VRNA_CONSTRAINT_DB_GQUAD 8192U |
'+' switch for structure constraint (base is involved in a gquad)
#define VRNA_CONSTRAINT_DB_ENFORCE_BP 16384U |
Switch for dot-bracket structure constraint to enforce base pairs.
This flag should be used to really enforce base pairs given in dot-bracket constraint rather than just weakly-enforcing them.
#define VRNA_CONSTRAINT_DB 256U |
Flag for vrna_add_constraints() to indicate that constraint is passed in pseudo dot-bracket notation.
#define VRNA_CONSTRAINT_FILE 512U |
Flag for vrna_add_constraints() to indicate that constraints are present in a text file.
void vrna_message_constraint_options | ( | unsigned int | option | ) |
Print a help message for pseudo dot-bracket structure constraint characters to stdout. (constraint support is specified by option parameter)
Currently available options are:
VRNA_CONSTRAINT_DB_PIPE (paired with another base)
VRNA_CONSTRAINT_DB_DOT (no constraint at all)
VRNA_CONSTRAINT_DB_X (base must not pair)
VRNA_CONSTRAINT_DB_ANG_BRACK (paired downstream/upstream)
VRNA_CONSTRAINT_DB_RND_BRACK (base i pairs base j)
pass a collection of options as one value like this:
vrna_message_constraints(option_1 | option_2 | option_n)
option | Option switch that tells which constraint help will be printed |
void vrna_message_constraints_all | ( | void | ) |
Print structure constraint characters to stdout (full constraint support)
void vrna_add_constraints | ( | vrna_fold_compound * | vc, |
const char * | constraint, | ||
unsigned int | options | ||
) |
Add constraints to a vrna_fold_compound data structure.
Use this function to add/update the hard/soft constraints The function allows for passing a string 'constraint' that can either be a filename that points to a constraints definition file or it may be a pseudo dot-bracket notation indicating hard constraints. Depending on the type of the string the user has to pass VRNA_CONSTRAINT_FILE or VRNA_CONSTRAINT_DB in the option parameter, respectively. If none of these to options are passed, no action is performed, other than to guarantee that at least a hard constraints data structure of type vrna_hc_t with default values is present in 'vc'. Already existing hard constraints are not touched.
In case, a psuedo dot-bracket string is passed as the second argument, the user has to specify, which characters are allowed to be interpreted as constraints by passing the corresponding options via the third parameter.
vc | The fold compound |
constraint | A string with either the filename of the constraint definitions or a pseudo dot-bracket notation of the hard constraint. May be NULL. |
options | The option flags |