Structure Class SPECIES

Package:

CL-SBML

Class Precedence List:

SPECIES, SBML-ELEMENT, SBML-BASE, STRUCTURE-CLASS, T.

Slots:

COMPARTMENT: default value NIL, type (OR NULL STRING COMPARTMENT), initarg :COMPARTMENT
INITIAL-AMOUNT: default value 0.0d0, type DOUBLE-FLOAT, initarg :INITIAL-AMOUNT
INITIAL-CONCENTRATION: default value 0,0d0, type DOUBLE-FLOAT, initarg :INITIAL-CONCENTRATION
SUBSTANCE-UNITS: default value NI, type (OR NULL STRING UNIT LIST), initarg :SUBSTANCE-UNITS
SPATIAL-UNITS: default value NI, type (OR NULL STRING UNIT LIST), initarg :SPATIAL-UNITS
HAS-ONLY-SUBSTANCE-UNITS-P: default value NIL, type BOOLEAN, initarg :HAS-ONLY-SUBSTANCE-UNITS-P
CHARGE: default value 0, type FIXNUM, initarg :CHARGE
CONSTANT-P: default value NIL, type BOOLEAN, initarg :CONSTANT-P

Description:

The representation of speciess in SBML.

The term species refers to chemical entities that take part in reactions. These include simple ions (e.g., protons, calcium), simple molecules (e.g., glucose, ATP), large molecules (e.g., RNA, polysaccharides, and proteins), and others. The Species data structure is intended to represent these entities.

The accessors SPECIES-COMPARTMENT, SPECIES-INITIAL-AMOUNT, SPECIES-INITIAL-CONCENTRATION, SPECIES-SUBSTANCE-UNITS, SPECIES-SPATIAL-UNITS, SPECIES-HAS-ONLY-SUBSTANCE-UNITS-P, SPECIES-CHARGE, and SPECIES-CONSTANT-P, are used to extract and set the structure fields.

Affected By:

None.

Exceptional Situations:

None.

Notes:

Types

SBML states that the values of the COMPARTMENT field should be of type SID (SId.) The definition here is more liberal, as the type specifier SID is defined in terms of SATISFIES, which is a notorious complication in the CL type system. If the need arises, the type specification of the slots can be made stricter.

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	Structure Class SPECIES Package: `CL-SBML` Class Precedence List: SPECIES, SBML-ELEMENT, SBML-BASE, STRUCTURE-CLASS, T. Slots: COMPARTMENT: default value NIL, type (OR NULL STRING COMPARTMENT), initarg :COMPARTMENT INITIAL-AMOUNT: default value 0.0d0, type DOUBLE-FLOAT, initarg :INITIAL-AMOUNT INITIAL-CONCENTRATION: default value 0,0d0, type DOUBLE-FLOAT, initarg :INITIAL-CONCENTRATION SUBSTANCE-UNITS: default value NI, type (OR NULL STRING UNIT LIST), initarg :SUBSTANCE-UNITS SPATIAL-UNITS: default value NI, type (OR NULL STRING UNIT LIST), initarg :SPATIAL-UNITS HAS-ONLY-SUBSTANCE-UNITS-P: default value NIL, type BOOLEAN, initarg :HAS-ONLY-SUBSTANCE-UNITS-P CHARGE: default value 0, type FIXNUM, initarg :CHARGE CONSTANT-P: default value NIL, type BOOLEAN, initarg :CONSTANT-P Description: The representation of speciess in SBML. The term species refers to chemical entities that take part in reactions. These include simple ions (e.g., protons, calcium), simple molecules (e.g., glucose, ATP), large molecules (e.g., RNA, polysaccharides, and proteins), and others. The Species data structure is intended to represent these entities. The accessors SPECIES-COMPARTMENT, SPECIES-INITIAL-AMOUNT, SPECIES-INITIAL-CONCENTRATION, SPECIES-SUBSTANCE-UNITS, SPECIES-SPATIAL-UNITS, SPECIES-HAS-ONLY-SUBSTANCE-UNITS-P, SPECIES-CHARGE, and SPECIES-CONSTANT-P, are used to extract and set the structure fields. Affected By: None. Exceptional Situations: None. See Also: SBML-ELEMENT, SPECIES-P, SPECIES-COMPARTMENT, SPECIES-INITIAL-AMOUNT, SPECIES-INITIAL-CONCENTRATION, SPECIES-SUBSTANCE-UNITS, SPECIES-SPATIAL-UNITS, SPECIES-HAS-ONLY-SUBSTANCE-UNITS-P, SPECIES-CHARGE, and SPECIES-CONSTANT-P, and MAKE-SPECIES. Notes: Types SBML states that the values of the COMPARTMENT field should be of type SID (`SId`.) The definition here is more liberal, as the type specifier SID is defined in terms of SATISFIES, which is a notorious complication in the CL type system. If the need arises, the type specification of the slots can be made stricter.
	News News in chronological order, most recent on top. 2005-05-06 Completed description.
© 2003-2005, Marco Antoniotti, all rights reserved.