MATLAB_SBML_STRUCTURE_FUNCTIONS\SPECIES

The functions allow users to create and work with the SBML Species structure.

Function are:

Species = Species_create(level(optional), version(optional) )

Takes

1. level, an integer representing an SBML level (optional)
2. version, an integer representing an SBML version (optional)

Returns

1. a MATLAB_SBML Species structure of the appropriate level and version

NOTE: the optional level and version preserve backwards compatibility a missing version argument will default to L1V2; L2V4 or L3V1 missing both arguments will default to L3V1

boundaryCondition = Species_getBoundaryCondition(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the boundaryCondition attribute

charge = Species_getCharge(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the charge attribute

compartment = Species_getCompartment(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the compartment attribute

constant = Species_getConstant(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the constant attribute

conversionFactor = Species_getConversionFactor(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the conversionFactor attribute

hasOnlySubstanceUnits = Species_getHasOnlySubstanceUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the hasOnlySubstanceUnits attribute

id = Species_getId(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the id attribute

initialAmount = Species_getInitialAmount(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the initialAmount attribute

initialConcentration = Species_getInitialConcentration(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the initialConcentration attribute

metaid = Species_getMetaid(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the metaid attribute

name = Species_getName(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the name attribute

sboTerm = Species_getSBOTerm(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the sboTerm attribute

spatialSizeUnits = Species_getSpatialSizeUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the spatialSizeUnits attribute

speciesType = Species_getSpeciesType(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the speciesType attribute

substanceUnits = Species_getSubstanceUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the substanceUnits attribute

units = Species_getUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the value of the units attribute

y = Species_isAssignedByRateRule(SBMLSpecies, SBMLRules)

Takes

1. SBMLSpecies, an SBML Species structure
2. SBMLRules; the array of rules from an SBML Model structure

Returns

y = - the index of the rateRule used to assigned value to the Species - 0 if the Species is not assigned by rateRule

!--------------------------------------------------------------------------- This file is part of SBMLToolbox. Please visit http://sbml.org for more information about SBML, and the latest version of SBMLToolbox.

Copyright (C) 2009-2016 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK

Copyright (C) 2006-2008 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. University of Hertfordshire, Hatfield, UK

Copyright (C) 2003-2005 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. Japan Science and Technology Agency, Japan 3. University of Hertfordshire, Hatfield, UK

SBMLToolbox is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this software distribution. ---------------------------------------------------------------------- -->

y = Species_isAssignedByRule(SBMLSpecies, SBMLRules)

Takes

1. SBMLSpecies, an SBML Species structure
2. SBMLRules; the array of rules from an SBML Model structure

Returns

y = - the index of the assignmentRule used to assigned value to the Species - 0 if the Species is not assigned by assignmentRule

!--------------------------------------------------------------------------- This file is part of SBMLToolbox. Please visit http://sbml.org for more information about SBML, and the latest version of SBMLToolbox.

Copyright (C) 2009-2016 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK

Copyright (C) 2006-2008 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. University of Hertfordshire, Hatfield, UK

Copyright (C) 2003-2005 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. Japan Science and Technology Agency, Japan 3. University of Hertfordshire, Hatfield, UK

SBMLToolbox is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this software distribution. ---------------------------------------------------------------------- -->

y = Species_isInAlgebraicRule(SBMLSpecies, SBMLRules)

Takes

1. SBMLSpecies, an SBML Species structure
2. SBMLRules; the array of rules from an SBML Model structure

Returns

y = - an array of the indices of any algebraicRules the id of the Species appears in - 0 if the Species appears in no algebraicRules

!--------------------------------------------------------------------------- This file is part of SBMLToolbox. Please visit http://sbml.org for more information about SBML, and the latest version of SBMLToolbox.

Copyright (C) 2009-2016 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK

Copyright (C) 2006-2008 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. University of Hertfordshire, Hatfield, UK

Copyright (C) 2003-2005 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. Japan Science and Technology Agency, Japan 3. University of Hertfordshire, Hatfield, UK

SBMLToolbox is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this software distribution. ---------------------------------------------------------------------- -->

value = Species_isSetCharge(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the charge attribute is set
   • 0 otherwise

value = Species_isSetCompartment(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the compartment attribute is set
   • 0 otherwise

value = Species_isSetConversionFactor(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the conversionFactor attribute is set
   • 0 otherwise

value = Species_isSetHasOnlySubstanceUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the hasOnlySubstanceUnits attribute is set
   • 0 otherwise

value = Species_isSetId(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the id attribute is set
   • 0 otherwise

value = Species_isSetInitialAmount(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the initialAmount attribute is set
   • 0 otherwise

value = Species_isSetInitialConcentration(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the initialConcentration attribute is set
   • 0 otherwise

value = Species_isSetMetaid(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the metaid attribute is set
   • 0 otherwise

value = Species_isSetName(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the name attribute is set
   • 0 otherwise

value = Species_isSetSBOTerm(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the sboTerm attribute is set
   • 0 otherwise

value = Species_isSetSpatialSizeUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the spatialSizeUnits attribute is set
   • 0 otherwise

value = Species_isSetSpeciesType(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the speciesType attribute is set
   • 0 otherwise

value = Species_isSetSubstanceUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the substanceUnits attribute is set
   • 0 otherwise

value = Species_isSetUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. value =
   • 1 if the units attribute is set
   • 0 otherwise

SBMLSpecies = Species_setBoundaryCondition(SBMLSpecies, boundaryCondition)

Takes

1. SBMLSpecies, an SBML Species structure
2. boundaryCondition, an integer (0/1) representing the value of boundaryCondition to be set

Returns

1. the SBML Species structure with the new value for the boundaryCondition attribute

SBMLSpecies = Species_setCharge(SBMLSpecies, charge)

Takes

1. SBMLSpecies, an SBML Species structure
2. charge, an integer representing the charge to be set

Returns

1. the SBML Species structure with the new value for the charge attribute

SBMLSpecies = Species_setCompartment(SBMLSpecies, compartment)

Takes

1. SBMLSpecies, an SBML Species structure
2. compartment; a string representing the compartment to be set

Returns

1. the SBML Species structure with the new value for the compartment attribute

SBMLSpecies = Species_setConstant(SBMLSpecies, constant)

Takes

1. SBMLSpecies, an SBML Species structure
2. constant, an integer (0/1) representing the value of constant to be set

Returns

1. the SBML Species structure with the new value for the constant attribute

SBMLSpecies = Species_setConversionFactor(SBMLSpecies, conversionFactor)

Takes

1. SBMLSpecies, an SBML Species structure
2. conversionFactor; a string representing the conversionFactor to be set

Returns

1. the SBML Species structure with the new value for the conversionFactor attribute

SBMLSpecies = Species_setHasOnlySubstanceUnits(SBMLSpecies, hasOnlySubstanceUnits)

Takes

1. SBMLSpecies, an SBML Species structure
2. hasOnlySubstanceUnits, an integer (0/1) representing the value of hasOnlySubstanceUnits to be set

Returns

1. the SBML Species structure with the new value for the hasOnlySubstanceUnits attribute

SBMLSpecies = Species_setId(SBMLSpecies, id)

Takes

1. SBMLSpecies, an SBML Species structure
2. id; a string representing the id to be set

Returns

1. the SBML Species structure with the new value for the id attribute

SBMLSpecies = Species_setInitialAmount(SBMLSpecies, initialAmount)

Takes

1. SBMLSpecies, an SBML Species structure
2. initialAmount; number representing the value of initialAmount to be set

Returns

1. the SBML Species structure with the new value for the initialAmount attribute

SBMLSpecies = Species_setInitialConcentration(SBMLSpecies, initialConcentration)

Takes

1. SBMLSpecies, an SBML Species structure
2. initialConcentration; number representing the value of initialConcentration to be set

Returns

1. the SBML Species structure with the new value for the initialConcentration attribute

SBMLSpecies = Species_setMetaid(SBMLSpecies, metaid)

Takes

1. SBMLSpecies, an SBML Species structure
2. metaid; a string representing the metaid to be set

Returns

1. the SBML Species structure with the new value for the metaid attribute

SBMLSpecies = Species_setName(SBMLSpecies, name)

Takes

1. SBMLSpecies, an SBML Species structure
2. name; a string representing the name to be set

Returns

1. the SBML Species structure with the new value for the name attribute

SBMLSpecies = Species_setSBOTerm(SBMLSpecies, sboTerm)

Takes

1. SBMLSpecies, an SBML Species structure
2. sboTerm, an integer representing the sboTerm to be set

Returns

1. the SBML Species structure with the new value for the sboTerm attribute

SBMLSpecies = Species_setSpatialSizeUnits(SBMLSpecies, spatialSizeUnits)

Takes

1. SBMLSpecies, an SBML Species structure
2. spatialSizeUnits; a string representing the spatialSizeUnits to be set

Returns

1. the SBML Species structure with the new value for the spatialSizeUnits attribute

SBMLSpecies = Species_setSpeciesType(SBMLSpecies, speciesType)

Takes

1. SBMLSpecies, an SBML Species structure
2. speciesType; a string representing the speciesType to be set

Returns

1. the SBML Species structure with the new value for the speciesType attribute

SBMLSpecies = Species_setSubstanceUnits(SBMLSpecies, substanceUnits)

Takes

1. SBMLSpecies, an SBML Species structure
2. substanceUnits; a string representing the substanceUnits to be set

Returns

1. the SBML Species structure with the new value for the substanceUnits attribute

SBMLSpecies = Species_setUnits(SBMLSpecies, units)

Takes

1. SBMLSpecies, an SBML Species structure
2. units; a string representing the units to be set

Returns

1. the SBML Species structure with the new value for the units attribute

SBMLSpecies = Species_unsetCharge(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the charge attribute unset

SBMLSpecies = Species_unsetCompartment(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the compartment attribute unset

SBMLSpecies = Species_unsetConversionFactor(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the conversionFactor attribute unset

SBMLSpecies = Species_unsetId(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the id attribute unset

SBMLSpecies = Species_unsetInitialAmount(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the initialAmount attribute unset

SBMLSpecies = Species_unsetInitialConcentration(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the initialConcentration attribute unset

SBMLSpecies = Species_unsetMetaid(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the metaid attribute unset

SBMLSpecies = Species_unsetName(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the name attribute unset

SBMLSpecies = Species_unsetSBOTerm(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the sboTerm attribute unset

SBMLSpecies = Species_unsetSpatialSizeUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the spatialSizeUnits attribute unset

SBMLSpecies = Species_unsetSpeciesType(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the speciesType attribute unset

SBMLSpecies = Species_unsetSubstanceUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the substanceUnits attribute unset

SBMLSpecies = Species_unsetUnits(SBMLSpecies)

Takes

1. SBMLSpecies, an SBML Species structure

Returns

1. the SBML Species structure with the units attribute unset