libSBML Perl API
libSBML 5.8.0 Perl API
|
Implementations of Reaction and ListOfReactions.
Functions | |
static SBase * | GetSpeciesRef (ListOf &items, const string &species) |
Used by getReactant(species), getProduct(species), and getModifier(species). More... | |
static const SBase * | GetSpeciesRef (const ListOf &items, const std::string &species) |
Simply calls non-const version above. More... | |
Reaction_t * | ListOfReactions_getById (ListOf_t *lo, const char *sid) |
Reaction_t * | ListOfReactions_removeById (ListOf_t *lo, const char *sid) |
Removes item in this ListOf items with the given id or NULL if no such item exists. More... | |
int | Reaction_addModifier (Reaction_t *r, const SpeciesReference_t *msr) |
Adds a copy of the given modifier (ModifierSpeciesReference) to this Reaction. More... | |
int | Reaction_addProduct (Reaction_t *r, const SpeciesReference_t *sr) |
Adds a copy of the given product (SpeciesReference) to this Reaction. More... | |
int | Reaction_addReactant (Reaction_t *r, const SpeciesReference_t *sr) |
Adds a copy of the given reactant (SpeciesReference) to this Reaction. More... | |
Reaction_t * | Reaction_clone (const Reaction_t *r) |
Reaction_t * | Reaction_create (unsigned int level, unsigned int version) |
Creates a new Reaction_t structure using the given SBML level and version values. More... | |
KineticLaw_t * | Reaction_createKineticLaw (Reaction_t *r) |
Creates a new KineticLaw for this Reaction and returns it. More... | |
SpeciesReference_t * | Reaction_createModifier (Reaction_t *r) |
Creates a new SpeciesReference, adds it to this Reaction's list of modifiers and returns it. More... | |
SpeciesReference_t * | Reaction_createProduct (Reaction_t *r) |
Creates a new SpeciesReference, adds it to this Reaction's list of products and returns it. More... | |
SpeciesReference_t * | Reaction_createReactant (Reaction_t *r) |
Creates a new SpeciesReference, adds it to this Reaction's list of reactants and returns it. More... | |
Reaction_t * | Reaction_createWithNS (SBMLNamespaces_t *sbmlns) |
Creates a new Reaction_t structure using the given SBMLNamespaces_t structure. More... | |
void | Reaction_free (Reaction_t *r) |
Frees the given Reaction. More... | |
const char * | Reaction_getCompartment (const Reaction_t *r) |
int | Reaction_getFast (const Reaction_t *r) |
const char * | Reaction_getId (const Reaction_t *r) |
KineticLaw_t * | Reaction_getKineticLaw (Reaction_t *r) |
ListOf_t * | Reaction_getListOfModifiers (Reaction_t *r) |
ListOf_t * | Reaction_getListOfProducts (Reaction_t *r) |
ListOf_t * | Reaction_getListOfReactants (Reaction_t *r) |
SpeciesReference_t * | Reaction_getModifier (Reaction_t *r, unsigned int n) |
SpeciesReference_t * | Reaction_getModifierBySpecies (Reaction_t *r, const char *species) |
const char * | Reaction_getName (const Reaction_t *r) |
const XMLNamespaces_t * | Reaction_getNamespaces (Reaction_t *r) |
Returns a list of XMLNamespaces_t associated with this Reaction_t structure. More... | |
unsigned int | Reaction_getNumModifiers (const Reaction_t *r) |
unsigned int | Reaction_getNumProducts (const Reaction_t *r) |
unsigned int | Reaction_getNumReactants (const Reaction_t *r) |
SpeciesReference_t * | Reaction_getProduct (Reaction_t *r, unsigned int n) |
SpeciesReference_t * | Reaction_getProductBySpecies (Reaction_t *r, const char *species) |
SpeciesReference_t * | Reaction_getReactant (Reaction_t *r, unsigned int n) |
SpeciesReference_t * | Reaction_getReactantBySpecies (Reaction_t *r, const char *species) |
int | Reaction_getReversible (const Reaction_t *r) |
int | Reaction_hasRequiredAttributes (Reaction_t *r) |
Predicate returning true or false depending on whether all the required attributes for this Reaction object have been set. More... | |
void | Reaction_initDefaults (Reaction_t *r) |
Initializes the fields of this Reaction to their defaults: More... | |
int | Reaction_isSetCompartment (const Reaction_t *r) |
int | Reaction_isSetFast (const Reaction_t *r) |
int | Reaction_isSetId (const Reaction_t *r) |
int | Reaction_isSetKineticLaw (const Reaction_t *r) |
int | Reaction_isSetName (const Reaction_t *r) |
int | Reaction_isSetReversible (const Reaction_t *r) |
SpeciesReference_t * | Reaction_removeModifier (Reaction_t *r, unsigned int n) |
Removes the nth modifier SpeciesReference_t object from this Reaction_t object and returns a pointer to it. More... | |
SpeciesReference_t * | Reaction_removeModifierBySpecies (Reaction_t *r, const char *species) |
Removes the modifier SpeciesReference_t object with the given "species" attribute from this Reaction_t object and returns a pointer to it. More... | |
SpeciesReference_t * | Reaction_removeProduct (Reaction_t *r, unsigned int n) |
Removes the nth product SpeciesReference_t object from this Reaction_t object and returns a pointer to it. More... | |
SpeciesReference_t * | Reaction_removeProductBySpecies (Reaction_t *r, const char *species) |
Removes the product SpeciesReference_t object with the given "species" attribute from this Reaction_t object and returns a pointer to it. More... | |
SpeciesReference_t * | Reaction_removeReactant (Reaction_t *r, unsigned int n) |
Removes the nth reactant SpeciesReference_t object from this Reaction_t object and returns a pointer to it. More... | |
SpeciesReference_t * | Reaction_removeReactantBySpecies (Reaction_t *r, const char *species) |
Removes the reactant SpeciesReference_t object with the given "species" attribute from this Reaction_t object and returns a pointer to it. More... | |
int | Reaction_setCompartment (Reaction_t *r, const char *compartment) |
Sets the compartment of this Reaction to a copy of compartment. More... | |
int | Reaction_setFast (Reaction_t *r, int value) |
Sets the fast status of this Reaction to value (boolean). More... | |
int | Reaction_setId (Reaction_t *r, const char *sid) |
Sets the id of this Reaction to a copy of sid. More... | |
int | Reaction_setKineticLaw (Reaction_t *r, const KineticLaw_t *kl) |
Sets the KineticLaw of this Reaction to a copy of the given KineticLaw. More... | |
int | Reaction_setName (Reaction_t *r, const char *name) |
Sets the name of this Reaction to a copy of name. More... | |
int | Reaction_setReversible (Reaction_t *r, int value) |
Sets the reversible status of this Reaction to value (boolean). More... | |
int | Reaction_unsetCompartment (Reaction_t *r) |
Unsets the compartment of this Reaction. More... | |
int | Reaction_unsetFast (Reaction_t *r) |
Unsets the fast status of this Reation. More... | |
int | Reaction_unsetKineticLaw (Reaction_t *r) |
Unsets the KineticLaw of this Reaction. More... | |
int | Reaction_unsetName (Reaction_t *r) |
Unsets the name of this Reaction. More... | |
Used by getReactant(species), getProduct(species), and getModifier(species).
Simply calls non-const version above.
Reaction_t* ListOfReactions_getById | ( | ListOf_t * | lo, |
const char * | sid | ||
) |
id
or NULL
if no such item exists. Reaction_t* ListOfReactions_removeById | ( | ListOf_t * | lo, |
const char * | sid | ||
) |
Removes item in this ListOf items with the given id
or NULL
if no such item exists.
The caller owns the returned item and is responsible for deleting it.
int Reaction_addModifier | ( | Reaction_t * | r, |
const SpeciesReference_t * | msr | ||
) |
Adds a copy of the given modifier (ModifierSpeciesReference) to this Reaction.
int Reaction_addProduct | ( | Reaction_t * | r, |
const SpeciesReference_t * | sr | ||
) |
Adds a copy of the given product (SpeciesReference) to this Reaction.
int Reaction_addReactant | ( | Reaction_t * | r, |
const SpeciesReference_t * | sr | ||
) |
Adds a copy of the given reactant (SpeciesReference) to this Reaction.
Reaction_t* Reaction_clone | ( | const Reaction_t * | r | ) |
Reaction_t* Reaction_create | ( | unsigned int | level, |
unsigned int | version | ||
) |
Creates a new Reaction_t structure using the given SBML level
and version
values.
level | an unsigned int, the SBML Level to assign to this Reaction |
version | an unsigned int, the SBML Version to assign to this Reaction |
level
and version
for the document override those used to create the Reaction. Despite this, the ability to supply the values at creation time is an important aid to creating valid SBML. Knowledge of the intended SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument. KineticLaw_t* Reaction_createKineticLaw | ( | Reaction_t * | r | ) |
Creates a new KineticLaw for this Reaction and returns it.
If this Reaction had a previous KineticLaw, it will be destroyed.
SpeciesReference_t* Reaction_createModifier | ( | Reaction_t * | r | ) |
Creates a new SpeciesReference, adds it to this Reaction's list of modifiers and returns it.
SpeciesReference_t* Reaction_createProduct | ( | Reaction_t * | r | ) |
Creates a new SpeciesReference, adds it to this Reaction's list of products and returns it.
SpeciesReference_t* Reaction_createReactant | ( | Reaction_t * | r | ) |
Creates a new SpeciesReference, adds it to this Reaction's list of reactants and returns it.
Reaction_t* Reaction_createWithNS | ( | SBMLNamespaces_t * | sbmlns | ) |
Creates a new Reaction_t structure using the given SBMLNamespaces_t structure.
sbmlns | SBMLNamespaces, a pointer to an SBMLNamespaces structure to assign to this Reaction |
sbmlns
namespaces for the document override those used to create the Reaction. Despite this, the ability to supply the values at creation time is an important aid to creating valid SBML. Knowledge of the intended SBML Level and Version determine whether it is valid to assign a particular value to an attribute, or whether it is valid to add an object to an existing SBMLDocument. void Reaction_free | ( | Reaction_t * | r | ) |
Frees the given Reaction.
const char* Reaction_getCompartment | ( | const Reaction_t * | r | ) |
int Reaction_getFast | ( | const Reaction_t * | r | ) |
const char* Reaction_getId | ( | const Reaction_t * | r | ) |
KineticLaw_t* Reaction_getKineticLaw | ( | Reaction_t * | r | ) |
ListOf_t* Reaction_getListOfModifiers | ( | Reaction_t * | r | ) |
ListOf_t* Reaction_getListOfProducts | ( | Reaction_t * | r | ) |
ListOf_t* Reaction_getListOfReactants | ( | Reaction_t * | r | ) |
SpeciesReference_t* Reaction_getModifier | ( | Reaction_t * | r, |
unsigned int | n | ||
) |
SpeciesReference_t* Reaction_getModifierBySpecies | ( | Reaction_t * | r, |
const char * | species | ||
) |
NULL
if no such modifier exists. const char* Reaction_getName | ( | const Reaction_t * | r | ) |
const XMLNamespaces_t* Reaction_getNamespaces | ( | Reaction_t * | r | ) |
Returns a list of XMLNamespaces_t associated with this Reaction_t structure.
r | the Reaction_t structure |
unsigned int Reaction_getNumModifiers | ( | const Reaction_t * | r | ) |
unsigned int Reaction_getNumProducts | ( | const Reaction_t * | r | ) |
unsigned int Reaction_getNumReactants | ( | const Reaction_t * | r | ) |
SpeciesReference_t* Reaction_getProduct | ( | Reaction_t * | r, |
unsigned int | n | ||
) |
SpeciesReference_t* Reaction_getProductBySpecies | ( | Reaction_t * | r, |
const char * | species | ||
) |
NULL
if no such product exists. SpeciesReference_t* Reaction_getReactant | ( | Reaction_t * | r, |
unsigned int | n | ||
) |
SpeciesReference_t* Reaction_getReactantBySpecies | ( | Reaction_t * | r, |
const char * | species | ||
) |
NULL
if no such reactant exists. int Reaction_getReversible | ( | const Reaction_t * | r | ) |
int Reaction_hasRequiredAttributes | ( | Reaction_t * | r | ) |
Predicate returning true
or false
depending on whether all the required attributes for this Reaction object have been set.
r | the Reaction_t structure to check. |
void Reaction_initDefaults | ( | Reaction_t * | r | ) |
Initializes the fields of this Reaction to their defaults:
int Reaction_isSetCompartment | ( | const Reaction_t * | r | ) |
int Reaction_isSetFast | ( | const Reaction_t * | r | ) |
In L1, fast is optional with a default of false, which means it is effectively always set. In L2, however, fast is optional with no default value, so it may or may not be set to a specific value.
int Reaction_isSetId | ( | const Reaction_t * | r | ) |
int Reaction_isSetKineticLaw | ( | const Reaction_t * | r | ) |
int Reaction_isSetName | ( | const Reaction_t * | r | ) |
int Reaction_isSetReversible | ( | const Reaction_t * | r | ) |
SpeciesReference_t* Reaction_removeModifier | ( | Reaction_t * | r, |
unsigned int | n | ||
) |
Removes the nth modifier SpeciesReference_t object from this Reaction_t object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
r | the Reaction_t structure |
n | the integer index of the modifier SpeciesReference_t to remove |
NULL
is returned if the given index is out of range. SpeciesReference_t* Reaction_removeModifierBySpecies | ( | Reaction_t * | r, |
const char * | species | ||
) |
Removes the modifier SpeciesReference_t object with the given "species" attribute from this Reaction_t object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
r | the Reaction_t structure |
species | the "species" attribute of the modifier SpeciesReference_t to remove |
NULL
is returned if no modifier SpeciesReference_t object with the "species" attribute exists in this Reaction. SpeciesReference_t* Reaction_removeProduct | ( | Reaction_t * | r, |
unsigned int | n | ||
) |
Removes the nth product SpeciesReference_t object from this Reaction_t object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
r | the Reaction_t structure |
n | the integer index of the product SpeciesReference_t to remove |
NULL
is returned if the given index is out of range. SpeciesReference_t* Reaction_removeProductBySpecies | ( | Reaction_t * | r, |
const char * | species | ||
) |
Removes the product SpeciesReference_t object with the given "species" attribute from this Reaction_t object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
r | the Reaction_t structure |
species | the "species" attribute of the product SpeciesReference_t to remove |
NULL
is returned if no product SpeciesReference_t object with the "species" attribute exists in this Reaction. SpeciesReference_t* Reaction_removeReactant | ( | Reaction_t * | r, |
unsigned int | n | ||
) |
Removes the nth reactant SpeciesReference_t object from this Reaction_t object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
r | the Reaction_t structure |
n | the integer index of the reactant SpeciesReference_t to remove |
NULL
is returned if the given index is out of range. SpeciesReference_t* Reaction_removeReactantBySpecies | ( | Reaction_t * | r, |
const char * | species | ||
) |
Removes the reactant SpeciesReference_t object with the given "species" attribute from this Reaction_t object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
r | the Reaction_t structure |
species | the "species" attribute of the reactant SpeciesReference_t to remove |
NULL
is returned if no reactant SpeciesReference_t object with the "species" attribute exists in this Reaction. int Reaction_setCompartment | ( | Reaction_t * | r, |
const char * | compartment | ||
) |
Sets the compartment of this Reaction to a copy of compartment.
int Reaction_setFast | ( | Reaction_t * | r, |
int | value | ||
) |
Sets the fast status of this Reaction to value (boolean).
int Reaction_setId | ( | Reaction_t * | r, |
const char * | sid | ||
) |
Sets the id of this Reaction to a copy of sid.
int Reaction_setKineticLaw | ( | Reaction_t * | r, |
const KineticLaw_t * | kl | ||
) |
Sets the KineticLaw of this Reaction to a copy of the given KineticLaw.
int Reaction_setName | ( | Reaction_t * | r, |
const char * | name | ||
) |
Sets the name of this Reaction to a copy of name.
int Reaction_setReversible | ( | Reaction_t * | r, |
int | value | ||
) |
Sets the reversible status of this Reaction to value (boolean).
int Reaction_unsetCompartment | ( | Reaction_t * | r | ) |
Unsets the compartment of this Reaction.
int Reaction_unsetFast | ( | Reaction_t * | r | ) |
Unsets the fast status of this Reation.
int Reaction_unsetKineticLaw | ( | Reaction_t * | r | ) |
Unsets the KineticLaw of this Reaction.
int Reaction_unsetName | ( | Reaction_t * | r | ) |
Unsets the name of this Reaction.