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; either
version 2.1 of the License, or any later version.
This software is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The
software and documentation provided hereunder is on an "as is"
basis, and the California Institute of Technology, the Japan
Science and Technology Agency, and the University of
Hertfordshire have no obligations to provide maintenance,
support, updates, enhancements or modifications. In no event
shall the California Institute of Technology, the Japan Science
and Technology Agency, or the University of Hertfordshire be
liable to any party for direct, indirect, special, incidental or
consequential damages, including lost profits, arising out of
the use of this software and its documentation, even if the
California Institute of Technology, the Japan Science and
Technology Agency, and/or the University of Hertfordshire have
been advised of the possibility of such damage. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library in the file named "LICENSE.txt"
included with the software distribution. A copy is also
available online at the Internet address
http://sbml.org/Software/SBMLToolbox/LICENSE.html for your
convenience. You may also write to obtain a copy from the Free
Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
MA 02111-1307 USA.
SBMLToolbox-4.1.0/FUNDING.txt 0000644 0000000 0000000 00000001427 11540617602 014157 0 ustar root root This and other projects of the SBML Team have been supported by the
following organizations: the National Institutes of Health (USA) under
grants R01 GM070923 and R01 GM077671; the International Joint Research
Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the Japanese
Ministry of Agriculture; the Japanese Ministry of Education, Culture,
Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the
DARPA IPTO Bio-Computation Program (USA); the Army Research Office's
Institute for Collaborative Biotechnologies (USA); the Air Force Office of
Scientific Research (USA); the California Institute of Technology (USA);
the University of Hertfordshire (UK); the Molecular Sciences Institute
(USA); the Systems Biology Institute (Japan); and Keio University (Japan).
SBMLToolbox-4.1.0/docs/ 0000755 0000000 0000000 00000000000 11704572216 013253 5 ustar root root SBMLToolbox-4.1.0/docs/validation.html 0000644 0000000 0000000 00000057656 11611210324 016300 0 ustar root root
This folder contains tests that checks that the structure supplied as argument
is of the appropriate form to represent the intended element of an SBML model.
Each check tests that the fields supplied within the structure match the fields
expected for an element of that type and SBML Level and Version.
Tried to make toc numbers have a fixed
width, so that the toc would be aligned, but the following didn't
do it, and nothing I could find could do it either. Why?
.tocnumber {
min-width: 2em !important;
}
*/
#toc,
.toc,
.mw-warning {
font-family: Helvetica, Arial, sans-serif;
border: 1px dotted #aaa;
padding: 5px;
margin: 15px 4px 15px 15px;
font-size: smaller;
font-weight: normal;
float: right;
background-color: #f9f9f9;
}
#toc h2,
.toc h2 {
font-family: Helvetica, Arial, sans-serif;
font-size: 9pt;
display: inline;
border: none;
padding: 0;
margin-top: 0;
}
#toc #toctitle,
.toc #toctitle,
#toc .toctitle,
.toc .toctitle {
font-family: Helvetica, Arial, sans-serif;
font-weight: normal;
font-size: 9pt;
text-align: center;
margin: 0;
padding: 0;
}
#toc ul,
.toc ul {
font-family: Helvetica, Arial, sans-serif;
font-size: 9pt;
font-weight: normal;
list-style-type: none;
list-style-image: none;
margin-left: 0;
padding-left: 0;
text-align: left;
}
#toc a {
font-weight: normal;
}
#toc ul li,
.toc ul li {
margin-left: 0;
margin-top: 0;
}
#toc ul ul,
.toc ul ul {
margin-left: 0;
}
#toc ul ul,
.toc ul ul {
font-family: Helvetica, Arial, sans-serif;
margin: 0 0 0 2em;
}
#toc .toctoggle,
.toc .toctoggle {
font-family: Helvetica, Arial, sans-serif;
font-size: smaller;
}
#toc td {
border: none;
padding: 0 3px 3px 3px;
}
.imagelist {
font-size: 8pt;
width: 100%;
}
.TablePager, .TablePager td, .TablePager th {
border: none;
padding: 0 0.15em 0 0.15em;
}
.icon {
vertical-align: middle;
padding-left: 2px;
padding-right: 2px;
}
td p {
padding: 0px;
margin: 0px;
}
/* --- Page bottom bling. Has to come after general settings. --- */
#flashyicons {
padding-bottom: 10px;
}
#flashyicons table {
margin-left: auto;
margin-right: auto;
margin-top: 6px;
margin-bottom: 10px;
border-width: 0px;
}
#flashyicons td.icon {
border-width: 0px;
padding: 0 10px 0 10px;
}
a.osi-icon {
display: block;
width: 80px;
height: 15px;
background: url(/skins/SBML/button-osi.gif) -80px 0 no-repeat;
text-decoration: none;
}
a:hover.osi-icon {
background-position: 0 0;
}
a.php-icon {
display: block;
width: 80px;
height: 15px;
background: url(/skins/SBML/button-php.gif) -80px 0 no-repeat;
text-decoration: none;
}
a:hover.php-icon {
background-position: 0 0;
}
a.gnu-icon {
display: block;
width: 80px;
height: 15px;
background: url(/skins/SBML/button-gnu.gif) -80px 0 no-repeat;
text-decoration: none;
}
a:hover.gnu-icon {
background-position: 0 0;
}
a.linux-icon {
display: block;
width: 80px;
height: 15px;
background: url(/skins/SBML/button-linux.gif) -80px 0 no-repeat;
text-decoration: none;
}
a:hover.linux-icon {
background-position: 0 0;
}
a.rss-icon {
display: block;
width: 80px;
height: 15px;
background: url(/skins/SBML/button-rss.gif) -80px 0 no-repeat;
text-decoration: none;
}
a:hover.rss-icon {
background-position: 0 0;
}
a.mediawiki-icon {
display: block;
width: 80px;
height: 15px;
background: url(/skins/SBML/button-mediawiki.gif) -80px 0 no-repeat;
text-decoration: none;
}
a:hover.mediawiki-icon {
background-position: 0 0;
}
.floatright {
margin-top: 1em !important;
}
/* --- Special cases for different areas of the site --- */
#workshop-quick-map table {
padding: 5px;
border: none;
}
#workshop-quick-map th {
padding: 5px 15px 5px 15px;
background-color: #fff;
border-top: none;
border-left: none;
border-right: none;
border-bottom: 1px solid #ccc;
}
#workshop-quick-map td {
padding: 5px 15px 5px 15px;
border: none;
}
/* To make a table collapsed when first viewed, put "collapsed"
in its class list. */
#past-events #collapsibleTable0 td,
#past-events #collapsibleTable1 td,
#past-events #collapsibleTable2 td
{
font-size: 8pt;
}
.float-right {
display: inline;
float: right;
}
.border-dotted {
border: 1px dotted #ccc;
}
.gray-border {
border: 1px solid #ccc;
}
.news-item-title {
font-weight: bold;
font-style: italic;
display: block;
}
.news-item-title h3 {
margin-bottom: 2px;
}
.news-item-abstract {
font-size: 8pt;
}
.news-item-date {
font-style: italic;
margin-right: 3px;
color: #937c7c;
}
#about-blurb {
font-size: 8pt;
line-height: 120%;
margin: 1.25em 1.75em 2em 0;
}
#about-blurb .icon {
padding-bottom: 1em;
}
.about-blurb-name {
display: inline;
font-weight: bold;
}
p.about-blurb-image {
text-align: center;
margin: 0 0 0.75em 0;
padding: 0px;
}
.about-blurb-text {
text-align: justify;
}
.page-Special_Allpages {
font-size: 8pt;
}
.no-margins {
margin: 0;
padding: 0;
}
/* --- Special effects libraries --- */
#stylefour {
position: relative;
display: block;
height: 39px;
background: transparent url(/skins/SBML/tab-bgOFF.gif) repeat-x top left;
}
#stylefour ul {
margin: 0;
padding: 0;
list-style-type: none;
width: auto;
}
#stylefour ul li {
display: block;
float: left;
margin: 0;
}
#stylefour ul li a {
display: block;
float: left;
color: #666;
text-decoration: none;
padding: 11px 7px 0 7px;
height: 23px;
background: transparent url(/skins/SBML/tab-bgDIVIDER.gif) no-repeat top right;
}
#stylefour ul li a:hover, #stylefour ul li a.current {
background: #fff url(/skins/SBML/tab-bgON.gif) no-repeat top right;
}
#navlinks ul {
color: #fff;
margin: 0;
padding: 0;
list-style-type: none;
width: auto;
}
#navlinks ul li {
display: block;
float: left;
margin: 0;
}
#navlinks ul li a {
display: block;
float: left;
color: #fff;
text-decoration: none;
padding: 0px 7px 0 7px;
}
#navlinks ul li a:visited {
color: #fff;
}
#navlinks ul li a:hover, #navlinks ul li a.current {
color: #000;
}
#searchbox {
float: right;
padding: 8px 10px 0 0;
width: auto;
margin: auto;
}
#searchbox img {
vertical-align: top;
}
#searchbox form,
#searchbox input,
#searchbox .searchform {
background: transparent url('osx-searchbox/srch_bg.gif') repeat-x top left;
display: inline;
font-size: 7pt;
text-decoration: none;
white-space: nowrap;
margin-bottom: 10px;
padding: 0px;
border: none;
height: 19px;
width: 100px;
vertical-align: middle;
}
/* 'height' in the following and padding in the next one interact for
positioning the placeholder text in the search box. */
#searchbox input {
vertical-align: top;
background-color: #ffffff;
color: #404040;
height: 15px;
}
#searchbox input.srch_fld {
padding-top: 4px;
}
/* Taken from monobook */
/*
** keep the whitespace in front of the ^=, hides rule from konqueror
** this is css3, the validator doesn't like it when validating as css2
*/
#article a.external,
#article a[href ^="gopher://"] {
background: url(external.png) center right no-repeat;
padding-right: 13px;
}
#article a[href ^="mailto:"],
.link-mailto {
background: url(mail_icon.gif) center right no-repeat;
padding-right: 18px;
}
#article a[href ^="news://"] {
background: url(news_icon.png) center right no-repeat;
padding-right: 18px;
}
#article a[href ^="ftp://"],
.link-ftp {
background: url(file_icon.gif) center right no-repeat;
padding-right: 18px;
}
#article a[href ^="irc://"],
.link-irc {
background: url(discussionitem_icon.gif) center right no-repeat;
padding-right: 18px;
}
#article a.external[href $=".ogg"], #article a.external[href $=".OGG"],
#article a.external[href $=".mid"], #article a.external[href $=".MID"],
#article a.external[href $=".midi"], #article a.external[href $=".MIDI"],
#article a.external[href $=".mp3"], #article a.external[href $=".MP3"],
#article a.external[href $=".wav"], #article a.external[href $=".WAV"],
#article a.external[href $=".wma"], #article a.external[href $=".WMA"],
.link-audio {
background: url("audio.png") center right no-repeat;
padding-right: 13px;
}
#article a.external[href $=".ogm"], #article a.external[href $=".OGM"],
#article a.external[href $=".avi"], #article a.external[href $=".AVI"],
#article a.external[href $=".mpeg"], #article a.external[href $=".MPEG"],
#article a.external[href $=".mpg"], #article a.external[href $=".MPG"],
.link-video {
background: url("video.png") center right no-repeat;
padding-right: 13px;
}
#article a.external[href $=".pdf"], #article a.external[href $=".PDF"],
#article a.external[href *=".pdf#"], #article a.external[href *=".PDF#"],
#article a.external[href *=".pdf?"], #article a.external[href *=".PDF?"],
.link-document {
background: url("document.png") center right no-repeat;
padding-right: 12px;
}
/* Print-specific things to hide */
.printfooter {
display: none;
}
#article img[alt ^="Image:"] {
vertical-align: middle;
}
tr.headers {
background: lightgray;
}
tr.headers2 {
background: navajowhite;
text-align: center;
}
td.footnote {
text-align: center;
font-size:small;
}
SBMLToolbox-4.1.0/docs/structureFields.html 0000644 0000000 0000000 00000065005 11611210324 017320 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\STRUCTFIELDNAMES
These functions return the fieldnames and default values for the MATLAB_SBML structures.
Function are:
[values] = getAlgebraicRuleDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML AlgebraicRule structure of the given level and version
NOTE: The corresponding fields present in an SBML AlgebraicRule structure can be found using
the function getAlgebraicRuleFieldnames
[fieldnames, num] = getAlgebraicRuleFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML AlgebraicRule structure of the given level and version
- the number of fieldnames
[values] = getAssignmentRuleDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML AssignmentRule structure of the given level and version
NOTE: The corresponding fields present in an SBML AssignmentRule structure can be found using
the function getAssignmentRuleFieldnames
[fieldnames, num] = getAssignmentRuleFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML AssignmentRule structure of the given level and version
- the number of fieldnames
[values] = getCompartmentDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Compartment structure of the given level and version
NOTE: The corresponding fields present in an SBML Compartment structure can be found using
the function getCompartmentFieldnames
[fieldnames, num] = getCompartmentFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Compartment structure of the given level and version
- the number of fieldnames
[values] = getCompartmentTypeDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML CompartmentType structure of the given level and version
NOTE: The corresponding fields present in an SBML CompartmentType structure can be found using
the function getCompartmentTypeFieldnames
[fieldnames, num] = getCompartmentTypeFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML CompartmentType structure of the given level and version
- the number of fieldnames
[values] = getCompartmentVolumeRuleDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML CompartmentVolumeRule structure of the given level and version
NOTE: The corresponding fields present in an SBML CompartmentVolumeRule structure can be found using
the function getCompartmentVolumeRuleFieldnames
[fieldnames, num] = getCompartmentVolumeRuleFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML CompartmentVolumeRule structure of the given level and version
- the number of fieldnames
[values] = getConstraintDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Constraint structure of the given level and version
NOTE: The corresponding fields present in an SBML Constraint structure can be found using
the function getConstraintFieldnames
[fieldnames, num] = getConstraintFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Constraint structure of the given level and version
- the number of fieldnames
[values] = getDefaultValues(typecode, level, version)
Takes
- typecode; a string representing the type of object being queried
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML structure of the given typecode, level and version
NOTE: The corresponding fields present in an SBML structure can be found using
the function getFieldnames
[values] = getDelayDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Delay structure of the given level and version
NOTE: The corresponding fields present in an SBML Delay structure can be found using
the function getDelayFieldnames
[fieldnames, num] = getDelayFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Delay structure of the given level and version
- the number of fieldnames
[values] = getEventAssignmentDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML EventAssignment structure of the given level and version
NOTE: The corresponding fields present in an SBML EventAssignment structure can be found using
the function getEventAssignmentFieldnames
[fieldnames, num] = getEventAssignmentFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML EventAssignment structure of the given level and version
- the number of fieldnames
[values] = getEventDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Event structure of the given level and version
NOTE: The corresponding fields present in an SBML Event structure can be found using
the function getEventFieldnames
[fieldnames, num] = getEventFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Event structure of the given level and version
- the number of fieldnames
[fieldnames, num] = getFieldnames(typecode, level, version)
Takes
- typecode; a string representing the type of object being queried
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML structure of the given typecode, level and version
- the number of fieldnames
[values] = getFunctionDefinitionDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML FunctionDefinition structure of the given level and version
NOTE: The corresponding fields present in an SBML FunctionDefinition structure can be found using
the function getFunctionDefinitionFieldnames
[fieldnames, num] = getFunctionDefinitionFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML FunctionDefinition structure of the given level and version
- the number of fieldnames
[values] = getInitialAssignmentDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML InitialAssignment structure of the given level and version
NOTE: The corresponding fields present in an SBML InitialAssignment structure can be found using
the function getInitialAssignmentFieldnames
[fieldnames, num] = getInitialAssignmentFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML InitialAssignment structure of the given level and version
- the number of fieldnames
[values] = getKineticLawDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML KineticLaw structure of the given level and version
NOTE: The corresponding fields present in an SBML KineticLaw structure can be found using
the function getKineticLawFieldnames
[fieldnames, num] = getKineticLawFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML KineticLaw structure of the given level and version
- the number of fieldnames
[values] = getLocalParameterDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML LocalParameter structure of the given level and version
NOTE: The corresponding fields present in an SBML LocalParameter structure can be found using
the function getLocalParameterFieldnames
[fieldnames, num] = getLocalParameterFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML LocalParameter structure of the given level and version
- the number of fieldnames
[values] = getModelDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Model structure of the given level and version
NOTE: The corresponding fields present in an SBML Model structure can be found using
the function getModelFieldnames
[fieldnames, num] = getModelFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Model structure of the given level and version
- the number of fieldnames
[values] = getModifierSpeciesReferenceDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML ModifierSpeciesReference structure of the given level and version
NOTE: The corresponding fields present in an SBML ModifierSpeciesReference structure can be found using
the function getModifierSpeciesReferenceFieldnames
[fieldnames, num] = getModifierSpeciesReferenceFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML ModifierSpeciesReference structure of the given level and version
- the number of fieldnames
[values] = getParameterDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Parameter structure of the given level and version
NOTE: The corresponding fields present in an SBML Parameter structure can be found using
the function getParameterFieldnames
[fieldnames, num] = getParameterFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Parameter structure of the given level and version
- the number of fieldnames
[values] = getParameterRuleDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML ParameterRule structure of the given level and version
NOTE: The corresponding fields present in an SBML ParameterRule structure can be found using
the function getParameterRuleFieldnames
[fieldnames, num] = getParameterRuleFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML ParameterRule structure of the given level and version
- the number of fieldnames
[values] = getPriorityDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Priority structure of the given level and version
NOTE: The corresponding fields present in an SBML Priority structure can be found using
the function getPriorityFieldnames
[fieldnames, num] = getPriorityFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Priority structure of the given level and version
- the number of fieldnames
[values] = getRateRuleDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML RateRule structure of the given level and version
NOTE: The corresponding fields present in an SBML RateRule structure can be found using
the function getRateRuleFieldnames
[fieldnames, num] = getRateRuleFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML RateRule structure of the given level and version
- the number of fieldnames
[values] = getReactionDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Reaction structure of the given level and version
NOTE: The corresponding fields present in an SBML Reaction structure can be found using
the function getReactionFieldnames
[fieldnames, num] = getReactionFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Reaction structure of the given level and version
- the number of fieldnames
[fieldnames, num] = getRuleFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Rule structure of the given level and version
- the number of fieldnames
[values] = getSpeciesConcentrationRuleDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML SpeciesConcentrationRule structure of the given level and version
NOTE: The corresponding fields present in an SBML SpeciesConcentrationRule structure can be found using
the function getSpeciesConcentrationRuleFieldnames
[fieldnames, num] = getSpeciesConcentrationRuleFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML SpeciesConcentrationRule structure of the given level and version
- the number of fieldnames
[values] = getSpeciesDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Species structure of the given level and version
NOTE: The corresponding fields present in an SBML Species structure can be found using
the function getSpeciesFieldnames
[fieldnames, num] = getSpeciesFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Species structure of the given level and version
- the number of fieldnames
[values] = getSpeciesReferenceDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML SpeciesReference structure of the given level and version
NOTE: The corresponding fields present in an SBML SpeciesReference structure can be found using
the function getSpeciesReferenceFieldnames
[fieldnames, num] = getSpeciesReferenceFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML SpeciesReference structure of the given level and version
- the number of fieldnames
[values] = getSpeciesTypeDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML SpeciesType structure of the given level and version
NOTE: The corresponding fields present in an SBML SpeciesType structure can be found using
the function getSpeciesTypeFieldnames
[fieldnames, num] = getSpeciesTypeFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML SpeciesType structure of the given level and version
- the number of fieldnames
[values] = getStoichiometryMathDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML StoichiometryMath structure of the given level and version
NOTE: The corresponding fields present in an SBML StoichiometryMath structure can be found using
the function getStoichiometryMathFieldnames
[fieldnames, num] = getStoichiometryMathFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML StoichiometryMath structure of the given level and version
- the number of fieldnames
[values] = getTriggerDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Trigger structure of the given level and version
NOTE: The corresponding fields present in an SBML Trigger structure can be found using
the function getTriggerFieldnames
[fieldnames, num] = getTriggerFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Trigger structure of the given level and version
- the number of fieldnames
[values] = getUnitDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML Unit structure of the given level and version
NOTE: The corresponding fields present in an SBML Unit structure can be found using
the function getUnitFieldnames
[values] = getUnitDefinitionDefaultValues(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of default values for an SBML UnitDefinition structure of the given level and version
NOTE: The corresponding fields present in an SBML UnitDefinition structure can be found using
the function getUnitDefinitionFieldnames
[fieldnames, num] = getUnitDefinitionFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML UnitDefinition structure of the given level and version
- the number of fieldnames
[fieldnames, num] = getUnitFieldnames(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- an array of fieldnames for an SBML Unit structure of the given level and version
- the number of fieldnames
valid = isValidLevelVersionCombination(level, version)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
Returns
- valid = 1 if the level and version combinbation represent a valid
specification of SBML supported by SBMLToolbox
NOTE: This function causes an error if the level/version arguments do
not represent a valid supported SBML format
SBMLModel = propagateLevelVersion(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with level and version fields added to all
sub structures
NOTE: This function facilitates keeping track of the level and version
of sub objects within a model
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MATLAB_SBML_STRUCTURE_FUNCTIONS
These are general functions for working with MATLAB_SBML structures.
Function are:
level = GetLevel(SBMLStructure)
Takes
- SBMLStructure, any SBML structure
Returns
- the SBML level corresponding to this structure
NOTE: it is not always possible to uniquely determine the level from a
structure. The most recent SBML level that matches will be reported.
[level, version] = GetLevelVersion(SBMLStructure)
Takes
- SBMLStructure, any SBML structure
Returns
- the SBML level corresponding to this structure
- the SBML version corresponding to this structure
NOTE: it is not always possible to uniquely determine the level/version from a
structure. The most recent SBML level/version that matches will be reported.
SBMLStructure = Object_create(typecode, level, version)
Takes
- typecode; a string representing the type of object being queried
- level; an integer representing an SBML level
- version; an integer representing an SBML version
Returns
- an SBML structure representing the given typecode, level and version
identical = areIdentical(SBMLStruct1, SBMLStruct2)
Takes
- SBMLStruct1, any SBML structure
- SBMLStruct2, any SBML structure
Returns
- identical =
- 1 if the structures are identical i.e. contain same fields and the same values
- 0 otherwise
SBMLToolbox-4.1.0/docs/structure-functions/ 0000755 0000000 0000000 00000000000 11704572220 017314 5 ustar root root SBMLToolbox-4.1.0/docs/structure-functions/unitDefinition.html 0000644 0000000 0000000 00000014735 11626400656 023212 0 ustar root root MATLABSBMLSTRUCTURE_FUNCTIONS\UNITDEFINITION
The functions allow users to create and work with the SBML UnitDefinition structure.
Function are:
SBMLUnitDefinition = UnitDefinition_addUnit(SBMLUnitDefinition, SBMLUnit)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
- SBMLUnit, an SBML Unit structure
Returns
- the SBML UnitDefinition structure with the SBML Unit structure added
UnitDefinition = UnitDefinition_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML UnitDefinition 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
SBMLUnitDefinition = UnitDefinition_createUnit(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the SBML UnitDefinition structure with a new SBML Unit structure added
id = UnitDefinition_getId(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the value of the id attribute
unit = UnitDefinition_getListOfUnits(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- an array of the unit structures
metaid = UnitDefinition_getMetaid(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the value of the metaid attribute
name = UnitDefinition_getName(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the value of the name attribute
numUnits = UnitDefinition_getNumUnits(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the value of the numUnits attribute
sboTerm = UnitDefinition_getSBOTerm(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the value of the sboTerm attribute
unit = UnitDefinition_getUnit(SBMLUnitDefinition, index)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
- index, an integer representing the index of SBML Unit structure
Returns
- the SBML Unit structure at the indexed position
value = UnitDefinition_isSetId(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = UnitDefinition_isSetMetaid(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = UnitDefinition_isSetName(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = UnitDefinition_isSetSBOTerm(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLUnitDefinition = UnitDefinition_setId(SBMLUnitDefinition, id)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
- id; a string representing the id to be set
Returns
- the SBML UnitDefinition structure with the new value for the id attribute
SBMLUnitDefinition = UnitDefinition_setMetaid(SBMLUnitDefinition, metaid)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
- metaid; a string representing the metaid to be set
Returns
- the SBML UnitDefinition structure with the new value for the metaid attribute
SBMLUnitDefinition = UnitDefinition_setName(SBMLUnitDefinition, name)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
- name; a string representing the name to be set
Returns
- the SBML UnitDefinition structure with the new value for the name attribute
SBMLUnitDefinition = UnitDefinition_setSBOTerm(SBMLUnitDefinition, sboTerm)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML UnitDefinition structure with the new value for the sboTerm attribute
SBMLUnitDefinition = UnitDefinition_unsetId(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the SBML UnitDefinition structure with the id attribute unset
SBMLUnitDefinition = UnitDefinition_unsetMetaid(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the SBML UnitDefinition structure with the metaid attribute unset
SBMLUnitDefinition = UnitDefinition_unsetName(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the SBML UnitDefinition structure with the name attribute unset
SBMLUnitDefinition = UnitDefinition_unsetSBOTerm(SBMLUnitDefinition)
Takes
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the SBML UnitDefinition structure with the sboTerm attribute unset
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MATLAB_SBML_STRUCTURE_FUNCTIONS\UNIT
The functions allow users to create and work with the SBML Unit structure.
Function are:
Unit = Unit_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Unit 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
exponent = Unit_getExponent(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the value of the exponent attribute
kind = Unit_getKind(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the value of the kind attribute
metaid = Unit_getMetaid(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the value of the metaid attribute
multiplier = Unit_getMultiplier(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the value of the multiplier attribute
offset = Unit_getOffset(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the value of the offset attribute
sboTerm = Unit_getSBOTerm(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the value of the sboTerm attribute
scale = Unit_getScale(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the value of the scale attribute
value = Unit_isSetExponent(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- value =
- 1 if the exponent attribute is set
- 0 otherwise
value = Unit_isSetKind(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- value =
- 1 if the kind attribute is set
- 0 otherwise
value = Unit_isSetMetaid(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Unit_isSetMultiplier(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- value =
- 1 if the multiplier attribute is set
- 0 otherwise
value = Unit_isSetOffset(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- value =
- 1 if the offset attribute is set
- 0 otherwise
value = Unit_isSetSBOTerm(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = Unit_isSetScale(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- value =
- 1 if the scale attribute is set
- 0 otherwise
SBMLUnit = Unit_setExponent(SBMLUnit, exponent)
Takes
- SBMLUnit, an SBML Unit structure
- exponent; number representing the value of exponent to be set
Returns
- the SBML Unit structure with the new value for the exponent attribute
SBMLUnit = Unit_setKind(SBMLUnit, kind)
Takes
- SBMLUnit, an SBML Unit structure
- kind; a string representing the kind to be set
Returns
- the SBML Unit structure with the new value for the kind attribute
SBMLUnit = Unit_setMetaid(SBMLUnit, metaid)
Takes
- SBMLUnit, an SBML Unit structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Unit structure with the new value for the metaid attribute
SBMLUnit = Unit_setMultiplier(SBMLUnit, multiplier)
Takes
- SBMLUnit, an SBML Unit structure
- multiplier; number representing the value of multiplier to be set
Returns
- the SBML Unit structure with the new value for the multiplier attribute
SBMLUnit = Unit_setOffset(SBMLUnit, offset)
Takes
- SBMLUnit, an SBML Unit structure
- offset, an integer representing the offset to be set
Returns
- the SBML Unit structure with the new value for the offset attribute
SBMLUnit = Unit_setSBOTerm(SBMLUnit, sboTerm)
Takes
- SBMLUnit, an SBML Unit structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Unit structure with the new value for the sboTerm attribute
SBMLUnit = Unit_setScale(SBMLUnit, scale)
Takes
- SBMLUnit, an SBML Unit structure
- scale; number representing the value of scale to be set
Returns
- the SBML Unit structure with the new value for the scale attribute
SBMLUnit = Unit_unsetExponent(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the SBML Unit structure with the exponent attribute unset
SBMLUnit = Unit_unsetKind(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the SBML Unit structure with the kind attribute unset
SBMLUnit = Unit_unsetMetaid(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the SBML Unit structure with the metaid attribute unset
SBMLUnit = Unit_unsetMultiplier(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the SBML Unit structure with the multiplier attribute unset
SBMLUnit = Unit_unsetOffset(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the SBML Unit structure with the offset attribute unset
SBMLUnit = Unit_unsetSBOTerm(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the SBML Unit structure with the sboTerm attribute unset
SBMLUnit = Unit_unsetScale(SBMLUnit)
Takes
- SBMLUnit, an SBML Unit structure
Returns
- the SBML Unit structure with the scale attribute unset
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MATLAB_SBML_STRUCTURE_FUNCTIONS\TRIGGER
The functions allow users to create and work with the SBML Trigger structure.
Function are:
Trigger = Trigger_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Trigger 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
initialValue = Trigger_getInitialValue(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- the value of the initialValue attribute
math = Trigger_getMath(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- the value of the math attribute
metaid = Trigger_getMetaid(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- the value of the metaid attribute
persistent = Trigger_getPersistent(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- the value of the persistent attribute
sboTerm = Trigger_getSBOTerm(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- the value of the sboTerm attribute
value = Trigger_isSetMath(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = Trigger_isSetMetaid(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Trigger_isSetSBOTerm(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLTrigger = Trigger_setInitialValue(SBMLTrigger, initialValue)
Takes
- SBMLTrigger, an SBML Trigger structure
- initialValue, an integer (0/1) representing the value of initialValue to be set
Returns
- the SBML Trigger structure with the new value for the initialValue attribute
SBMLTrigger = Trigger_setMath(SBMLTrigger, math)
Takes
- SBMLTrigger, an SBML Trigger structure
- math; string representing the math expression math to be set
Returns
- the SBML Trigger structure with the new value for the math attribute
SBMLTrigger = Trigger_setMetaid(SBMLTrigger, metaid)
Takes
- SBMLTrigger, an SBML Trigger structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Trigger structure with the new value for the metaid attribute
SBMLTrigger = Trigger_setPersistent(SBMLTrigger, persistent)
Takes
- SBMLTrigger, an SBML Trigger structure
- persistent, an integer (0/1) representing the value of persistent to be set
Returns
- the SBML Trigger structure with the new value for the persistent attribute
SBMLTrigger = Trigger_setSBOTerm(SBMLTrigger, sboTerm)
Takes
- SBMLTrigger, an SBML Trigger structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Trigger structure with the new value for the sboTerm attribute
SBMLTrigger = Trigger_unsetMath(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- the SBML Trigger structure with the math attribute unset
SBMLTrigger = Trigger_unsetMetaid(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- the SBML Trigger structure with the metaid attribute unset
SBMLTrigger = Trigger_unsetSBOTerm(SBMLTrigger)
Takes
- SBMLTrigger, an SBML Trigger structure
Returns
- the SBML Trigger structure with the sboTerm attribute unset
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MATLAB_SBML_STRUCTURE_FUNCTIONS\STOICHIOMETRYMATH
The functions allow users to create and work with the SBML StoichiometryMath structure.
Function are:
StoichiometryMath = StoichiometryMath_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML StoichiometryMath 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
math = StoichiometryMath_getMath(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- the value of the math attribute
metaid = StoichiometryMath_getMetaid(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- the value of the metaid attribute
sboTerm = StoichiometryMath_getSBOTerm(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- the value of the sboTerm attribute
value = StoichiometryMath_isSetMath(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = StoichiometryMath_isSetMetaid(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = StoichiometryMath_isSetSBOTerm(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLStoichiometryMath = StoichiometryMath_setMath(SBMLStoichiometryMath, math)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
- math; string representing the math expression math to be set
Returns
- the SBML StoichiometryMath structure with the new value for the math attribute
SBMLStoichiometryMath = StoichiometryMath_setMetaid(SBMLStoichiometryMath, metaid)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
- metaid; a string representing the metaid to be set
Returns
- the SBML StoichiometryMath structure with the new value for the metaid attribute
SBMLStoichiometryMath = StoichiometryMath_setSBOTerm(SBMLStoichiometryMath, sboTerm)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML StoichiometryMath structure with the new value for the sboTerm attribute
SBMLStoichiometryMath = StoichiometryMath_unsetMath(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- the SBML StoichiometryMath structure with the math attribute unset
SBMLStoichiometryMath = StoichiometryMath_unsetMetaid(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- the SBML StoichiometryMath structure with the metaid attribute unset
SBMLStoichiometryMath = StoichiometryMath_unsetSBOTerm(SBMLStoichiometryMath)
Takes
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- the SBML StoichiometryMath structure with the sboTerm attribute unset
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MATLAB_SBML_STRUCTURE_FUNCTIONS\SPECIESTYPE
The functions allow users to create and work with the SBML SpeciesType structure.
Function are:
SpeciesType = SpeciesType_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML SpeciesType 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
id = SpeciesType_getId(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the value of the id attribute
metaid = SpeciesType_getMetaid(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the value of the metaid attribute
name = SpeciesType_getName(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the value of the name attribute
sboTerm = SpeciesType_getSBOTerm(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the value of the sboTerm attribute
value = SpeciesType_isSetId(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = SpeciesType_isSetMetaid(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = SpeciesType_isSetName(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = SpeciesType_isSetSBOTerm(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLSpeciesType = SpeciesType_setId(SBMLSpeciesType, id)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
- id; a string representing the id to be set
Returns
- the SBML SpeciesType structure with the new value for the id attribute
SBMLSpeciesType = SpeciesType_setMetaid(SBMLSpeciesType, metaid)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
- metaid; a string representing the metaid to be set
Returns
- the SBML SpeciesType structure with the new value for the metaid attribute
SBMLSpeciesType = SpeciesType_setName(SBMLSpeciesType, name)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
- name; a string representing the name to be set
Returns
- the SBML SpeciesType structure with the new value for the name attribute
SBMLSpeciesType = SpeciesType_setSBOTerm(SBMLSpeciesType, sboTerm)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML SpeciesType structure with the new value for the sboTerm attribute
SBMLSpeciesType = SpeciesType_unsetId(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the SBML SpeciesType structure with the id attribute unset
SBMLSpeciesType = SpeciesType_unsetMetaid(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the SBML SpeciesType structure with the metaid attribute unset
SBMLSpeciesType = SpeciesType_unsetName(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the SBML SpeciesType structure with the name attribute unset
SBMLSpeciesType = SpeciesType_unsetSBOTerm(SBMLSpeciesType)
Takes
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the SBML SpeciesType structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/speciesReference.html 0000644 0000000 0000000 00000037575 11703262406 023476 0 ustar root root MATLABSBMLSTRUCTURE_FUNCTIONS\SPECIESREFERENCE
The functions allow users to create and work with the SBML SpeciesReference structure.
Function are:
SpeciesReference = SpeciesReference_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML SpeciesReference 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
SBMLSpeciesReference = SpeciesReference_createStoichiometryMath(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with a new SBML StoichiometryMath structure added
constant = SpeciesReference_getConstant(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the value of the constant attribute
denominator = SpeciesReference_getDenominator(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the value of the denominator attribute
id = SpeciesReference_getId(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the value of the id attribute
metaid = SpeciesReference_getMetaid(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the value of the metaid attribute
name = SpeciesReference_getName(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the value of the name attribute
sboTerm = SpeciesReference_getSBOTerm(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the value of the sboTerm attribute
species = SpeciesReference_getSpecies(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the value of the species attribute
stoichiometry = SpeciesReference_getStoichiometry(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the value of the stoichiometry attribute
stoichiometryMath = SpeciesReference_getStoichiometryMath(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML StoichiometryMath structure
y = SpeciesReference_isAssignedByRateRule(SBMLSpeciesReference, SBMLRules)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- the index of the rateRule used to assigned value to the SpeciesReference
- 0 if the SpeciesReference 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) 2009-2012 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 = SpeciesReference_isAssignedByRule(SBMLSpeciesReference, SBMLRules)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- the index of the assignmentRule used to assigned value to the SpeciesReference
- 0 if the SpeciesReference 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) 2009-2012 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 = SpeciesReference_isInAlgebraicRule(SBMLSpeciesReference, SBMLRules)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- an array of the indices of any algebraicRules the id of the SpeciesReference appears in
- 0 if the SpeciesReference 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) 2009-2012 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 = SpeciesReference_isSetDenominator(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- value =
- 1 if the denominator attribute is set
- 0 otherwise
value = SpeciesReference_isSetId(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = SpeciesReference_isSetMetaid(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = SpeciesReference_isSetName(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = SpeciesReference_isSetSBOTerm(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = SpeciesReference_isSetSpecies(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- value =
- 1 if the species attribute is set
- 0 otherwise
value = SpeciesReference_isSetStoichiometry(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- value =
- 1 if the stoichiometry attribute is set
- 0 otherwise
value = SpeciesReference_isSetStoichiometryMath(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- value =
- 1 if the stoichiometryMath structure is set
- 0 otherwise
SBMLSpeciesReference = SpeciesReference_setConstant(SBMLSpeciesReference, constant)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- constant, an integer (0/1) representing the value of constant to be set
Returns
- the SBML SpeciesReference structure with the new value for the constant attribute
SBMLSpeciesReference = SpeciesReference_setDenominator(SBMLSpeciesReference, denominator)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- denominator, an integer representing the denominator to be set
Returns
- the SBML SpeciesReference structure with the new value for the denominator attribute
SBMLSpeciesReference = SpeciesReference_setId(SBMLSpeciesReference, id)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- id; a string representing the id to be set
Returns
- the SBML SpeciesReference structure with the new value for the id attribute
SBMLSpeciesReference = SpeciesReference_setMetaid(SBMLSpeciesReference, metaid)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- metaid; a string representing the metaid to be set
Returns
- the SBML SpeciesReference structure with the new value for the metaid attribute
SBMLSpeciesReference = SpeciesReference_setName(SBMLSpeciesReference, name)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- name; a string representing the name to be set
Returns
- the SBML SpeciesReference structure with the new value for the name attribute
SBMLSpeciesReference = SpeciesReference_setSBOTerm(SBMLSpeciesReference, sboTerm)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML SpeciesReference structure with the new value for the sboTerm attribute
SBMLSpeciesReference = SpeciesReference_setSpecies(SBMLSpeciesReference, species)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- species; a string representing the species to be set
Returns
- the SBML SpeciesReference structure with the new value for the species attribute
SBMLSpeciesReference = SpeciesReference_setStoichiometry(SBMLSpeciesReference, stoichiometry)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- stoichiometry; number representing the value of stoichiometry to be set
Returns
- the SBML SpeciesReference structure with the new value for the stoichiometry attribute
SBMLSpeciesReference = SpeciesReference_setStoichiometryMath(SBMLSpeciesReference, SBMLStoichiometryMath)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
- SBMLStoichiometryMath, an SBML StoichiometryMath structure
Returns
- the SBML SpeciesReference structure with the new value for the stoichiometryMath field
SBMLSpeciesReference = SpeciesReference_unsetDenominator(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with the denominator attribute unset
SBMLSpeciesReference = SpeciesReference_unsetId(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with the id attribute unset
SBMLSpeciesReference = SpeciesReference_unsetMetaid(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with the metaid attribute unset
SBMLSpeciesReference = SpeciesReference_unsetName(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with the name attribute unset
SBMLSpeciesReference = SpeciesReference_unsetSBOTerm(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with the sboTerm attribute unset
SBMLSpeciesReference = SpeciesReference_unsetSpecies(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with the species attribute unset
SBMLSpeciesReference = SpeciesReference_unsetStoichiometry(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with the stoichiometry attribute unset
SBMLSpeciesReference = SpeciesReference_unsetStoichiometryMath(SBMLSpeciesReference)
Takes
- SBMLSpeciesReference, an SBML SpeciesReference structure
Returns
- the SBML SpeciesReference structure with the stoichiometryMath field unset
SBMLToolbox-4.1.0/docs/structure-functions/speciesConcentrationRule.html 0000644 0000000 0000000 00000012155 11611210762 025215 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\SPECIESCONCENTRATIONRULE
The functions allow users to create and work with the SBML SpeciesConcentrationRule structure.
Function are:
SpeciesConcentrationRule = SpeciesConcentrationRule_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML SpeciesConcentrationRule 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
formula = SpeciesConcentrationRule_getFormula(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- the value of the formula attribute
species = SpeciesConcentrationRule_getSpecies(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- the value of the species attribute
type = SpeciesConcentrationRule_getType(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- the value of the type attribute
value = SpeciesConcentrationRule_isSetFormula(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- value =
- 1 if the formula attribute is set
- 0 otherwise
value = SpeciesConcentrationRule_isSetSpecies(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- value =
- 1 if the species attribute is set
- 0 otherwise
value = SpeciesConcentrationRule_isSetType(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- value =
- 1 if the type attribute is set
- 0 otherwise
SBMLSpeciesConcentrationRule = SpeciesConcentrationRule_setFormula(SBMLSpeciesConcentrationRule, formula)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
- formula; a string representing the formula to be set
Returns
- the SBML SpeciesConcentrationRule structure with the new value for the formula attribute
SBMLSpeciesConcentrationRule = SpeciesConcentrationRule_setSpecies(SBMLSpeciesConcentrationRule, species)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
- species; a string representing the species to be set
Returns
- the SBML SpeciesConcentrationRule structure with the new value for the species attribute
SBMLSpeciesConcentrationRule = SpeciesConcentrationRule_setType(SBMLSpeciesConcentrationRule, type)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
- type; a string representing the type to be set
Returns
- the SBML SpeciesConcentrationRule structure with the new value for the type attribute
SBMLSpeciesConcentrationRule = SpeciesConcentrationRule_unsetFormula(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- the SBML SpeciesConcentrationRule structure with the formula attribute unset
SBMLSpeciesConcentrationRule = SpeciesConcentrationRule_unsetSpecies(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- the SBML SpeciesConcentrationRule structure with the species attribute unset
SBMLSpeciesConcentrationRule = SpeciesConcentrationRule_unsetType(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- the SBML SpeciesConcentrationRule structure with the type attribute unset
SBMLSpeciesConcentrationRule = SpeciesConcentrationRule_unsetVariable(SBMLSpeciesConcentrationRule)
Takes
- SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
Returns
- the SBML SpeciesConcentrationRule structure with the variable attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/species.html 0000644 0000000 0000000 00000051405 11703262406 021643 0 ustar root root
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
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- 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
- SBMLSpecies, an SBML Species structure
Returns
- the value of the boundaryCondition attribute
charge = Species_getCharge(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the charge attribute
compartment = Species_getCompartment(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the compartment attribute
constant = Species_getConstant(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the constant attribute
conversionFactor = Species_getConversionFactor(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the conversionFactor attribute
hasOnlySubstanceUnits = Species_getHasOnlySubstanceUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the hasOnlySubstanceUnits attribute
id = Species_getId(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the id attribute
initialAmount = Species_getInitialAmount(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the initialAmount attribute
initialConcentration = Species_getInitialConcentration(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the initialConcentration attribute
metaid = Species_getMetaid(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the metaid attribute
name = Species_getName(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the name attribute
sboTerm = Species_getSBOTerm(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the sboTerm attribute
spatialSizeUnits = Species_getSpatialSizeUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the spatialSizeUnits attribute
speciesType = Species_getSpeciesType(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the speciesType attribute
substanceUnits = Species_getSubstanceUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the substanceUnits attribute
units = Species_getUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the value of the units attribute
y = Species_isAssignedByRateRule(SBMLSpecies, SBMLRules)
Takes
- SBMLSpecies, an SBML Species structure
- 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) 2009-2012 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
- SBMLSpecies, an SBML Species structure
- 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) 2009-2012 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
- SBMLSpecies, an SBML Species structure
- 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) 2009-2012 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
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the charge attribute is set
- 0 otherwise
value = Species_isSetCompartment(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the compartment attribute is set
- 0 otherwise
value = Species_isSetConversionFactor(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the conversionFactor attribute is set
- 0 otherwise
value = Species_isSetHasOnlySubstanceUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the hasOnlySubstanceUnits attribute is set
- 0 otherwise
value = Species_isSetId(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = Species_isSetInitialAmount(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the initialAmount attribute is set
- 0 otherwise
value = Species_isSetInitialConcentration(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the initialConcentration attribute is set
- 0 otherwise
value = Species_isSetMetaid(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Species_isSetName(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = Species_isSetSBOTerm(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = Species_isSetSpatialSizeUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the spatialSizeUnits attribute is set
- 0 otherwise
value = Species_isSetSpeciesType(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the speciesType attribute is set
- 0 otherwise
value = Species_isSetSubstanceUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the substanceUnits attribute is set
- 0 otherwise
value = Species_isSetUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- value =
- 1 if the units attribute is set
- 0 otherwise
SBMLSpecies = Species_setBoundaryCondition(SBMLSpecies, boundaryCondition)
Takes
- SBMLSpecies, an SBML Species structure
- boundaryCondition, an integer (0/1) representing the value of boundaryCondition to be set
Returns
- the SBML Species structure with the new value for the boundaryCondition attribute
SBMLSpecies = Species_setCharge(SBMLSpecies, charge)
Takes
- SBMLSpecies, an SBML Species structure
- charge, an integer representing the charge to be set
Returns
- the SBML Species structure with the new value for the charge attribute
SBMLSpecies = Species_setCompartment(SBMLSpecies, compartment)
Takes
- SBMLSpecies, an SBML Species structure
- compartment; a string representing the compartment to be set
Returns
- the SBML Species structure with the new value for the compartment attribute
SBMLSpecies = Species_setConstant(SBMLSpecies, constant)
Takes
- SBMLSpecies, an SBML Species structure
- constant, an integer (0/1) representing the value of constant to be set
Returns
- the SBML Species structure with the new value for the constant attribute
SBMLSpecies = Species_setConversionFactor(SBMLSpecies, conversionFactor)
Takes
- SBMLSpecies, an SBML Species structure
- conversionFactor; a string representing the conversionFactor to be set
Returns
- the SBML Species structure with the new value for the conversionFactor attribute
SBMLSpecies = Species_setHasOnlySubstanceUnits(SBMLSpecies, hasOnlySubstanceUnits)
Takes
- SBMLSpecies, an SBML Species structure
- hasOnlySubstanceUnits, an integer (0/1) representing the value of hasOnlySubstanceUnits to be set
Returns
- the SBML Species structure with the new value for the hasOnlySubstanceUnits attribute
SBMLSpecies = Species_setId(SBMLSpecies, id)
Takes
- SBMLSpecies, an SBML Species structure
- id; a string representing the id to be set
Returns
- the SBML Species structure with the new value for the id attribute
SBMLSpecies = Species_setInitialAmount(SBMLSpecies, initialAmount)
Takes
- SBMLSpecies, an SBML Species structure
- initialAmount; number representing the value of initialAmount to be set
Returns
- the SBML Species structure with the new value for the initialAmount attribute
SBMLSpecies = Species_setInitialConcentration(SBMLSpecies, initialConcentration)
Takes
- SBMLSpecies, an SBML Species structure
- initialConcentration; number representing the value of initialConcentration to be set
Returns
- the SBML Species structure with the new value for the initialConcentration attribute
SBMLSpecies = Species_setMetaid(SBMLSpecies, metaid)
Takes
- SBMLSpecies, an SBML Species structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Species structure with the new value for the metaid attribute
SBMLSpecies = Species_setName(SBMLSpecies, name)
Takes
- SBMLSpecies, an SBML Species structure
- name; a string representing the name to be set
Returns
- the SBML Species structure with the new value for the name attribute
SBMLSpecies = Species_setSBOTerm(SBMLSpecies, sboTerm)
Takes
- SBMLSpecies, an SBML Species structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Species structure with the new value for the sboTerm attribute
SBMLSpecies = Species_setSpatialSizeUnits(SBMLSpecies, spatialSizeUnits)
Takes
- SBMLSpecies, an SBML Species structure
- spatialSizeUnits; a string representing the spatialSizeUnits to be set
Returns
- the SBML Species structure with the new value for the spatialSizeUnits attribute
SBMLSpecies = Species_setSpeciesType(SBMLSpecies, speciesType)
Takes
- SBMLSpecies, an SBML Species structure
- speciesType; a string representing the speciesType to be set
Returns
- the SBML Species structure with the new value for the speciesType attribute
SBMLSpecies = Species_setSubstanceUnits(SBMLSpecies, substanceUnits)
Takes
- SBMLSpecies, an SBML Species structure
- substanceUnits; a string representing the substanceUnits to be set
Returns
- the SBML Species structure with the new value for the substanceUnits attribute
SBMLSpecies = Species_setUnits(SBMLSpecies, units)
Takes
- SBMLSpecies, an SBML Species structure
- units; a string representing the units to be set
Returns
- the SBML Species structure with the new value for the units attribute
SBMLSpecies = Species_unsetCharge(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the charge attribute unset
SBMLSpecies = Species_unsetCompartment(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the compartment attribute unset
SBMLSpecies = Species_unsetConversionFactor(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the conversionFactor attribute unset
SBMLSpecies = Species_unsetId(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the id attribute unset
SBMLSpecies = Species_unsetInitialAmount(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the initialAmount attribute unset
SBMLSpecies = Species_unsetInitialConcentration(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the initialConcentration attribute unset
SBMLSpecies = Species_unsetMetaid(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the metaid attribute unset
SBMLSpecies = Species_unsetName(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the name attribute unset
SBMLSpecies = Species_unsetSBOTerm(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the sboTerm attribute unset
SBMLSpecies = Species_unsetSpatialSizeUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the spatialSizeUnits attribute unset
SBMLSpecies = Species_unsetSpeciesType(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the speciesType attribute unset
SBMLSpecies = Species_unsetSubstanceUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the substanceUnits attribute unset
SBMLSpecies = Species_unsetUnits(SBMLSpecies)
Takes
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Species structure with the units attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/rule.html 0000644 0000000 0000000 00000005042 11626400656 021160 0 ustar root root MATLABSBMLSTRUCTURE_FUNCTIONS\RULE
The functions allow users to create and work with the SBML Rule structure.
Function are:
Rule = Rule_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Rule 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
formula = Rule_getFormula(SBMLRule)
Takes
- SBMLRule, an SBML Rule structure
Returns
- the value of the formula attribute
sboTerm = Rule_getSBOTerm(SBMLRule)
Takes
- SBMLRule, an SBML Rule structure
Returns
- the value of the sboTerm attribute
value = Rule_isSetFormula(SBMLRule)
Takes
- SBMLRule, an SBML Rule structure
Returns
- value =
- 1 if the formula attribute is set
- 0 otherwise
value = Rule_isSetSBOTerm(SBMLRule)
Takes
- SBMLRule, an SBML Rule structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLRule = Rule_setFormula(SBMLRule, formula)
Takes
- SBMLRule, an SBML Rule structure
- formula; a string representing the formula to be set
Returns
- the SBML Rule structure with the new value for the formula attribute
SBMLRule = Rule_setSBOTerm(SBMLRule, sboTerm)
Takes
- SBMLRule, an SBML Rule structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Rule structure with the new value for the sboTerm attribute
SBMLRule = Rule_unsetFormula(SBMLRule)
Takes
- SBMLRule, an SBML Rule structure
Returns
- the SBML Rule structure with the formula attribute unset
SBMLRule = Rule_unsetSBOTerm(SBMLRule)
Takes
- SBMLRule, an SBML Rule structure
Returns
- the SBML Rule structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/reaction.html 0000644 0000000 0000000 00000033362 11626400656 022023 0 ustar root root MATLABSBMLSTRUCTURE_FUNCTIONS\REACTION
The functions allow users to create and work with the SBML Reaction structure.
Function are:
SBMLReaction = Reaction_addModifier(SBMLReaction, SBMLModifier)
Takes
- SBMLReaction, an SBML Reaction structure
- SBMLModifier, an SBML Modifier structure
Returns
- the SBML Reaction structure with the SBML Modifier structure added
SBMLReaction = Reaction_addProduct(SBMLReaction, SBMLProduct)
Takes
- SBMLReaction, an SBML Reaction structure
- SBMLProduct, an SBML Product structure
Returns
- the SBML Reaction structure with the SBML Product structure added
SBMLReaction = Reaction_addReactant(SBMLReaction, SBMLReactant)
Takes
- SBMLReaction, an SBML Reaction structure
- SBMLReactant, an SBML Reactant structure
Returns
- the SBML Reaction structure with the SBML Reactant structure added
Reaction = Reaction_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Reaction 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
SBMLReaction = Reaction_createKineticLaw(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with a new SBML KineticLaw structure added
SBMLReaction = Reaction_createModifier(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with a new SBML ModifierSpeciesReference structure added
SBMLReaction = Reaction_createProduct(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with a new SBML SpeciesReference structure added
SBMLReaction = Reaction_createReactant(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with a new SBML SpeciesReference structure added
compartment = Reaction_getCompartment(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the value of the compartment attribute
fast = Reaction_getFast(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the value of the fast attribute
id = Reaction_getId(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the value of the id attribute
kineticLaw = Reaction_getKineticLaw(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML KineticLaw structure
modifier = Reaction_getListOfModifiers(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- an array of the modifier structures
product = Reaction_getListOfProducts(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- an array of the product structures
reactant = Reaction_getListOfReactants(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- an array of the reactant structures
metaid = Reaction_getMetaid(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the value of the metaid attribute
modifier = Reaction_getModifier(SBMLReaction, index)
Takes
- SBMLReaction, an SBML Reaction structure
- index, an integer representing the index of SBML Modifier structure
Returns
- the SBML Modifier structure at the indexed position
modifier = Reaction_getModifierById(SBMLReaction, id)
Takes
- SBMLReaction, an SBML Reaction structure
- id; a string representing the id of SBML Modifier structure
Returns
- the SBML Modifier structure that has this id
name = Reaction_getName(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the value of the name attribute
num = Reaction_getNumModifiers(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the number of SBML Modifier structures present in the Reaction
num = Reaction_getNumProducts(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the number of SBML Product structures present in the Reaction
num = Reaction_getNumReactants(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the number of SBML Reactant structures present in the Reaction
product = Reaction_getProduct(SBMLReaction, index)
Takes
- SBMLReaction, an SBML Reaction structure
- index, an integer representing the index of SBML Product structure
Returns
- the SBML Product structure at the indexed position
product = Reaction_getProductById(SBMLReaction, id)
Takes
- SBMLReaction, an SBML Reaction structure
- id; a string representing the id of SBML Product structure
Returns
- the SBML Product structure that has this id
reactant = Reaction_getReactant(SBMLReaction, index)
Takes
- SBMLReaction, an SBML Reaction structure
- index, an integer representing the index of SBML Reactant structure
Returns
- the SBML Reactant structure at the indexed position
reactant = Reaction_getReactantById(SBMLReaction, id)
Takes
- SBMLReaction, an SBML Reaction structure
- id; a string representing the id of SBML Reactant structure
Returns
- the SBML Reactant structure that has this id
reversible = Reaction_getReversible(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the value of the reversible attribute
sboTerm = Reaction_getSBOTerm(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the value of the sboTerm attribute
value = Reaction_isSetCompartment(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- value =
- 1 if the compartment attribute is set
- 0 otherwise
value = Reaction_isSetFast(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- value =
- 1 if the fast attribute is set
- 0 otherwise
value = Reaction_isSetId(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = Reaction_isSetKineticLaw(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- value =
- 1 if the kineticLaw structure is set
- 0 otherwise
value = Reaction_isSetMetaid(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Reaction_isSetName(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = Reaction_isSetReversible(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- value =
- 1 if the reversible attribute is set
- 0 otherwise
value = Reaction_isSetSBOTerm(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLReaction = Reaction_setCompartment(SBMLReaction, compartment)
Takes
- SBMLReaction, an SBML Reaction structure
- compartment; a string representing the compartment to be set
Returns
- the SBML Reaction structure with the new value for the compartment attribute
SBMLReaction = Reaction_setFast(SBMLReaction, fast)
Takes
- SBMLReaction, an SBML Reaction structure
- fast, an integer (0/1) representing the value of fast to be set
Returns
- the SBML Reaction structure with the new value for the fast attribute
SBMLReaction = Reaction_setId(SBMLReaction, id)
Takes
- SBMLReaction, an SBML Reaction structure
- id; a string representing the id to be set
Returns
- the SBML Reaction structure with the new value for the id attribute
SBMLReaction = Reaction_setKineticLaw(SBMLReaction, SBMLKineticLaw)
Takes
- SBMLReaction, an SBML Reaction structure
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML Reaction structure with the new value for the kineticLaw field
SBMLReaction = Reaction_setMetaid(SBMLReaction, metaid)
Takes
- SBMLReaction, an SBML Reaction structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Reaction structure with the new value for the metaid attribute
SBMLReaction = Reaction_setName(SBMLReaction, name)
Takes
- SBMLReaction, an SBML Reaction structure
- name; a string representing the name to be set
Returns
- the SBML Reaction structure with the new value for the name attribute
SBMLReaction = Reaction_setReversible(SBMLReaction, reversible)
Takes
- SBMLReaction, an SBML Reaction structure
- reversible, an integer (0/1) representing the value of reversible to be set
Returns
- the SBML Reaction structure with the new value for the reversible attribute
SBMLReaction = Reaction_setSBOTerm(SBMLReaction, sboTerm)
Takes
- SBMLReaction, an SBML Reaction structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Reaction structure with the new value for the sboTerm attribute
SBMLReaction = Reaction_unsetCompartment(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with the compartment attribute unset
SBMLReaction = Reaction_unsetFast(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with the fast attribute unset
SBMLReaction = Reaction_unsetId(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with the id attribute unset
SBMLReaction = Reaction_unsetKineticLaw(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with the kineticLaw field unset
SBMLReaction = Reaction_unsetMetaid(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with the metaid attribute unset
SBMLReaction = Reaction_unsetName(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with the name attribute unset
SBMLReaction = Reaction_unsetReversible(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with the reversible attribute unset
SBMLReaction = Reaction_unsetSBOTerm(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Reaction structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/rateRule.html 0000644 0000000 0000000 00000011464 11611210762 021770 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\RATERULE
The functions allow users to create and work with the SBML RateRule structure.
Function are:
RateRule = RateRule_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML RateRule 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
formula = RateRule_getFormula(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- the value of the formula attribute
metaid = RateRule_getMetaid(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- the value of the metaid attribute
sboTerm = RateRule_getSBOTerm(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- the value of the sboTerm attribute
variable = RateRule_getVariable(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- the value of the variable attribute
value = RateRule_isSetFormula(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- value =
- 1 if the formula attribute is set
- 0 otherwise
value = RateRule_isSetMetaid(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = RateRule_isSetSBOTerm(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = RateRule_isSetVariable(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- value =
- 1 if the variable attribute is set
- 0 otherwise
SBMLRateRule = RateRule_setFormula(SBMLRateRule, formula)
Takes
- SBMLRateRule, an SBML RateRule structure
- formula; a string representing the formula to be set
Returns
- the SBML RateRule structure with the new value for the formula attribute
SBMLRateRule = RateRule_setMetaid(SBMLRateRule, metaid)
Takes
- SBMLRateRule, an SBML RateRule structure
- metaid; a string representing the metaid to be set
Returns
- the SBML RateRule structure with the new value for the metaid attribute
SBMLRateRule = RateRule_setSBOTerm(SBMLRateRule, sboTerm)
Takes
- SBMLRateRule, an SBML RateRule structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML RateRule structure with the new value for the sboTerm attribute
SBMLRateRule = RateRule_setVariable(SBMLRateRule, variable)
Takes
- SBMLRateRule, an SBML RateRule structure
- variable; a string representing the variable to be set
Returns
- the SBML RateRule structure with the new value for the variable attribute
SBMLRateRule = RateRule_unsetFormula(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- the SBML RateRule structure with the formula attribute unset
SBMLRateRule = RateRule_unsetMetaid(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- the SBML RateRule structure with the metaid attribute unset
SBMLRateRule = RateRule_unsetSBOTerm(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- the SBML RateRule structure with the sboTerm attribute unset
SBMLRateRule = RateRule_unsetVariable(SBMLRateRule)
Takes
- SBMLRateRule, an SBML RateRule structure
Returns
- the SBML RateRule structure with the variable attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/priority.html 0000644 0000000 0000000 00000007416 11611210760 022066 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\PRIORITY
The functions allow users to create and work with the SBML Priority structure.
Function are:
Priority = Priority_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Priority 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
math = Priority_getMath(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- the value of the math attribute
metaid = Priority_getMetaid(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- the value of the metaid attribute
sboTerm = Priority_getSBOTerm(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- the value of the sboTerm attribute
value = Priority_isSetMath(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = Priority_isSetMetaid(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Priority_isSetSBOTerm(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLPriority = Priority_setMath(SBMLPriority, math)
Takes
- SBMLPriority, an SBML Priority structure
- math; string representing the math expression math to be set
Returns
- the SBML Priority structure with the new value for the math attribute
SBMLPriority = Priority_setMetaid(SBMLPriority, metaid)
Takes
- SBMLPriority, an SBML Priority structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Priority structure with the new value for the metaid attribute
SBMLPriority = Priority_setSBOTerm(SBMLPriority, sboTerm)
Takes
- SBMLPriority, an SBML Priority structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Priority structure with the new value for the sboTerm attribute
SBMLPriority = Priority_unsetMath(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- the SBML Priority structure with the math attribute unset
SBMLPriority = Priority_unsetMetaid(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- the SBML Priority structure with the metaid attribute unset
SBMLPriority = Priority_unsetSBOTerm(SBMLPriority)
Takes
- SBMLPriority, an SBML Priority structure
Returns
- the SBML Priority structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/parameterRule.html 0000644 0000000 0000000 00000012173 11611210760 023011 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\PARAMETERRULE
The functions allow users to create and work with the SBML ParameterRule structure.
Function are:
ParameterRule = ParameterRule_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML ParameterRule 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
formula = ParameterRule_getFormula(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- the value of the formula attribute
name = ParameterRule_getName(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- the value of the name attribute
type = ParameterRule_getType(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- the value of the type attribute
units = ParameterRule_getUnits(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- the value of the units attribute
value = ParameterRule_isSetFormula(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- value =
- 1 if the formula attribute is set
- 0 otherwise
value = ParameterRule_isSetName(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = ParameterRule_isSetType(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- value =
- 1 if the type attribute is set
- 0 otherwise
value = ParameterRule_isSetUnits(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- value =
- 1 if the units attribute is set
- 0 otherwise
SBMLParameterRule = ParameterRule_setFormula(SBMLParameterRule, formula)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
- formula; a string representing the formula to be set
Returns
- the SBML ParameterRule structure with the new value for the formula attribute
SBMLParameterRule = ParameterRule_setName(SBMLParameterRule, name)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
- name; a string representing the name to be set
Returns
- the SBML ParameterRule structure with the new value for the name attribute
SBMLParameterRule = ParameterRule_setType(SBMLParameterRule, type)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
- type; a string representing the type to be set
Returns
- the SBML ParameterRule structure with the new value for the type attribute
SBMLParameterRule = ParameterRule_setUnits(SBMLParameterRule, units)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
- units; a string representing the units to be set
Returns
- the SBML ParameterRule structure with the new value for the units attribute
SBMLParameterRule = ParameterRule_unsetFormula(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- the SBML ParameterRule structure with the formula attribute unset
SBMLParameterRule = ParameterRule_unsetName(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- the SBML ParameterRule structure with the name attribute unset
SBMLParameterRule = ParameterRule_unsetType(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- the SBML ParameterRule structure with the type attribute unset
SBMLParameterRule = ParameterRule_unsetUnits(SBMLParameterRule)
Takes
- SBMLParameterRule, an SBML ParameterRule structure
Returns
- the SBML ParameterRule structure with the units attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/parameter.html 0000644 0000000 0000000 00000030027 11703262406 022165 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\PARAMETER
The functions allow users to create and work with the SBML Parameter structure.
Function are:
Parameter = Parameter_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Parameter 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
constant = Parameter_getConstant(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the value of the constant attribute
id = Parameter_getId(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the value of the id attribute
metaid = Parameter_getMetaid(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the value of the metaid attribute
name = Parameter_getName(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the value of the name attribute
sboTerm = Parameter_getSBOTerm(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the value of the sboTerm attribute
units = Parameter_getUnits(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the value of the units attribute
value = Parameter_getValue(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the value of the value attribute
y = Parameter_isAssignedByRateRule(SBMLParameter, SBMLRules)
Takes
- SBMLParameter, an SBML Parameter structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- the index of the rateRule used to assigned value to the Parameter
- 0 if the Parameter 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) 2009-2012 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 = Parameter_isAssignedByRule(SBMLParameter, SBMLRules)
Takes
- SBMLParameter, an SBML Parameter structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- the index of the assignmentRule used to assigned value to the Parameter
- 0 if the Parameter 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) 2009-2012 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 = Parameter_isInAlgebraicRule(SBMLParameter, SBMLRules)
Takes
- SBMLParameter, an SBML Parameter structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- an array of the indices of any algebraicRules the id of the Parameter appears in
- 0 if the Parameter 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) 2009-2012 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 = Parameter_isSetId(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = Parameter_isSetMetaid(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Parameter_isSetName(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = Parameter_isSetSBOTerm(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = Parameter_isSetUnits(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- value =
- 1 if the units attribute is set
- 0 otherwise
value = Parameter_isSetValue(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- value =
- 1 if the value attribute is set
- 0 otherwise
SBMLParameter = Parameter_setConstant(SBMLParameter, constant)
Takes
- SBMLParameter, an SBML Parameter structure
- constant, an integer (0/1) representing the value of constant to be set
Returns
- the SBML Parameter structure with the new value for the constant attribute
SBMLParameter = Parameter_setId(SBMLParameter, id)
Takes
- SBMLParameter, an SBML Parameter structure
- id; a string representing the id to be set
Returns
- the SBML Parameter structure with the new value for the id attribute
SBMLParameter = Parameter_setMetaid(SBMLParameter, metaid)
Takes
- SBMLParameter, an SBML Parameter structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Parameter structure with the new value for the metaid attribute
SBMLParameter = Parameter_setName(SBMLParameter, name)
Takes
- SBMLParameter, an SBML Parameter structure
- name; a string representing the name to be set
Returns
- the SBML Parameter structure with the new value for the name attribute
SBMLParameter = Parameter_setSBOTerm(SBMLParameter, sboTerm)
Takes
- SBMLParameter, an SBML Parameter structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Parameter structure with the new value for the sboTerm attribute
SBMLParameter = Parameter_setUnits(SBMLParameter, units)
Takes
- SBMLParameter, an SBML Parameter structure
- units; a string representing the units to be set
Returns
- the SBML Parameter structure with the new value for the units attribute
SBMLParameter = Parameter_setValue(SBMLParameter, value)
Takes
- SBMLParameter, an SBML Parameter structure
- value; number representing the value of value to be set
Returns
- the SBML Parameter structure with the new value for the value attribute
SBMLParameter = Parameter_unsetId(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the SBML Parameter structure with the id attribute unset
SBMLParameter = Parameter_unsetMetaid(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the SBML Parameter structure with the metaid attribute unset
SBMLParameter = Parameter_unsetName(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the SBML Parameter structure with the name attribute unset
SBMLParameter = Parameter_unsetSBOTerm(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the SBML Parameter structure with the sboTerm attribute unset
SBMLParameter = Parameter_unsetUnits(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the SBML Parameter structure with the units attribute unset
SBMLParameter = Parameter_unsetValue(SBMLParameter)
Takes
- SBMLParameter, an SBML Parameter structure
Returns
- the SBML Parameter structure with the value attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/modifierSpeciesReference.html 0000644 0000000 0000000 00000016534 11611210654 025141 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\MODIFIERSPECIESREFERENCE
The functions allow users to create and work with the SBML ModifierSpeciesReference structure.
Function are:
ModifierSpeciesReference = ModifierSpeciesReference_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML ModifierSpeciesReference 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
id = ModifierSpeciesReference_getId(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the value of the id attribute
metaid = ModifierSpeciesReference_getMetaid(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the value of the metaid attribute
name = ModifierSpeciesReference_getName(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the value of the name attribute
sboTerm = ModifierSpeciesReference_getSBOTerm(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the value of the sboTerm attribute
species = ModifierSpeciesReference_getSpecies(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the value of the species attribute
value = ModifierSpeciesReference_isSetId(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = ModifierSpeciesReference_isSetMetaid(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = ModifierSpeciesReference_isSetName(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = ModifierSpeciesReference_isSetSBOTerm(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = ModifierSpeciesReference_isSetSpecies(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- value =
- 1 if the species attribute is set
- 0 otherwise
SBMLModifierSpeciesReference = ModifierSpeciesReference_setId(SBMLModifierSpeciesReference, id)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
- id; a string representing the id to be set
Returns
- the SBML ModifierSpeciesReference structure with the new value for the id attribute
SBMLModifierSpeciesReference = ModifierSpeciesReference_setMetaid(SBMLModifierSpeciesReference, metaid)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
- metaid; a string representing the metaid to be set
Returns
- the SBML ModifierSpeciesReference structure with the new value for the metaid attribute
SBMLModifierSpeciesReference = ModifierSpeciesReference_setName(SBMLModifierSpeciesReference, name)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
- name; a string representing the name to be set
Returns
- the SBML ModifierSpeciesReference structure with the new value for the name attribute
SBMLModifierSpeciesReference = ModifierSpeciesReference_setSBOTerm(SBMLModifierSpeciesReference, sboTerm)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML ModifierSpeciesReference structure with the new value for the sboTerm attribute
SBMLModifierSpeciesReference = ModifierSpeciesReference_setSpecies(SBMLModifierSpeciesReference, species)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
- species; a string representing the species to be set
Returns
- the SBML ModifierSpeciesReference structure with the new value for the species attribute
SBMLModifierSpeciesReference = ModifierSpeciesReference_unsetId(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the SBML ModifierSpeciesReference structure with the id attribute unset
SBMLModifierSpeciesReference = ModifierSpeciesReference_unsetMetaid(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the SBML ModifierSpeciesReference structure with the metaid attribute unset
SBMLModifierSpeciesReference = ModifierSpeciesReference_unsetName(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the SBML ModifierSpeciesReference structure with the name attribute unset
SBMLModifierSpeciesReference = ModifierSpeciesReference_unsetSBOTerm(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the SBML ModifierSpeciesReference structure with the sboTerm attribute unset
SBMLModifierSpeciesReference = ModifierSpeciesReference_unsetSpecies(SBMLModifierSpeciesReference)
Takes
- SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
Returns
- the SBML ModifierSpeciesReference structure with the species attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/model.html 0000644 0000000 0000000 00000102365 11660457476 021331 0 ustar root root MATLAB_SBML_STRUCTURE_FUNCTIONS\MODEL
The functions allow users to create and work with the SBML Model structure.
Function are:
SBMLModel = Model_addCompartment(SBMLModel, SBMLCompartment)
Takes
- SBMLModel, an SBML Model structure
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Model structure with the SBML Compartment structure added
SBMLModel = Model_addCompartmentType(SBMLModel, SBMLCompartmentType)
Takes
- SBMLModel, an SBML Model structure
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the SBML Model structure with the SBML CompartmentType structure added
SBMLModel = Model_addConstraint(SBMLModel, SBMLConstraint)
Takes
- SBMLModel, an SBML Model structure
- SBMLConstraint, an SBML Constraint structure
Returns
- the SBML Model structure with the SBML Constraint structure added
SBMLModel = Model_addEvent(SBMLModel, SBMLEvent)
Takes
- SBMLModel, an SBML Model structure
- SBMLEvent, an SBML Event structure
Returns
- the SBML Model structure with the SBML Event structure added
SBMLModel = Model_addFunctionDefinition(SBMLModel, SBMLFunctionDefinition)
Takes
- SBMLModel, an SBML Model structure
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the SBML Model structure with the SBML FunctionDefinition structure added
SBMLModel = Model_addInitialAssignment(SBMLModel, SBMLInitialAssignment)
Takes
- SBMLModel, an SBML Model structure
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the SBML Model structure with the SBML InitialAssignment structure added
SBMLModel = Model_addParameter(SBMLModel, SBMLParameter)
Takes
- SBMLModel, an SBML Model structure
- SBMLParameter, an SBML Parameter structure
Returns
- the SBML Model structure with the SBML Parameter structure added
SBMLModel = Model_addReaction(SBMLModel, SBMLReaction)
Takes
- SBMLModel, an SBML Model structure
- SBMLReaction, an SBML Reaction structure
Returns
- the SBML Model structure with the SBML Reaction structure added
SBMLModel = Model_addRule(SBMLModel, SBMLRule)
Takes
- SBMLModel, an SBML Model structure
- SBMLRule, an SBML Rule structure
Returns
- the SBML Model structure with the SBML Rule structure added
SBMLModel = Model_addSpecies(SBMLModel, SBMLSpecies)
Takes
- SBMLModel, an SBML Model structure
- SBMLSpecies, an SBML Species structure
Returns
- the SBML Model structure with the SBML Species structure added
SBMLModel = Model_addSpeciesType(SBMLModel, SBMLSpeciesType)
Takes
- SBMLModel, an SBML Model structure
- SBMLSpeciesType, an SBML SpeciesType structure
Returns
- the SBML Model structure with the SBML SpeciesType structure added
SBMLModel = Model_addUnitDefinition(SBMLModel, SBMLUnitDefinition)
Takes
- SBMLModel, an SBML Model structure
- SBMLUnitDefinition, an SBML UnitDefinition structure
Returns
- the SBML Model structure with the SBML UnitDefinition structure added
Model = Model_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Model 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
SBMLModel = Model_createCompartment(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML Compartment structure added
SBMLModel = Model_createCompartmentType(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML CompartmentType structure added
SBMLModel = Model_createConstraint(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML Constraint structure added
SBMLModel = Model_createEvent(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML Event structure added
SBMLModel = Model_createFunctionDefinition(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML FunctionDefinition structure added
SBMLModel = Model_createInitialAssignment(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML InitialAssignment structure added
SBMLModel = Model_createParameter(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML Parameter structure added
SBMLModel = Model_createReaction(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML Reaction structure added
SBMLModel = Model_createRule(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML Rule structure added
SBMLModel = Model_createSpecies(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML Species structure added
SBMLModel = Model_createSpeciesType(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML SpeciesType structure added
SBMLModel = Model_createUnitDefinition(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the SBML UnitDefinition structure added
areaUnits = Model_getAreaUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the areaUnits attribute
assignmentRule = Model_getAssignmentRuleByVariable(SBMLModel, variable)
Takes
- SBMLModel, an SBML Model structure
- variable; a string representing the variable of SBML AssignmentRule structure
Returns
- the SBML AssignmentRule structure that has this variable
compartment = Model_getCompartment(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML Compartment structure
Returns
- the SBML Compartment structure at the indexed position
compartment = Model_getCompartmentById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML Compartment structure
Returns
- the SBML Compartment structure that has this id
compartmentType = Model_getCompartmentType(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML CompartmentType structure
Returns
- the SBML CompartmentType structure at the indexed position
compartmentType = Model_getCompartmentTypeById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML CompartmentType structure
Returns
- the SBML CompartmentType structure that has this id
constraint = Model_getConstraint(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML Constraint structure
Returns
- the SBML Constraint structure at the indexed position
conversionFactor = Model_getConversionFactor(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the conversionFactor attribute
event = Model_getEvent(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML Event structure
Returns
- the SBML Event structure at the indexed position
event = Model_getEventById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML Event structure
Returns
- the SBML Event structure that has this id
extentUnits = Model_getExtentUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the extentUnits attribute
functionDefinition = Model_getFunctionDefinition(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML FunctionDefinition structure
Returns
- the SBML FunctionDefinition structure at the indexed position
functionDefinition = Model_getFunctionDefinitionById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML FunctionDefinition structure
Returns
- the SBML FunctionDefinition structure that has this id
functionIds = Model_getFunctionIds(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the functionIds attribute
id = Model_getId(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the id attribute
initialAssignment = Model_getInitialAssignment(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML InitialAssignment structure
Returns
- the SBML InitialAssignment structure at the indexed position
initialAssignment = Model_getInitialAssignmentBySymbol(SBMLModel, symbol)
Takes
- SBMLModel, an SBML Model structure
- symbol; a string representing the symbol of SBML InitialAssignment structure
Returns
- the SBML InitialAssignment structure that has this symbol
lengthUnits = Model_getLengthUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the lengthUnits attribute
algebraicRule = Model_getListOfAlgebraicRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the algebraicRule structures
assignmentRule = Model_getListOfAssignmentRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the assignmentRule structures
listOf = Model_getListOfByTypecode(SBMLModel, typecode)
Takes
- SBMLModel, an SBML Model structure
- typecode; a string representing the typecode of SBML ListOf structure
Returns
- the SBML ListOf structure that has this typecode
compartmentType = Model_getListOfCompartmentTypes(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the compartmentType structures
compartment = Model_getListOfCompartments(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the compartment structures
constraint = Model_getListOfConstraints(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the constraint structures
event = Model_getListOfEvents(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the event structures
functionDefinition = Model_getListOfFunctionDefinitions(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the functionDefinition structures
initialAssignment = Model_getListOfInitialAssignments(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the initialAssignment structures
parameter = Model_getListOfParameters(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the parameter structures
rateRule = Model_getListOfRateRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the rateRule structures
reaction = Model_getListOfReactions(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the reaction structures
rule = Model_getListOfRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the rule structures
species = Model_getListOfSpecies(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the species structures
speciesType = Model_getListOfSpeciesTypes(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the speciesType structures
species = Model_getListOfSpeciess(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the species structures
unitDefinition = Model_getListOfUnitDefinitions(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of the unitDefinition structures
metaid = Model_getMetaid(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the metaid attribute
name = Model_getName(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the name attribute
num = Model_getNumAlgebraicRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML AlgebraicRule structures present in the Model
num = Model_getNumAssignmentRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML AssignmentRule structures present in the Model
num = Model_getNumCompartmentTypes(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML CompartmentType structures present in the Model
num = Model_getNumCompartments(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML Compartment structures present in the Model
num = Model_getNumConstraints(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML Constraint structures present in the Model
num = Model_getNumEvents(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML Event structures present in the Model
num = Model_getNumFunctionDefinitions(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML FunctionDefinition structures present in the Model
num = Model_getNumInitialAssignments(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML InitialAssignment structures present in the Model
num = Model_getNumParameters(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML Parameter structures present in the Model
num = Model_getNumRateRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML RateRule structures present in the Model
num = Model_getNumReactions(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML Reaction structures present in the Model
num = Model_getNumRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML Rule structures present in the Model
num = Model_getNumSpecies(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML Species structures present in the Model
num = Model_getNumSpeciesTypes(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML SpeciesType structures present in the Model
num = Model_getNumSpeciess(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML Species structures present in the Model
num = Model_getNumUnitDefinitions(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the number of SBML UnitDefinition structures present in the Model
parameter = Model_getParameter(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML Parameter structure
Returns
- the SBML Parameter structure at the indexed position
parameter = Model_getParameterById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML Parameter structure
Returns
- the SBML Parameter structure that has this id
rateRule = Model_getRateRuleByVariable(SBMLModel, variable)
Takes
- SBMLModel, an SBML Model structure
- variable; a string representing the variable of SBML RateRule structure
Returns
- the SBML RateRule structure that has this variable
reaction = Model_getReaction(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML Reaction structure
Returns
- the SBML Reaction structure at the indexed position
reaction = Model_getReactionById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML Reaction structure
Returns
- the SBML Reaction structure that has this id
rule = Model_getRule(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML Rule structure
Returns
- the SBML Rule structure at the indexed position
sBMLlevel = ModelgetSBML_level(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the sBML_level attribute
sBMLversion = ModelgetSBML_version(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the sBML_version attribute
sboTerm = Model_getSBOTerm(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the sboTerm attribute
species = Model_getSpecies(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML Species structure
Returns
- the SBML Species structure at the indexed position
species = Model_getSpeciesById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML Species structure
Returns
- the SBML Species structure that has this id
speciesType = Model_getSpeciesType(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML SpeciesType structure
Returns
- the SBML SpeciesType structure at the indexed position
speciesType = Model_getSpeciesTypeById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML SpeciesType structure
Returns
- the SBML SpeciesType structure that has this id
substanceUnits = Model_getSubstanceUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the substanceUnits attribute
timeUnits = Model_getTimeUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the timeUnits attribute
unitDefinition = Model_getUnitDefinition(SBMLModel, index)
Takes
- SBMLModel, an SBML Model structure
- index, an integer representing the index of SBML UnitDefinition structure
Returns
- the SBML UnitDefinition structure at the indexed position
unitDefinition = Model_getUnitDefinitionById(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id of SBML UnitDefinition structure
Returns
- the SBML UnitDefinition structure that has this id
volumeUnits = Model_getVolumeUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the value of the volumeUnits attribute
value = Model_isSetAreaUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the areaUnits attribute is set
- 0 otherwise
value = Model_isSetConversionFactor(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the conversionFactor attribute is set
- 0 otherwise
value = Model_isSetExtentUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the extentUnits attribute is set
- 0 otherwise
value = Model_isSetId(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = Model_isSetLengthUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the lengthUnits attribute is set
- 0 otherwise
value = Model_isSetMetaid(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Model_isSetName(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = ModelisSetSBMLlevel(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the sBML_level attribute is set
- 0 otherwise
value = ModelisSetSBMLversion(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the sBML_version attribute is set
- 0 otherwise
value = Model_isSetSBOTerm(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = Model_isSetSubstanceUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the substanceUnits attribute is set
- 0 otherwise
value = Model_isSetTimeUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the timeUnits attribute is set
- 0 otherwise
value = Model_isSetVolumeUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- value =
- 1 if the volumeUnits attribute is set
- 0 otherwise
SBMLModel = Model_setAreaUnits(SBMLModel, areaUnits)
Takes
- SBMLModel, an SBML Model structure
- areaUnits; a string representing the areaUnits to be set
Returns
- the SBML Model structure with the new value for the areaUnits attribute
SBMLModel = Model_setConversionFactor(SBMLModel, conversionFactor)
Takes
- SBMLModel, an SBML Model structure
- conversionFactor; a string representing the conversionFactor to be set
Returns
- the SBML Model structure with the new value for the conversionFactor attribute
SBMLModel = Model_setExtentUnits(SBMLModel, extentUnits)
Takes
- SBMLModel, an SBML Model structure
- extentUnits; a string representing the extentUnits to be set
Returns
- the SBML Model structure with the new value for the extentUnits attribute
SBMLModel = Model_setId(SBMLModel, id)
Takes
- SBMLModel, an SBML Model structure
- id; a string representing the id to be set
Returns
- the SBML Model structure with the new value for the id attribute
SBMLModel = Model_setLengthUnits(SBMLModel, lengthUnits)
Takes
- SBMLModel, an SBML Model structure
- lengthUnits; a string representing the lengthUnits to be set
Returns
- the SBML Model structure with the new value for the lengthUnits attribute
SBMLModel = Model_setMetaid(SBMLModel, metaid)
Takes
- SBMLModel, an SBML Model structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Model structure with the new value for the metaid attribute
SBMLModel = Model_setName(SBMLModel, name)
Takes
- SBMLModel, an SBML Model structure
- name; a string representing the name to be set
Returns
- the SBML Model structure with the new value for the name attribute
SBMLModel = Model_setSBOTerm(SBMLModel, sboTerm)
Takes
- SBMLModel, an SBML Model structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Model structure with the new value for the sboTerm attribute
SBMLModel = Model_setSubstanceUnits(SBMLModel, substanceUnits)
Takes
- SBMLModel, an SBML Model structure
- substanceUnits; a string representing the substanceUnits to be set
Returns
- the SBML Model structure with the new value for the substanceUnits attribute
SBMLModel = Model_setTimeUnits(SBMLModel, timeUnits)
Takes
- SBMLModel, an SBML Model structure
- timeUnits; a string representing the timeUnits to be set
Returns
- the SBML Model structure with the new value for the timeUnits attribute
SBMLModel = Model_setVolumeUnits(SBMLModel, volumeUnits)
Takes
- SBMLModel, an SBML Model structure
- volumeUnits; a string representing the volumeUnits to be set
Returns
- the SBML Model structure with the new value for the volumeUnits attribute
SBMLModel = Model_unsetAreaUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the areaUnits attribute unset
SBMLModel = Model_unsetConversionFactor(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the conversionFactor attribute unset
SBMLModel = Model_unsetExtentUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the extentUnits attribute unset
SBMLModel = Model_unsetId(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the id attribute unset
SBMLModel = Model_unsetLengthUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the lengthUnits attribute unset
SBMLModel = Model_unsetMetaid(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the metaid attribute unset
SBMLModel = Model_unsetName(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the name attribute unset
SBMLModel = Model_unsetSBOTerm(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the sboTerm attribute unset
SBMLModel = Model_unsetSubstanceUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the substanceUnits attribute unset
SBMLModel = Model_unsetTimeUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the timeUnits attribute unset
SBMLModel = Model_unsetVolumeUnits(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the SBML Model structure with the volumeUnits attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/localParameter.html 0000644 0000000 0000000 00000016625 11611210654 023144 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\LOCALPARAMETER
The functions allow users to create and work with the SBML LocalParameter structure.
Function are:
LocalParameter = LocalParameter_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML LocalParameter 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
id = LocalParameter_getId(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the value of the id attribute
metaid = LocalParameter_getMetaid(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the value of the metaid attribute
name = LocalParameter_getName(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the value of the name attribute
sboTerm = LocalParameter_getSBOTerm(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the value of the sboTerm attribute
units = LocalParameter_getUnits(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the value of the units attribute
value = LocalParameter_getValue(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the value of the value attribute
value = LocalParameter_isSetId(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = LocalParameter_isSetMetaid(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = LocalParameter_isSetName(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = LocalParameter_isSetSBOTerm(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = LocalParameter_isSetUnits(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- value =
- 1 if the units attribute is set
- 0 otherwise
value = LocalParameter_isSetValue(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- value =
- 1 if the value attribute is set
- 0 otherwise
SBMLLocalParameter = LocalParameter_setId(SBMLLocalParameter, id)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
- id; a string representing the id to be set
Returns
- the SBML LocalParameter structure with the new value for the id attribute
SBMLLocalParameter = LocalParameter_setMetaid(SBMLLocalParameter, metaid)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
- metaid; a string representing the metaid to be set
Returns
- the SBML LocalParameter structure with the new value for the metaid attribute
SBMLLocalParameter = LocalParameter_setName(SBMLLocalParameter, name)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
- name; a string representing the name to be set
Returns
- the SBML LocalParameter structure with the new value for the name attribute
SBMLLocalParameter = LocalParameter_setSBOTerm(SBMLLocalParameter, sboTerm)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML LocalParameter structure with the new value for the sboTerm attribute
SBMLLocalParameter = LocalParameter_setUnits(SBMLLocalParameter, units)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
- units; a string representing the units to be set
Returns
- the SBML LocalParameter structure with the new value for the units attribute
SBMLLocalParameter = LocalParameter_setValue(SBMLLocalParameter, value)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
- value; number representing the value of value to be set
Returns
- the SBML LocalParameter structure with the new value for the value attribute
SBMLLocalParameter = LocalParameter_unsetId(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the SBML LocalParameter structure with the id attribute unset
SBMLLocalParameter = LocalParameter_unsetMetaid(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the SBML LocalParameter structure with the metaid attribute unset
SBMLLocalParameter = LocalParameter_unsetName(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the SBML LocalParameter structure with the name attribute unset
SBMLLocalParameter = LocalParameter_unsetSBOTerm(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the SBML LocalParameter structure with the sboTerm attribute unset
SBMLLocalParameter = LocalParameter_unsetUnits(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the SBML LocalParameter structure with the units attribute unset
SBMLLocalParameter = LocalParameter_unsetValue(SBMLLocalParameter)
Takes
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the SBML LocalParameter structure with the value attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/kineticLaw.html 0000644 0000000 0000000 00000025126 11626400656 022310 0 ustar root root MATLABSBMLSTRUCTURE_FUNCTIONS\KINETICLAW
The functions allow users to create and work with the SBML KineticLaw structure.
Function are:
SBMLKineticLaw = KineticLaw_addLocalParameter(SBMLKineticLaw, SBMLLocalParameter)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- SBMLLocalParameter, an SBML LocalParameter structure
Returns
- the SBML KineticLaw structure with the SBML LocalParameter structure added
SBMLKineticLaw = KineticLaw_addParameter(SBMLKineticLaw, SBMLParameter)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- SBMLParameter, an SBML Parameter structure
Returns
- the SBML KineticLaw structure with the SBML Parameter structure added
KineticLaw = KineticLaw_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML KineticLaw 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
SBMLKineticLaw = KineticLaw_createLocalParameter(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML KineticLaw structure with a new SBML LocalParameter structure added
SBMLKineticLaw = KineticLaw_createParameter(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML KineticLaw structure with a new SBML Parameter structure added
formula = KineticLaw_getFormula(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the value of the formula attribute
localParameter = KineticLaw_getListOfLocalParameters(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- an array of the localParameter structures
parameter = KineticLaw_getListOfParameters(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- an array of the parameter structures
localParameter = KineticLaw_getLocalParameter(SBMLKineticLaw, index)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- index, an integer representing the index of SBML LocalParameter structure
Returns
- the SBML LocalParameter structure at the indexed position
math = KineticLaw_getMath(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the value of the math attribute
metaid = KineticLaw_getMetaid(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the value of the metaid attribute
num = KineticLaw_getNumLocalParameters(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the number of SBML LocalParameter structures present in the KineticLaw
num = KineticLaw_getNumParameters(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the number of SBML Parameter structures present in the KineticLaw
parameter = KineticLaw_getParameter(SBMLKineticLaw, index)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- index, an integer representing the index of SBML Parameter structure
Returns
- the SBML Parameter structure at the indexed position
sboTerm = KineticLaw_getSBOTerm(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the value of the sboTerm attribute
substanceUnits = KineticLaw_getSubstanceUnits(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the value of the substanceUnits attribute
timeUnits = KineticLaw_getTimeUnits(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the value of the timeUnits attribute
value = KineticLaw_isSetFormula(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- value =
- 1 if the formula attribute is set
- 0 otherwise
value = KineticLaw_isSetMath(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = KineticLaw_isSetMetaid(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = KineticLaw_isSetSBOTerm(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = KineticLaw_isSetSubstanceUnits(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- value =
- 1 if the substanceUnits attribute is set
- 0 otherwise
value = KineticLaw_isSetTimeUnits(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- value =
- 1 if the timeUnits attribute is set
- 0 otherwise
SBMLKineticLaw = KineticLaw_setFormula(SBMLKineticLaw, formula)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- formula; a string representing the formula to be set
Returns
- the SBML KineticLaw structure with the new value for the formula attribute
SBMLKineticLaw = KineticLaw_setFormulaFromMath(SBMLKineticLaw, formulaFromMath)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- formulaFromMath; a string representing the formulaFromMath to be set
Returns
- the SBML KineticLaw structure with the new value for the formulaFromMath attribute
SBMLKineticLaw = KineticLaw_setMath(SBMLKineticLaw, math)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- math; string representing the math expression math to be set
Returns
- the SBML KineticLaw structure with the new value for the math attribute
SBMLKineticLaw = KineticLaw_setMathFromFormula(SBMLKineticLaw, mathFromFormula)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- mathFromFormula; string representing the math expression mathFromFormula to be set
Returns
- the SBML KineticLaw structure with the new value for the mathFromFormula attribute
SBMLKineticLaw = KineticLaw_setMetaid(SBMLKineticLaw, metaid)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- metaid; a string representing the metaid to be set
Returns
- the SBML KineticLaw structure with the new value for the metaid attribute
SBMLKineticLaw = KineticLaw_setSBOTerm(SBMLKineticLaw, sboTerm)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML KineticLaw structure with the new value for the sboTerm attribute
SBMLKineticLaw = KineticLaw_setSubstanceUnits(SBMLKineticLaw, substanceUnits)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- substanceUnits; a string representing the substanceUnits to be set
Returns
- the SBML KineticLaw structure with the new value for the substanceUnits attribute
SBMLKineticLaw = KineticLaw_setTimeUnits(SBMLKineticLaw, timeUnits)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
- timeUnits; a string representing the timeUnits to be set
Returns
- the SBML KineticLaw structure with the new value for the timeUnits attribute
SBMLKineticLaw = KineticLaw_unsetFormula(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML KineticLaw structure with the formula attribute unset
SBMLKineticLaw = KineticLaw_unsetMath(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML KineticLaw structure with the math attribute unset
SBMLKineticLaw = KineticLaw_unsetMetaid(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML KineticLaw structure with the metaid attribute unset
SBMLKineticLaw = KineticLaw_unsetSBOTerm(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML KineticLaw structure with the sboTerm attribute unset
SBMLKineticLaw = KineticLaw_unsetSubstanceUnits(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML KineticLaw structure with the substanceUnits attribute unset
SBMLKineticLaw = KineticLaw_unsetTimeUnits(SBMLKineticLaw)
Takes
- SBMLKineticLaw, an SBML KineticLaw structure
Returns
- the SBML KineticLaw structure with the timeUnits attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/initialAssignment.html 0000644 0000000 0000000 00000013003 11611210654 023656 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\INITIALASSIGNMENT
The functions allow users to create and work with the SBML InitialAssignment structure.
Function are:
InitialAssignment = InitialAssignment_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML InitialAssignment 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
math = InitialAssignment_getMath(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the value of the math attribute
metaid = InitialAssignment_getMetaid(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the value of the metaid attribute
sboTerm = InitialAssignment_getSBOTerm(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the value of the sboTerm attribute
symbol = InitialAssignment_getSymbol(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the value of the symbol attribute
value = InitialAssignment_isSetMath(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = InitialAssignment_isSetMetaid(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = InitialAssignment_isSetSBOTerm(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = InitialAssignment_isSetSymbol(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- value =
- 1 if the symbol attribute is set
- 0 otherwise
SBMLInitialAssignment = InitialAssignment_setMath(SBMLInitialAssignment, math)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
- math; string representing the math expression math to be set
Returns
- the SBML InitialAssignment structure with the new value for the math attribute
SBMLInitialAssignment = InitialAssignment_setMetaid(SBMLInitialAssignment, metaid)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
- metaid; a string representing the metaid to be set
Returns
- the SBML InitialAssignment structure with the new value for the metaid attribute
SBMLInitialAssignment = InitialAssignment_setSBOTerm(SBMLInitialAssignment, sboTerm)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML InitialAssignment structure with the new value for the sboTerm attribute
SBMLInitialAssignment = InitialAssignment_setSymbol(SBMLInitialAssignment, symbol)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
- symbol; a string representing the symbol to be set
Returns
- the SBML InitialAssignment structure with the new value for the symbol attribute
SBMLInitialAssignment = InitialAssignment_unsetMath(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the SBML InitialAssignment structure with the math attribute unset
SBMLInitialAssignment = InitialAssignment_unsetMetaid(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the SBML InitialAssignment structure with the metaid attribute unset
SBMLInitialAssignment = InitialAssignment_unsetSBOTerm(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the SBML InitialAssignment structure with the sboTerm attribute unset
SBMLInitialAssignment = InitialAssignment_unsetSymbol(SBMLInitialAssignment)
Takes
- SBMLInitialAssignment, an SBML InitialAssignment structure
Returns
- the SBML InitialAssignment structure with the symbol attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/functionDefinition.html 0000644 0000000 0000000 00000015320 11611210654 024036 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\FUNCTIONDEFINITION
The functions allow users to create and work with the SBML FunctionDefinition structure.
Function are:
FunctionDefinition = FunctionDefinition_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML FunctionDefinition 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
id = FunctionDefinition_getId(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the value of the id attribute
math = FunctionDefinition_getMath(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the value of the math attribute
metaid = FunctionDefinition_getMetaid(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the value of the metaid attribute
name = FunctionDefinition_getName(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the value of the name attribute
sboTerm = FunctionDefinition_getSBOTerm(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the value of the sboTerm attribute
value = FunctionDefinition_isSetId(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = FunctionDefinition_isSetMath(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = FunctionDefinition_isSetMetaid(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = FunctionDefinition_isSetName(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = FunctionDefinition_isSetSBOTerm(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLFunctionDefinition = FunctionDefinition_setId(SBMLFunctionDefinition, id)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
- id; a string representing the id to be set
Returns
- the SBML FunctionDefinition structure with the new value for the id attribute
SBMLFunctionDefinition = FunctionDefinition_setMath(SBMLFunctionDefinition, math)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
- math; string representing the math expression math to be set
Returns
- the SBML FunctionDefinition structure with the new value for the math attribute
SBMLFunctionDefinition = FunctionDefinition_setMetaid(SBMLFunctionDefinition, metaid)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
- metaid; a string representing the metaid to be set
Returns
- the SBML FunctionDefinition structure with the new value for the metaid attribute
SBMLFunctionDefinition = FunctionDefinition_setName(SBMLFunctionDefinition, name)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
- name; a string representing the name to be set
Returns
- the SBML FunctionDefinition structure with the new value for the name attribute
SBMLFunctionDefinition = FunctionDefinition_setSBOTerm(SBMLFunctionDefinition, sboTerm)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML FunctionDefinition structure with the new value for the sboTerm attribute
SBMLFunctionDefinition = FunctionDefinition_unsetId(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the SBML FunctionDefinition structure with the id attribute unset
SBMLFunctionDefinition = FunctionDefinition_unsetMath(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the SBML FunctionDefinition structure with the math attribute unset
SBMLFunctionDefinition = FunctionDefinition_unsetMetaid(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the SBML FunctionDefinition structure with the metaid attribute unset
SBMLFunctionDefinition = FunctionDefinition_unsetName(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the SBML FunctionDefinition structure with the name attribute unset
SBMLFunctionDefinition = FunctionDefinition_unsetSBOTerm(SBMLFunctionDefinition)
Takes
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- the SBML FunctionDefinition structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/eventAssignment.html 0000644 0000000 0000000 00000012561 11611210654 023356 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\EVENTASSIGNMENT
The functions allow users to create and work with the SBML EventAssignment structure.
Function are:
EventAssignment = EventAssignment_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML EventAssignment 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
math = EventAssignment_getMath(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the value of the math attribute
metaid = EventAssignment_getMetaid(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the value of the metaid attribute
sboTerm = EventAssignment_getSBOTerm(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the value of the sboTerm attribute
variable = EventAssignment_getVariable(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the value of the variable attribute
value = EventAssignment_isSetMath(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = EventAssignment_isSetMetaid(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = EventAssignment_isSetSBOTerm(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = EventAssignment_isSetVariable(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- value =
- 1 if the variable attribute is set
- 0 otherwise
SBMLEventAssignment = EventAssignment_setMath(SBMLEventAssignment, math)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
- math; string representing the math expression math to be set
Returns
- the SBML EventAssignment structure with the new value for the math attribute
SBMLEventAssignment = EventAssignment_setMetaid(SBMLEventAssignment, metaid)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
- metaid; a string representing the metaid to be set
Returns
- the SBML EventAssignment structure with the new value for the metaid attribute
SBMLEventAssignment = EventAssignment_setSBOTerm(SBMLEventAssignment, sboTerm)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML EventAssignment structure with the new value for the sboTerm attribute
SBMLEventAssignment = EventAssignment_setVariable(SBMLEventAssignment, variable)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
- variable; a string representing the variable to be set
Returns
- the SBML EventAssignment structure with the new value for the variable attribute
SBMLEventAssignment = EventAssignment_unsetMath(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the SBML EventAssignment structure with the math attribute unset
SBMLEventAssignment = EventAssignment_unsetMetaid(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the SBML EventAssignment structure with the metaid attribute unset
SBMLEventAssignment = EventAssignment_unsetSBOTerm(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the SBML EventAssignment structure with the sboTerm attribute unset
SBMLEventAssignment = EventAssignment_unsetVariable(SBMLEventAssignment)
Takes
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the SBML EventAssignment structure with the variable attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/event.html 0000644 0000000 0000000 00000025346 11626400656 021343 0 ustar root root MATLABSBMLSTRUCTURE_FUNCTIONS\EVENT
The functions allow users to create and work with the SBML Event structure.
Function are:
SBMLEvent = Event_addEventAssignment(SBMLEvent, SBMLEventAssignment)
Takes
- SBMLEvent, an SBML Event structure
- SBMLEventAssignment, an SBML EventAssignment structure
Returns
- the SBML Event structure with the SBML EventAssignment structure added
Event = Event_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Event 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
SBMLEvent = Event_createDelay(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with a new SBML Delay structure added
SBMLEvent = Event_acreateEventAssignment(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with a new SBML EventAssignment structure added
SBMLEvent = Event_createPriority(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with a new SBML Priority structure added
SBMLEvent = Event_createTrigger(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with a new SBML Trigger structure added
delay = Event_getDelay(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Delay structure
eventAssignment = Event_getEventAssignment(SBMLEvent, index)
Takes
- SBMLEvent, an SBML Event structure
- index, an integer representing the index of SBML EventAssignment structure
Returns
- the SBML EventAssignment structure at the indexed position
id = Event_getId(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the value of the id attribute
eventAssignment = Event_getListOfEventAssignments(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- an array of the eventAssignment structures
metaid = Event_getMetaid(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the value of the metaid attribute
name = Event_getName(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the value of the name attribute
num = Event_getNumEventAssignments(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the number of SBML EventAssignment structures present in the Event
priority = Event_getPriority(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Priority structure
sboTerm = Event_getSBOTerm(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the value of the sboTerm attribute
timeUnits = Event_getTimeUnits(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the value of the timeUnits attribute
trigger = Event_getTrigger(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Trigger structure
useValuesFromTriggerTime = Event_getUseValuesFromTriggerTime(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the value of the useValuesFromTriggerTime attribute
value = Event_isSetDelay(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- value =
- 1 if the delay structure is set
- 0 otherwise
value = Event_isSetId(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = Event_isSetMetaid(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Event_isSetName(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = Event_isSetPriority(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- value =
- 1 if the priority structure is set
- 0 otherwise
value = Event_isSetSBOTerm(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = Event_isSetTimeUnits(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- value =
- 1 if the timeUnits attribute is set
- 0 otherwise
value = Event_isSetTrigger(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- value =
- 1 if the trigger structure is set
- 0 otherwise
SBMLEvent = Event_setDelay(SBMLEvent, SBMLDelay)
Takes
- SBMLEvent, an SBML Event structure
- SBMLDelay, an SBML Delay structure
Returns
- the SBML Event structure with the new value for the delay field
SBMLEvent = Event_setId(SBMLEvent, id)
Takes
- SBMLEvent, an SBML Event structure
- id; a string representing the id to be set
Returns
- the SBML Event structure with the new value for the id attribute
SBMLEvent = Event_setMetaid(SBMLEvent, metaid)
Takes
- SBMLEvent, an SBML Event structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Event structure with the new value for the metaid attribute
SBMLEvent = Event_setName(SBMLEvent, name)
Takes
- SBMLEvent, an SBML Event structure
- name; a string representing the name to be set
Returns
- the SBML Event structure with the new value for the name attribute
SBMLEvent = Event_setPriority(SBMLEvent, SBMLPriority)
Takes
- SBMLEvent, an SBML Event structure
- SBMLPriority, an SBML Priority structure
Returns
- the SBML Event structure with the new value for the priority field
SBMLEvent = Event_setSBOTerm(SBMLEvent, sboTerm)
Takes
- SBMLEvent, an SBML Event structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Event structure with the new value for the sboTerm attribute
SBMLEvent = Event_setTimeUnits(SBMLEvent, timeUnits)
Takes
- SBMLEvent, an SBML Event structure
- timeUnits; a string representing the timeUnits to be set
Returns
- the SBML Event structure with the new value for the timeUnits attribute
SBMLEvent = Event_setTrigger(SBMLEvent, SBMLTrigger)
Takes
- SBMLEvent, an SBML Event structure
- SBMLTrigger, an SBML Trigger structure
Returns
- the SBML Event structure with the new value for the trigger field
SBMLEvent = Event_setUseValuesFromTriggerTime(SBMLEvent, useValuesFromTriggerTime)
Takes
- SBMLEvent, an SBML Event structure
- useValuesFromTriggerTime, an integer (0/1) representing the value of useValuesFromTriggerTime to be set
Returns
- the SBML Event structure with the new value for the useValuesFromTriggerTime attribute
SBMLEvent = Event_unsetDelay(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with the delay field unset
SBMLEvent = Event_unsetId(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with the id attribute unset
SBMLEvent = Event_unsetMetaid(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with the metaid attribute unset
SBMLEvent = Event_unsetName(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with the name attribute unset
SBMLEvent = Event_unsetPriority(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with the priority field unset
SBMLEvent = Event_unsetSBOTerm(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with the sboTerm attribute unset
SBMLEvent = Event_unsetTimeUnits(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with the timeUnits attribute unset
SBMLEvent = Event_unsetTrigger(SBMLEvent)
Takes
- SBMLEvent, an SBML Event structure
Returns
- the SBML Event structure with the trigger field unset
SBMLToolbox-4.1.0/docs/structure-functions/delay.html 0000644 0000000 0000000 00000007113 11611210542 021273 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\DELAY
The functions allow users to create and work with the SBML Delay structure.
Function are:
Delay = Delay_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Delay 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
math = Delay_getMath(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- the value of the math attribute
metaid = Delay_getMetaid(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- the value of the metaid attribute
sboTerm = Delay_getSBOTerm(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- the value of the sboTerm attribute
value = Delay_isSetMath(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = Delay_isSetMetaid(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Delay_isSetSBOTerm(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLDelay = Delay_setMath(SBMLDelay, math)
Takes
- SBMLDelay, an SBML Delay structure
- math; string representing the math expression math to be set
Returns
- the SBML Delay structure with the new value for the math attribute
SBMLDelay = Delay_setMetaid(SBMLDelay, metaid)
Takes
- SBMLDelay, an SBML Delay structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Delay structure with the new value for the metaid attribute
SBMLDelay = Delay_setSBOTerm(SBMLDelay, sboTerm)
Takes
- SBMLDelay, an SBML Delay structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Delay structure with the new value for the sboTerm attribute
SBMLDelay = Delay_unsetMath(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- the SBML Delay structure with the math attribute unset
SBMLDelay = Delay_unsetMetaid(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- the SBML Delay structure with the metaid attribute unset
SBMLDelay = Delay_unsetSBOTerm(SBMLDelay)
Takes
- SBMLDelay, an SBML Delay structure
Returns
- the SBML Delay structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/constraint.html 0000644 0000000 0000000 00000011674 11611210542 022370 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\CONSTRAINT
The functions allow users to create and work with the SBML Constraint structure.
Function are:
Constraint = Constraint_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Constraint 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
math = Constraint_getMath(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- the value of the math attribute
message = Constraint_getMessage(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- the value of the message attribute
metaid = Constraint_getMetaid(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- the value of the metaid attribute
sboTerm = Constraint_getSBOTerm(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- the value of the sboTerm attribute
value = Constraint_isSetMath(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- value =
- 1 if the math attribute is set
- 0 otherwise
value = Constraint_isSetMessage(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- value =
- 1 if the message attribute is set
- 0 otherwise
value = Constraint_isSetMetaid(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Constraint_isSetSBOTerm(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLConstraint = Constraint_setMath(SBMLConstraint, math)
Takes
- SBMLConstraint, an SBML Constraint structure
- math; string representing the math expression math to be set
Returns
- the SBML Constraint structure with the new value for the math attribute
SBMLConstraint = Constraint_setMessage(SBMLConstraint, message)
Takes
- SBMLConstraint, an SBML Constraint structure
- message; a string representing the message to be set
Returns
- the SBML Constraint structure with the new value for the message attribute
SBMLConstraint = Constraint_setMetaid(SBMLConstraint, metaid)
Takes
- SBMLConstraint, an SBML Constraint structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Constraint structure with the new value for the metaid attribute
SBMLConstraint = Constraint_setSBOTerm(SBMLConstraint, sboTerm)
Takes
- SBMLConstraint, an SBML Constraint structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Constraint structure with the new value for the sboTerm attribute
SBMLConstraint = Constraint_unsetMath(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- the SBML Constraint structure with the math attribute unset
SBMLConstraint = Constraint_unsetMessage(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- the SBML Constraint structure with the message attribute unset
SBMLConstraint = Constraint_unsetMetaid(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- the SBML Constraint structure with the metaid attribute unset
SBMLConstraint = Constraint_unsetSBOTerm(SBMLConstraint)
Takes
- SBMLConstraint, an SBML Constraint structure
Returns
- the SBML Constraint structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/compartmentVolumeRule.html 0000644 0000000 0000000 00000011207 11611210540 024543 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\COMPARTMENTVOLUMERULE
The functions allow users to create and work with the SBML CompartmentVolumeRule structure.
Function are:
CompartmentVolumeRule = CompartmentVolumeRule_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML CompartmentVolumeRule 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
compartment = CompartmentVolumeRule_getCompartment(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- the value of the compartment attribute
formula = CompartmentVolumeRule_getFormula(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- the value of the formula attribute
type = CompartmentVolumeRule_getType(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- the value of the type attribute
value = CompartmentVolumeRule_isSetCompartment(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- value =
- 1 if the compartment attribute is set
- 0 otherwise
value = CompartmentVolumeRule_isSetFormula(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- value =
- 1 if the formula attribute is set
- 0 otherwise
value = CompartmentVolumeRule_isSetType(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- value =
- 1 if the type attribute is set
- 0 otherwise
SBMLCompartmentVolumeRule = CompartmentVolumeRule_setCompartment(SBMLCompartmentVolumeRule, compartment)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
- compartment; a string representing the compartment to be set
Returns
- the SBML CompartmentVolumeRule structure with the new value for the compartment attribute
SBMLCompartmentVolumeRule = CompartmentVolumeRule_setFormula(SBMLCompartmentVolumeRule, formula)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
- formula; a string representing the formula to be set
Returns
- the SBML CompartmentVolumeRule structure with the new value for the formula attribute
SBMLCompartmentVolumeRule = CompartmentVolumeRule_setType(SBMLCompartmentVolumeRule, type)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
- type; a string representing the type to be set
Returns
- the SBML CompartmentVolumeRule structure with the new value for the type attribute
SBMLCompartmentVolumeRule = CompartmentVolumeRule_unsetCompartment(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- the SBML CompartmentVolumeRule structure with the compartment attribute unset
SBMLCompartmentVolumeRule = CompartmentVolumeRule_unsetFormula(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- the SBML CompartmentVolumeRule structure with the formula attribute unset
SBMLCompartmentVolumeRule = CompartmentVolumeRule_unsetType(SBMLCompartmentVolumeRule)
Takes
- SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
Returns
- the SBML CompartmentVolumeRule structure with the type attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/compartmentType.html 0000644 0000000 0000000 00000012433 11611210540 023367 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\COMPARTMENTTYPE
The functions allow users to create and work with the SBML CompartmentType structure.
Function are:
CompartmentType = CompartmentType_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML CompartmentType 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
id = CompartmentType_getId(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the value of the id attribute
metaid = CompartmentType_getMetaid(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the value of the metaid attribute
name = CompartmentType_getName(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the value of the name attribute
sboTerm = CompartmentType_getSBOTerm(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the value of the sboTerm attribute
value = CompartmentType_isSetId(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = CompartmentType_isSetMetaid(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = CompartmentType_isSetName(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = CompartmentType_isSetSBOTerm(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLCompartmentType = CompartmentType_setId(SBMLCompartmentType, id)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
- id; a string representing the id to be set
Returns
- the SBML CompartmentType structure with the new value for the id attribute
SBMLCompartmentType = CompartmentType_setMetaid(SBMLCompartmentType, metaid)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
- metaid; a string representing the metaid to be set
Returns
- the SBML CompartmentType structure with the new value for the metaid attribute
SBMLCompartmentType = CompartmentType_setName(SBMLCompartmentType, name)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
- name; a string representing the name to be set
Returns
- the SBML CompartmentType structure with the new value for the name attribute
SBMLCompartmentType = CompartmentType_setSBOTerm(SBMLCompartmentType, sboTerm)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML CompartmentType structure with the new value for the sboTerm attribute
SBMLCompartmentType = CompartmentType_unsetId(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the SBML CompartmentType structure with the id attribute unset
SBMLCompartmentType = CompartmentType_unsetMetaid(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the SBML CompartmentType structure with the metaid attribute unset
SBMLCompartmentType = CompartmentType_unsetName(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the SBML CompartmentType structure with the name attribute unset
SBMLCompartmentType = CompartmentType_unsetSBOTerm(SBMLCompartmentType)
Takes
- SBMLCompartmentType, an SBML CompartmentType structure
Returns
- the SBML CompartmentType structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/compartment.html 0000644 0000000 0000000 00000041427 11703262406 022544 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\COMPARTMENT
The functions allow users to create and work with the SBML Compartment structure.
Function are:
Compartment = Compartment_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML Compartment 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
compartmentType = Compartment_getCompartmentType(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the compartmentType attribute
constant = Compartment_getConstant(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the constant attribute
id = Compartment_getId(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the id attribute
metaid = Compartment_getMetaid(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the metaid attribute
name = Compartment_getName(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the name attribute
outside = Compartment_getOutside(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the outside attribute
sboTerm = Compartment_getSBOTerm(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the sboTerm attribute
size = Compartment_getSize(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the size attribute
spatialDimensions = Compartment_getSpatialDimensions(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the spatialDimensions attribute
units = Compartment_getUnits(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the units attribute
volume = Compartment_getVolume(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the value of the volume attribute
y = Compartment_isAssignedByRateRule(SBMLCompartment, SBMLRules)
Takes
- SBMLCompartment, an SBML Compartment structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- the index of the rateRule used to assigned value to the Compartment
- 0 if the Compartment 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) 2009-2012 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 = Compartment_isAssignedByRule(SBMLCompartment, SBMLRules)
Takes
- SBMLCompartment, an SBML Compartment structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- the index of the assignmentRule used to assigned value to the Compartment
- 0 if the Compartment 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) 2009-2012 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 = Compartment_isInAlgebraicRule(SBMLCompartment, SBMLRules)
Takes
- SBMLCompartment, an SBML Compartment structure
- SBMLRules; the array of rules from an SBML Model structure
Returns
y =
- an array of the indices of any algebraicRules the id of the Compartment appears in
- 0 if the Compartment 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) 2009-2012 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 = Compartment_isSetCompartmentType(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the compartmentType attribute is set
- 0 otherwise
value = Compartment_isSetId(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the id attribute is set
- 0 otherwise
value = Compartment_isSetMetaid(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = Compartment_isSetName(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the name attribute is set
- 0 otherwise
value = Compartment_isSetOutside(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the outside attribute is set
- 0 otherwise
value = Compartment_isSetSBOTerm(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = Compartment_isSetSize(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the size attribute is set
- 0 otherwise
value = Compartment_isSetSpatialDimensions(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the spatialDimensions attribute is set
- 0 otherwise
value = Compartment_isSetUnits(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the units attribute is set
- 0 otherwise
value = Compartment_isSetVolume(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- value =
- 1 if the volume attribute is set
- 0 otherwise
SBMLCompartment = Compartment_setCompartmentType(SBMLCompartment, compartmentType)
Takes
- SBMLCompartment, an SBML Compartment structure
- compartmentType; a string representing the compartmentType to be set
Returns
- the SBML Compartment structure with the new value for the compartmentType attribute
SBMLCompartment = Compartment_setConstant(SBMLCompartment, constant)
Takes
- SBMLCompartment, an SBML Compartment structure
- constant, an integer (0/1) representing the value of constant to be set
Returns
- the SBML Compartment structure with the new value for the constant attribute
SBMLCompartment = Compartment_setId(SBMLCompartment, id)
Takes
- SBMLCompartment, an SBML Compartment structure
- id; a string representing the id to be set
Returns
- the SBML Compartment structure with the new value for the id attribute
SBMLCompartment = Compartment_setMetaid(SBMLCompartment, metaid)
Takes
- SBMLCompartment, an SBML Compartment structure
- metaid; a string representing the metaid to be set
Returns
- the SBML Compartment structure with the new value for the metaid attribute
SBMLCompartment = Compartment_setName(SBMLCompartment, name)
Takes
- SBMLCompartment, an SBML Compartment structure
- name; a string representing the name to be set
Returns
- the SBML Compartment structure with the new value for the name attribute
SBMLCompartment = Compartment_setOutside(SBMLCompartment, outside)
Takes
- SBMLCompartment, an SBML Compartment structure
- outside; a string representing the outside to be set
Returns
- the SBML Compartment structure with the new value for the outside attribute
SBMLCompartment = Compartment_setSBOTerm(SBMLCompartment, sboTerm)
Takes
- SBMLCompartment, an SBML Compartment structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML Compartment structure with the new value for the sboTerm attribute
SBMLCompartment = Compartment_setSize(SBMLCompartment, size)
Takes
- SBMLCompartment, an SBML Compartment structure
- size; number representing the value of size to be set
Returns
- the SBML Compartment structure with the new value for the size attribute
SBMLCompartment = Compartment_setSpatialDimensions(SBMLCompartment, spatialDimensions)
Takes
- SBMLCompartment, an SBML Compartment structure
- spatialDimensions; number representing the value of spatialDimensions to be set
Returns
- the SBML Compartment structure with the new value for the spatialDimensions attribute
SBMLCompartment = Compartment_setUnits(SBMLCompartment, units)
Takes
- SBMLCompartment, an SBML Compartment structure
- units; a string representing the units to be set
Returns
- the SBML Compartment structure with the new value for the units attribute
SBMLCompartment = Compartment_setVolume(SBMLCompartment, volume)
Takes
- SBMLCompartment, an SBML Compartment structure
- volume; number representing the value of volume to be set
Returns
- the SBML Compartment structure with the new value for the volume attribute
SBMLCompartment = Compartment_unsetCompartmentType(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the compartmentType attribute unset
SBMLCompartment = Compartment_unsetId(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the id attribute unset
SBMLCompartment = Compartment_unsetMetaid(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the metaid attribute unset
SBMLCompartment = Compartment_unsetName(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the name attribute unset
SBMLCompartment = Compartment_unsetOutside(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the outside attribute unset
SBMLCompartment = Compartment_unsetSBOTerm(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the sboTerm attribute unset
SBMLCompartment = Compartment_unsetSize(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the size attribute unset
SBMLCompartment = Compartment_unsetSpatialDimensions(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the spatialDimensions attribute unset
SBMLCompartment = Compartment_unsetUnits(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the units attribute unset
SBMLCompartment = Compartment_unsetVolume(SBMLCompartment)
Takes
- SBMLCompartment, an SBML Compartment structure
Returns
- the SBML Compartment structure with the volume attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/assignmentRule.html 0000644 0000000 0000000 00000012462 11611210540 023176 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\ASSIGNMENTRULE
The functions allow users to create and work with the SBML AssignmentRule structure.
Function are:
AssignmentRule = AssignmentRule_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML AssignmentRule 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
formula = AssignmentRule_getFormula(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- the value of the formula attribute
metaid = AssignmentRule_getMetaid(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- the value of the metaid attribute
sboTerm = AssignmentRule_getSBOTerm(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- the value of the sboTerm attribute
variable = AssignmentRule_getVariable(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- the value of the variable attribute
value = AssignmentRule_isSetFormula(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- value =
- 1 if the formula attribute is set
- 0 otherwise
value = AssignmentRule_isSetMetaid(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = AssignmentRule_isSetSBOTerm(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = AssignmentRule_isSetVariable(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- value =
- 1 if the variable attribute is set
- 0 otherwise
SBMLAssignmentRule = AssignmentRule_setFormula(SBMLAssignmentRule, formula)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
- formula; a string representing the formula to be set
Returns
- the SBML AssignmentRule structure with the new value for the formula attribute
SBMLAssignmentRule = AssignmentRule_setMetaid(SBMLAssignmentRule, metaid)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
- metaid; a string representing the metaid to be set
Returns
- the SBML AssignmentRule structure with the new value for the metaid attribute
SBMLAssignmentRule = AssignmentRule_setSBOTerm(SBMLAssignmentRule, sboTerm)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML AssignmentRule structure with the new value for the sboTerm attribute
SBMLAssignmentRule = AssignmentRule_setVariable(SBMLAssignmentRule, variable)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
- variable; a string representing the variable to be set
Returns
- the SBML AssignmentRule structure with the new value for the variable attribute
SBMLAssignmentRule = AssignmentRule_unsetFormula(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- the SBML AssignmentRule structure with the formula attribute unset
SBMLAssignmentRule = AssignmentRule_unsetMetaid(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- the SBML AssignmentRule structure with the metaid attribute unset
SBMLAssignmentRule = AssignmentRule_unsetSBOTerm(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- the SBML AssignmentRule structure with the sboTerm attribute unset
SBMLAssignmentRule = AssignmentRule_unsetVariable(SBMLAssignmentRule)
Takes
- SBMLAssignmentRule, an SBML AssignmentRule structure
Returns
- the SBML AssignmentRule structure with the variable attribute unset
SBMLToolbox-4.1.0/docs/structure-functions/algebraicRule.html 0000644 0000000 0000000 00000010151 11611210364 022734 0 ustar root root
MATLAB_SBML_STRUCTURE_FUNCTIONS\ALGEBRAICRULE
The functions allow users to create and work with the SBML AlgebraicRule structure.
Function are:
AlgebraicRule = AlgebraicRule_create(level(optional), version(optional) )
Takes
- level, an integer representing an SBML level (optional)
- version, an integer representing an SBML version (optional)
Returns
- a MATLAB_SBML AlgebraicRule 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
formula = AlgebraicRule_getFormula(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- the value of the formula attribute
metaid = AlgebraicRule_getMetaid(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- the value of the metaid attribute
sboTerm = AlgebraicRule_getSBOTerm(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- the value of the sboTerm attribute
value = AlgebraicRule_isSetFormula(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- value =
- 1 if the formula attribute is set
- 0 otherwise
value = AlgebraicRule_isSetMetaid(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
value = AlgebraicRule_isSetSBOTerm(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLAlgebraicRule = AlgebraicRule_setFormula(SBMLAlgebraicRule, formula)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
- formula; a string representing the formula to be set
Returns
- the SBML AlgebraicRule structure with the new value for the formula attribute
SBMLAlgebraicRule = AlgebraicRule_setMetaid(SBMLAlgebraicRule, metaid)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
- metaid; a string representing the metaid to be set
Returns
- the SBML AlgebraicRule structure with the new value for the metaid attribute
SBMLAlgebraicRule = AlgebraicRule_setSBOTerm(SBMLAlgebraicRule, sboTerm)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
- sboTerm, an integer representing the sboTerm to be set
Returns
- the SBML AlgebraicRule structure with the new value for the sboTerm attribute
SBMLAlgebraicRule = AlgebraicRule_unsetFormula(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- the SBML AlgebraicRule structure with the formula attribute unset
SBMLAlgebraicRule = AlgebraicRule_unsetMetaid(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- the SBML AlgebraicRule structure with the metaid attribute unset
SBMLAlgebraicRule = AlgebraicRule_unsetSBOTerm(SBMLAlgebraicRule)
Takes
- SBMLAlgebraicRule, an SBML AlgebraicRule structure
Returns
- the SBML AlgebraicRule structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/structure/ 0000755 0000000 0000000 00000000000 11704572220 015306 5 ustar root root SBMLToolbox-4.1.0/docs/structure/unitdefinition.html 0000644 0000000 0000000 00000016663 11626412302 021235 0 ustar root root
UnitDefinition
typecode = SBML_UNIT_DEFINITION
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
| unit |
array of structures |
|
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
| unit |
array of structures |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
| unit |
array of structures |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
| unit |
array of structures |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
| unit |
array of structures |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
| unit |
array of structures |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
| unit |
array of structures |
|
SBMLToolbox-4.1.0/docs/structure/unit.html 0000644 0000000 0000000 00000017723 11626412302 017162 0 ustar root root
Unit
typecode = SBML_UNIT
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
kind |
string |
exponent |
integer |
scale |
boolean |
|
typecode |
as above |
notes |
string |
annotation |
string |
kind |
string |
exponent |
integer |
scale |
boolean |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
kind |
string |
exponent |
integer |
scale |
boolean |
multiplier |
double |
offset |
double |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
kind |
string |
exponent |
integer |
scale |
boolean |
multiplier |
double |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
kind |
string |
exponent |
integer |
scale |
boolean |
multiplier |
double |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
kind |
string |
exponent |
integer |
scale |
boolean |
multiplier |
double |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
kind |
string |
exponent |
double |
scale |
double |
multiplier |
double |
|
SBMLToolbox-4.1.0/docs/structure/trigger.html 0000644 0000000 0000000 00000007771 11626412302 017650 0 ustar root root
Trigger
typecode = SBML_TRIGGER
SBML Level 1
|
The Trigger component is not part of SBML Level 1 Version 1
|
The Trigger component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The Trigger component is not part of SBML Level 2 Version 1
|
The Trigger component is not part of SBML Level 2 Version 2
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
persistent |
boolean |
initialValue |
boolean |
math |
string |
|
SBMLToolbox-4.1.0/docs/structure/stoichiometrymath.html 0000644 0000000 0000000 00000006234 11626412302 021752 0 ustar root root
StoichiometryMath
typecode = SBML_STOICHIOMETRY_MATH
SBML Level 1
|
The StoichiometryMath component is not part of SBML Level 1 Version 1
|
The StoichiometryMath component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The StoichiometryMath component is not part of SBML Level 2 Version 1
|
The StoichiometryMath component is not part of SBML Level 2 Version 2
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
|
SBML Level 3
|
The StoichiometryMath component is not part of SBML Level 3 Version 1
|
SBMLToolbox-4.1.0/docs/structure/speciestype.html 0000644 0000000 0000000 00000007774 11626412302 020545 0 ustar root root
SpeciesType
typecode = SBML_SPECIES_TYPE
SBML Level 1
|
The SpeciesType component is not part of SBML Level 1 Version 1
|
The SpeciesType component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The SpeciesType component is not part of SBML Level 2 Version 1
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
|
SBML Level 3
|
The SpeciesType component is not part of SBML Level 3 Version 1
|
SBMLToolbox-4.1.0/docs/structure/speciesreference.html 0000644 0000000 0000000 00000021035 11626412302 021504 0 ustar root root
SpeciesReference
typecode = SBML_SPECIES_REFERENCE
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
species |
string |
stoichiometry |
integer |
denominator |
integer |
|
typecode |
as above |
notes |
string |
annotation |
string |
species |
string |
stoichiometry |
integer |
denominator |
integer |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
species |
string |
stoichiometry |
double |
denominator |
integer |
stoichiometryMath |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
species |
string |
id |
string |
name |
string |
sboTerm |
integer |
stoichiometry |
double |
stoichiometryMath |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
species |
string |
id |
string |
name |
string |
stoichiometry |
double |
| stoichiometryMath |
structure |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
species |
string |
id |
string |
name |
string |
stoichiometry |
double |
| stoichiometryMath |
structure |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
species |
string |
id |
string |
name |
string |
stoichiometry |
double |
constant |
boolean |
isSetStoichiometry |
boolean |
|
SBMLToolbox-4.1.0/docs/structure/speciesconcentrationrule.html 0000644 0000000 0000000 00000007555 11626412302 023317 0 ustar root root
SpeciesConcentrationRule
typecode = SBML_SPECIES_CONCENTRATION_RULE
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
type |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
notes |
string |
annotation |
string |
type |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBML Level 2
|
The SpeciesConcentrationRule component is not part of SBML Level 2 Version 1
|
The SpeciesConcentrationRule component is not part of SBML Level 2 Version 2
|
|
The SpeciesConcentrationRule component is not part of SBML Level 2 Version 3
|
The SpeciesConcentrationRule component is not part of SBML Level 2 Version 4
|
SBML Level 3
|
The SpeciesConcentrationRule component is not part of SBML Level 3 Version 1
|
SBMLToolbox-4.1.0/docs/structure/species.html 0000644 0000000 0000000 00000032270 11626412302 017630 0 ustar root root
Species
typecode = SBML_SPECIES
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
compartment |
string |
initialAmount |
double |
units |
string |
boundaryCondition |
boolean |
charge |
double |
isSetInitialAmount |
boolean |
isSetCharge |
boolean |
|
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
compartment |
string |
initialAmount |
double |
units |
string |
boundaryCondition |
boolean |
charge |
double |
isSetInitialAmount |
boolean |
isSetCharge |
boolean |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
compartment |
string |
initialAmount |
double |
initialConcentration |
double |
substanceUnits |
string |
spatialSizeUnits |
string |
hasOnlySubstanceUnits |
boolean |
boundaryCondition |
boolean |
charge |
double |
constant |
boolean |
isSetInitialAmount |
boolean |
isSetInitialConcentration |
boolean |
isSetCharge |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
speciesType |
string |
compartment |
string |
initialAmount |
double |
initialConcentration |
double |
substanceUnits |
string |
spatialSizeUnits |
string |
hasOnlySubstanceUnits |
boolean |
boundaryCondition |
boolean |
charge |
double |
constant |
boolean |
isSetInitialAmount |
boolean |
isSetInitialConcentration |
boolean |
isSetCharge |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
speciesType |
string |
compartment |
string |
initialAmount |
double |
initialConcentration |
double |
substanceUnits |
string |
hasOnlySubstanceUnits |
boolean |
boundaryCondition |
boolean |
charge |
double |
constant |
boolean |
isSetInitialAmount |
boolean |
isSetInitialConcentration |
boolean |
isSetCharge |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
speciesType |
string |
compartment |
string |
initialAmount |
double |
initialConcentration |
double |
substanceUnits |
string |
hasOnlySubstanceUnits |
boolean |
boundaryCondition |
boolean |
charge |
double |
constant |
boolean |
isSetInitialAmount |
boolean |
isSetInitialConcentration |
boolean |
isSetCharge |
boolean |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
compartment |
string |
initialAmount |
double |
initialConcentration |
double |
substanceUnits |
string |
hasOnlySubstanceUnits |
boolean |
boundaryCondition |
boolean |
constant |
boolean |
isSetInitialAmount |
boolean |
isSetInitialConcentration |
boolean |
conversionFactor |
string |
|
SBMLToolbox-4.1.0/docs/structure/rule.html 0000644 0000000 0000000 00000003375 11626415222 017154 0 ustar root root
Rule
SBML Level 1
SBML Level 2
SBML Level 3
SBMLToolbox-4.1.0/docs/structure/reaction.html 0000644 0000000 0000000 00000026273 11626412302 020007 0 ustar root root
Reaction
typecode = SBML_REACTION
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
| reactant |
array of structures |
| product |
array of structures |
| kineticLaw |
structure |
reversible |
boolean |
fast |
boolean |
|
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
| reactant |
array of structures |
| product |
array of structures |
| kineticLaw |
structure |
reversible |
boolean |
fast |
boolean |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
| reactant |
array of structures |
| product |
array of structures |
| modifier |
array of structures |
| kineticLaw |
structure |
reversible |
boolean |
fast |
boolean |
isSetFast |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
| reactant |
array of structures |
| product |
array of structures |
| modifier |
array of structures |
| kineticLaw |
structure |
reversible |
boolean |
fast |
boolean |
sboTerm |
integer |
isSetFast |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
| reactant |
array of structures |
| product |
array of structures |
| modifier |
array of structures |
| kineticLaw |
structure |
reversible |
boolean |
fast |
boolean |
isSetFast |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
| reactant |
array of structures |
| product |
array of structures |
| modifier |
array of structures |
| kineticLaw |
structure |
reversible |
boolean |
fast |
boolean |
isSetFast |
boolean |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
| reactant |
array of structures |
| product |
array of structures |
| modifier |
array of structures |
| kineticLaw |
structure |
reversible |
boolean |
fast |
boolean |
isSetFast |
boolean |
compartment |
string |
|
SBMLToolbox-4.1.0/docs/structure/raterule.html 0000644 0000000 0000000 00000016441 11626412302 020022 0 ustar root root
RateRule
typecode = SBML_RATE_RULE
SBML Level 1
|
The RateRule component is not part of SBML Level 1 Version 1
|
The RateRule component is not part of SBML Level 1 Version 2
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBMLToolbox-4.1.0/docs/structure/priority.html 0000644 0000000 0000000 00000004526 11626412302 020061 0 ustar root root
Priority
typecode = SBML_PRIORITY
SBML Level 1
|
The Priority component is not part of SBML Level 1 Version 1
|
The Priority component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The Priority component is not part of SBML Level 2 Version 1
|
The Priority component is not part of SBML Level 2 Version 2
|
|
The Priority component is not part of SBML Level 2 Version 3
|
The Priority component is not part of SBML Level 2 Version 4
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
|
SBMLToolbox-4.1.0/docs/structure/parameterrule.html 0000644 0000000 0000000 00000007424 11626412302 021050 0 ustar root root
ParameterRule
typecode = SBML_PARAMETER_RULE
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
type |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
notes |
string |
annotation |
string |
type |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBML Level 2
|
The ParameterRule component is not part of SBML Level 2 Version 1
|
The ParameterRule component is not part of SBML Level 2 Version 2
|
|
The ParameterRule component is not part of SBML Level 2 Version 3
|
The ParameterRule component is not part of SBML Level 2 Version 4
|
SBML Level 3
|
The ParameterRule component is not part of SBML Level 3 Version 1
|
SBMLToolbox-4.1.0/docs/structure/parameter.html 0000644 0000000 0000000 00000021645 11626412302 020161 0 ustar root root
Parameter
typecode = SBML_PARAMETER
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
value |
double |
units |
string |
isSetValue |
boolean |
|
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
value |
double |
units |
string |
isSetValue |
boolean |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
value |
double |
units |
string |
constant |
boolean |
isSetValue |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
value |
double |
units |
string |
constant |
boolean |
sboTerm |
integer |
isSetValue |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
value |
double |
units |
string |
constant |
boolean |
isSetValue |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
value |
double |
units |
string |
constant |
boolean |
isSetValue |
boolean |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
value |
double |
units |
string |
constant |
boolean |
isSetValue |
boolean |
|
SBMLToolbox-4.1.0/docs/structure/modifierspeciesreference.html 0000644 0000000 0000000 00000013717 11626412302 023233 0 ustar root root
ModifierSpeciesReference
typecode = SBML_MODIFIER_SPECIES_REFERENCE
SBML Level 1
|
The ModifierSpeciesReference component is not part of SBML Level 1 Version 1
|
The ModifierSpeciesReference component is not part of SBML Level 1 Version 2
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
species |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
species |
string |
id |
string |
name |
string |
sboTerm |
integer |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
species |
string |
id |
string |
name |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
species |
string |
id |
string |
name |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
species |
string |
id |
string |
name |
string |
|
SBMLToolbox-4.1.0/docs/structure/model.html 0000644 0000000 0000000 00000037704 11626412302 017304 0 ustar root root
Model
typecode = SBML_MODEL
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
SBML_level |
double |
SBML_version |
double |
name |
string |
| unitDefinition |
array of structures |
| compartment |
array of structures |
| species |
array of structures |
| parameter |
array of structures |
| rule |
array of structures |
| reaction |
array of structures |
|
typecode |
as above |
notes |
string |
annotation |
string |
SBML_level |
double |
SBML_version |
double |
name |
string |
| unitDefinition |
array of structures |
| compartment |
array of structures |
| species |
array of structures |
| parameter |
array of structures |
| rule |
array of structures |
| reaction |
array of structures |
|
SBML Level 2
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
SBML_level |
double |
SBML_version |
double |
name |
string |
id |
string |
sboTerm |
integer |
| functionDefinition |
array of structures |
| unitDefinition |
array of structures |
| compartment |
array of structures |
| species |
array of structures |
| parameter |
array of structures |
| initialAssignment |
array of structures |
| rule |
array of structures |
| constraint |
array of structures |
| reaction |
array of structures |
| event |
array of structures |
substanceUnits |
string |
timeUnits |
string |
lengthUnits |
string |
areaUnits |
string |
volumeUnits |
string |
extentUnits |
string |
conversionFactor |
string |
|
SBMLToolbox-4.1.0/docs/structure/localparameter.html 0000644 0000000 0000000 00000005324 11626412302 021170 0 ustar root root
LocalParameter
typecode = SBML_LOCAL_PARAMETER
SBML Level 1
|
The LocalParameter component is not part of SBML Level 1 Version 1
|
The LocalParameter component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The LocalParameter component is not part of SBML Level 2 Version 1
|
The LocalParameter component is not part of SBML Level 2 Version 2
|
|
The LocalParameter component is not part of SBML Level 2 Version 3
|
The LocalParameter component is not part of SBML Level 2 Version 4
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
value |
double |
units |
string |
isSetValue |
boolean |
|
SBMLToolbox-4.1.0/docs/structure/kineticlaw.html 0000644 0000000 0000000 00000020044 11626412302 020323 0 ustar root root
KineticLaw
typecode = SBML_KINETIC_LAW
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
formula |
string |
| parameter |
array of structures |
timeUnits |
string |
substanceUnits |
string |
|
typecode |
as above |
notes |
string |
annotation |
string |
formula |
string |
| parameter |
array of structures |
timeUnits |
string |
substanceUnits |
string |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
formula |
string |
math |
string |
| parameter |
array of structures |
timeUnits |
string |
substanceUnits |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
formula |
string |
math |
string |
| parameter |
array of structures |
sboTerm |
integer |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
math |
string |
| parameter |
array of structures |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
math |
string |
| parameter |
array of structures |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
| localParameter |
array of structures |
|
SBMLToolbox-4.1.0/docs/structure/initialassignment.html 0000644 0000000 0000000 00000011714 11626412302 021717 0 ustar root root
InitialAssignment
typecode = SBML_INITIAL_ASSIGNMENT
SBML Level 1
|
The InitialAssignment component is not part of SBML Level 1 Version 1
|
The InitialAssignment component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The InitialAssignment component is not part of SBML Level 2 Version 1
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
symbol |
string |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
symbol |
string |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
symbol |
string |
math |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
symbol |
string |
math |
string |
|
SBMLToolbox-4.1.0/docs/structure/functiondefinition.html 0000644 0000000 0000000 00000014077 11626412302 022100 0 ustar root root
FunctionDefinition
typecode = SBML_FUNCTION_DEFINITION
SBML Level 1
|
The FunctionDefinition component is not part of SBML Level 1 Version 1
|
The FunctionDefinition component is not part of SBML Level 1 Version 2
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
math |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
math |
string |
|
SBMLToolbox-4.1.0/docs/structure/eventassignment.html 0000644 0000000 0000000 00000013276 11626412302 021414 0 ustar root root
EventAssignment
typecode = SBML_EVENT_ASSIGNMENT
SBML Level 1
|
The EventAssignment component is not part of SBML Level 1 Version 1
|
The EventAssignment component is not part of SBML Level 1 Version 2
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
variable |
string |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
variable |
string |
sboTerm |
integer |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
variable |
string |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
variable |
string |
math |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
variable |
string |
math |
string |
|
SBMLToolbox-4.1.0/docs/structure/event.html 0000644 0000000 0000000 00000017071 11626412302 017320 0 ustar root root
Event
typecode = SBML_EVENT
SBML Level 1
|
The Event component is not part of SBML Level 1 Version 1
|
The Event component is not part of SBML Level 1 Version 2
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
trigger |
string |
delay |
string |
timeUnits |
string |
| eventAssignment |
array of structures |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
trigger |
string |
delay |
string |
timeUnits |
string |
sboTerm |
integer |
| eventAssignment |
array of structures |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
| trigger |
structure |
| delay |
structure |
| eventAssignment |
array of structures |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
useValuesFromTriggerTime |
boolean |
| trigger |
structure |
| delay |
structure |
| eventAssignment |
array of structures |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
useValuesFromTriggerTime |
boolean |
| trigger |
structure |
| delay |
structure |
| priority |
structure |
| eventAssignment |
array of structures |
|
SBMLToolbox-4.1.0/docs/structure/delay.html 0000644 0000000 0000000 00000007473 11626412302 017302 0 ustar root root
Delay
typecode = SBML_DELAY
SBML Level 1
|
The Delay component is not part of SBML Level 1 Version 1
|
The Delay component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The Delay component is not part of SBML Level 2 Version 1
|
The Delay component is not part of SBML Level 2 Version 2
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
|
SBMLToolbox-4.1.0/docs/structure/constraint.html 0000644 0000000 0000000 00000011645 11626412302 020364 0 ustar root root
Constraint
typecode = SBML_CONSTRAINT
SBML Level 1
|
The Constraint component is not part of SBML Level 1 Version 1
|
The Constraint component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The Constraint component is not part of SBML Level 2 Version 1
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
message |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
message |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
message |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
math |
string |
message |
string |
|
SBMLToolbox-4.1.0/docs/structure/compartmentvolumerule.html 0000644 0000000 0000000 00000007525 11626412302 022653 0 ustar root root
CompartmentVolumeRule
typecode = SBML_COMPARTMENT_VOLUME_RULE
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
type |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
notes |
string |
annotation |
string |
type |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBML Level 2
|
The CompartmentVolumeRule component is not part of SBML Level 2 Version 1
|
The CompartmentVolumeRule component is not part of SBML Level 2 Version 2
|
|
The CompartmentVolumeRule component is not part of SBML Level 2 Version 3
|
The CompartmentVolumeRule component is not part of SBML Level 2 Version 4
|
SBML Level 3
|
The CompartmentVolumeRule component is not part of SBML Level 3 Version 1
|
SBMLToolbox-4.1.0/docs/structure/compartmenttype.html 0000644 0000000 0000000 00000010030 11626412302 021416 0 ustar root root
CompartmentType
typecode = SBML_COMPARTMENT_TYPE
SBML Level 1
|
The CompartmentType component is not part of SBML Level 1 Version 1
|
The CompartmentType component is not part of SBML Level 1 Version 2
|
SBML Level 2
|
The CompartmentType component is not part of SBML Level 2 Version 1
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
|
SBML Level 3
|
The CompartmentType component is not part of SBML Level 3 Version 1
|
SBMLToolbox-4.1.0/docs/structure/compartment.html 0000644 0000000 0000000 00000024755 11626412302 020537 0 ustar root root
Compartment
typecode = SBML_COMPARTMENT
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
volume |
double |
units |
string |
outside |
string |
isSetVolume |
boolean |
|
typecode |
as above |
notes |
string |
annotation |
string |
name |
string |
volume |
double |
units |
string |
outside |
string |
isSetVolume |
boolean |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
spatialDimensions |
integer |
size |
double |
units |
string |
outside |
string |
constant |
boolean |
isSetSize |
boolean |
isSetVolume |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
name |
string |
id |
string |
compartmentType |
string |
spatialDimensions |
integer |
size |
double |
units |
string |
outside |
string |
constant |
boolean |
isSetSize |
boolean |
isSetVolume |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
compartmentType |
string |
spatialDimensions |
integer |
size |
double |
units |
string |
outside |
string |
constant |
boolean |
isSetSize |
boolean |
isSetVolume |
boolean |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
compartmentType |
string |
spatialDimensions |
integer |
size |
double |
units |
string |
outside |
string |
constant |
boolean |
isSetSize |
boolean |
isSetVolume |
boolean |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
name |
string |
id |
string |
spatialDimensions |
integer |
size |
double |
units |
string |
constant |
boolean |
isSetSize |
boolean |
isSetSpatialDimensions |
boolean |
|
SBMLToolbox-4.1.0/docs/structure/assignmentrule.html 0000644 0000000 0000000 00000016477 11626412302 021250 0 ustar root root
AssignmentRule
typecode = SBML_ASSIGNMENT_RULE
SBML Level 1
|
The AssignmentRule component is not part of SBML Level 1 Version 1
|
The AssignmentRule component is not part of SBML Level 1 Version 2
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBMLToolbox-4.1.0/docs/structure/algebraicrule.html 0000644 0000000 0000000 00000022702 11626412300 020773 0 ustar root root
AlgebraicRule
typecode = SBML_ALGEBRAIC_RULE
SBML Level 1
typecode |
as above |
notes |
string |
annotation |
string |
type |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
notes |
string |
annotation |
string |
type |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBML Level 2
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
units |
string |
|
SBML Level 3
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
formula |
string |
variable |
string |
species |
string |
compartment |
string |
name |
string |
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SBMLToolbox-4.1.0/docs/simulation.html 0000644 0000000 0000000 00000014232 11704012754 016323 0 ustar root root
SIMULATION
The functions allow users to simulate SBML Models.
Function are:
[analysis] = AnalyseSpecies(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- a structure detailing the species and how they are manipulated
within the model
EXAMPLE:
Using the model from toolbox/Test/test-data/algebraicRules.xml
analysis = AnalyseSpecies(m)
analysis =
1x5 struct array with fields:
Name
constant
boundaryCondition
initialValue
hasAmountOnly
isConcentration
compartment
ChangedByReaction
KineticLaw
ChangedByRateRule
RateRule
ChangedByAssignmentRule
AssignmentRule
InAlgebraicRule
AlgebraicRule
ConvertedToAssignRule
ConvertedRule
analysis(1) =
Name: {'S1'}
constant: 0
boundaryCondition: 0
initialValue: 0.0300
hasAmountOnly: 0
isConcentration: 0
compartment: 'compartment'
ChangedByReaction: 1
KineticLaw: {' - (k*S1)'}
ChangedByRateRule: 0
RateRule: ''
ChangedByAssignmentRule: 0
AssignmentRule: ''
InAlgebraicRule: 1
AlgebraicRule: {{1x1 cell}}
ConvertedToAssignRule: 0
ConvertedRule: ''
[analysis] = AnalyseVaryingParameters(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- a structure detailing any parameters that are not constant and how they are manipulated
within the model
EXAMPLE:
Using the model from toolbox/Test/test-data/algebraicRules.xml
analysis = AnalyseVaryingParameters(m)
analysis =
Name: {'s2'}
initialValue: 4
ChangedByRateRule: 0
RateRule: ''
ChangedByAssignmentRule: 0
AssignmentRule: ''
InAlgebraicRule: 1
AlgebraicRule: {{1x1 cell}}
ConvertedToAssignRule: 1
ConvertedRule: '-(-S2-S3)'
elements = DealWithPiecewise(formula)
Takes
- formula, a string representation of a math expression that contains the MathML piecewise function
Returns
- an array of the three components of the piecewise function
EXAMPLE:
elements = DealWithPiecewise('piecewise(le(s2,4),1.5,0.05)')
= 'le(s2,4)' '1.5' '0.05'
NOTE: The function cannot deal with a piecewise statement with more
than three elements.
elements = GetArgumentsFromLambdaFunction(formula)
Takes
- formula, a string representation of a math expression that contains the MathML lambda function
Returns
- an array of the components of the lambda function
EXAMPLE:
elements = GetArgumentsFromLambdaFunction('lambda(x, x+0.5)')
= 'x' 'x+0.5'
elements = GetArgumentsFromLambdaFunction('lambda(x, y, x + y)')
= 'x' 'y' 'x+y'
OutputODEFunction
NOTE: This function is deprecated. Use SolveODEFunction instead.
SolveODEFunction(varargin)
Takes
- a MATLAB_SBML model structure (required argument)
- time limit (default = 10)
- number of time steps (default lets the solver decide)
- a flag to indicate whether to output species values in amount/concentration
1 amount, 0 concentration (default)
- a flag to indicate whether to output the simulation data as
a comma separated variable (csv) file
1 output 0 no output (default)
- a filename (this is needed if WriteODEFunction was used with a
filename)
Returns
- an array of time values
- an array of the values of variables at each time point; species will
be in concentration or amount as specified by input arguments
Outputs
- a file 'name.csv' with the data results (if the flag to output such a
file is set to 1.
NOTE: the results are generated using ode45 solver (MATLAB) or lsode
(Octave)
WriteEventAssignmentFunction(SBMLModel, name)
Takes
- SBMLModel, an SBML Model structure
- name, a string representing the name of the ode function being used
Outputs
- a file 'name_eventAssign.m' defining a function that assigns values following an event
(for use with the event option of MATLABs ode solvers)
NOTE: This function is called from WriteODEFunction when a model with
events is encountered.
WriteEventHandlerFunction(SBMLModel, name)
Takes
- SBMLModel, an SBML Model structure
- name, a string representing the name of the ode function being used
Outputs
- a file 'name_events.m' defining a function that tests whether events
have been triggered
(for use with the event option of MATLABs ode solvers)
NOTE: This function is called from WriteODEFunction when a model with
events is encountered.
WriteODEFunction(SBMLModel, name(optional))
Takes
- SBMLModel, an SBML Model structure
- name, an optional string representing the name of the ode function to be used
Outputs
- a file 'name.m' defining a function that defines the ode equations of
the model for use with the ode solvers
(if no name supplied the model id will be used)
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SBMLToolbox 4.1 API
This manual describes the application programming interface (API) of
SBMLToolbox, an open-source (LGPL) MATLAB/Octave toolbox for writing and
manipulating content in the Systems Biology Markup Language (SBML). This
version of SBMLToolbox supports all releases of SBML up through Level 3 Version 1
Core Release 1. For more information about SBML, please visit http://sbml.org on the Internet.
All functions can be used in both the MATLAB and Octave environments.
Installation
Functions
MATLAB_SBML Structure Functions
MATLAB_SBML Structures
The following sections detail the structures of individual component types.
Level 3 FBC package
This version of SBMLToolbox (4.1.0) includes support for creating and manipulating structures representing the SBML L3 Flux Boubd Constraints (fbc) package.
Acknowledgements
This and other projects of the SBML Team have been supported by the
following organizations: the National Institutes of Health (USA) under
grants R01 GM070923 and R01 GM077671; the International Joint Research
Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the Japanese
Ministry of Agriculture; the Japanese Ministry of Education, Culture,
Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the
DARPA IPTO Bio-Computation Program (USA); the Army Research Office's
Institute for Collaborative Biotechnologies (USA); the Air Force Office of
Scientific Research (USA); the California Institute of Technology (USA);
the University of Hertfordshire (UK); the Molecular Sciences Institute
(USA); the Systems Biology Institute (Japan); and Keio University (Japan).
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Known issues
Simulating the SBML Test Suite
SBMLToolbox correctly simulates about 50% of the models in the SBML Test-suite.
There are 7 cases where comparison of the output reports that the test failed.
- 00676
- 00677
- 00678
- 00712
- 00713
- 00714
- 00954
These are cases where the number of variables with data
output by SBMLToolbox does not match the number of variables used in the comparison. The data output by SBMLToolbox is however correct.
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Installation
SBMLToolbox consists of scripts only. No compilation is required.
The import and export of SBML requires the installation of libSBML binding
for either MATLAB or Octave. This is available via the
libSBML page.
To install
- Start MATLAB/Octave
- Navigate to the SBMLToolbox/toolbox directory
- Run the install.m script found in that directory
The install.m script
- Reports whether the appropriate libSBML binding is available
- Adds the directories in the toolbox to the Path
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General functions
Functions in the top-level toolbox directory.
Function are:
installed = isBindingInstalled()
Returns
- installed =
- 1 if the libSBML executables have been installed
- 0 otherwise
install()
- Reports whether the appropriate libSBML binding is available
- Adds the directories in the toolbox to the Path
See installation
SBMLToolbox-4.1.0/docs/fbc_package/ 0000755 0000000 0000000 00000000000 11704572220 015453 5 ustar root root SBMLToolbox-4.1.0/docs/fbc_package/structure-functions/ 0000755 0000000 0000000 00000000000 11704572220 021521 5 ustar root root SBMLToolbox-4.1.0/docs/fbc_package/structure-functions/objective.html 0000644 0000000 0000000 00000014025 11702543302 024360 0 ustar root root FBC_PACKAGE\MATLAB_SBML_STRUCTURES\OBJECTIVE
The functions allow users to create and work with the SBML FBC Objective structure.
Function are:
SBMLObjective = Objective_addFluxObjective(SBMLObjective, SBMLFluxObjective)
Takes
- SBMLObjective, an SBML Objective structure
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the SBML Objective structure with the SBML FluxObjective structure added
Objective = Objective_create(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- a MATLAB_SBML FBC Objective structure of the appropriate level, version and pkgVersion
SBMLObjective = Objective_createFluxObjective(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the SBML Objective structure with a new SBML FluxObjective structure added
fluxObjective = Objective_getFluxObjective(SBMLObjective, index)
Takes
- SBMLObjective, an SBML Objective structure
- index, an integer representing the index of SBML FluxObjective structure
Returns
- the SBML FluxObjective structure at the indexed position
id = Objective_getId(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the value of the fbc_id attribute
fluxObjective = Objective_getListOfFluxObjectives(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- an array of the fluxObjective structures
metaid = Objective_getMetaid(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the value of the metaid attribute
num = Objective_getNumFluxObjectives(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the number of SBML FluxObjective structures present in the Objective
sboTerm = Objective_getSBOTerm(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the value of the sboTerm attribute
type = Objective_getType(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the value of the fbc_type attribute
id = Objective_isSetId(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- value =
- 1 if the fbc_id attribute is set
- 0 otherwise
metaid = Objective_isSetMetaid(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
sboTerm = Objective_isSetSBOTerm(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
type = Objective_isSetType(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- value =
- 1 if the fbc_type attribute is set
- 0 otherwise
SBMLObjective = Objective_setId(SBMLObjective, id)
Takes
- SBMLObjective, an SBML Objective structure
- id, a string representing the fbc_id to be set
Returns
- the SBML FBC Objective structure with the new value for the fbc_id attribute
SBMLObjective = Objective_setMetaid(SBMLObjective, metaid)
Takes
- SBMLObjective, an SBML Objective structure
- metaid, a string representing the metaid to be set
Returns
- the SBML FBC Objective structure with the new value for the metaid attribute
SBMLObjective = Objective_setSBOTerm(SBMLObjective, sboTerm)
Takes
- SBMLObjective, an SBML Objective structure
- sboTerm, a number representing the sboTerm to be set
Returns
- the SBML FBC Objective structure with the new value for the sboTerm attribute
SBMLObjective = Objective_setType(SBMLObjective, type)
Takes
- SBMLObjective, an SBML Objective structure
- type, a string representing the fbc_type to be set
Returns
- the SBML FBC Objective structure with the new value for the fbc_type attribute
SBMLObjective = Objective_unsetId(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the SBML FBC Objective structure with the fbc_id attribute unset
SBMLObjective = Objective_unsetMetaid(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the SBML FBC Objective structure with the metaid attribute unset
SBMLObjective = Objective_unsetSBOTerm(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the SBML FBC Objective structure with the sboTerm attribute unset
SBMLObjective = Objective_unsetType(SBMLObjective)
Takes
- SBMLObjective, an SBML Objective structure
Returns
- the SBML FBC Objective structure with the fbc_type attribute unset
SBMLToolbox-4.1.0/docs/fbc_package/structure-functions/fluxObjective.html 0000644 0000000 0000000 00000012172 11660503634 025227 0 ustar root root FBC_PACKAGE\MATLAB_SBML_STRUCTURES\FLUXOBJECTIVE
The functions allow users to create and work with the SBML FBC FluxObjective structure.
Function are:
FluxObjective = FluxObjective_create(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- a MATLAB_SBML FBC FluxObjective structure of the appropriate level, version and pkgVersion
coefficient = FluxObjective_getCoefficient(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the value of the fbc_coefficient attribute
metaid = FluxObjective_getMetaid(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the value of the metaid attribute
reaction = FluxObjective_getReaction(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the value of the fbc_reaction attribute
sboTerm = FluxObjective_getSBOTerm(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the value of the sboTerm attribute
coefficient = FluxObjective_isSetCoefficient(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- value =
- 1 if the fbc_coefficient attribute is set
- 0 otherwise
metaid = FluxObjective_isSetMetaid(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
reaction = FluxObjective_isSetReaction(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- value =
- 1 if the fbc_reaction attribute is set
- 0 otherwise
sboTerm = FluxObjective_isSetSBOTerm(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
SBMLFluxObjective = FluxObjective_setCoefficient(SBMLFluxObjective, coefficient)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
- coefficient, a number representing the fbc_coefficient to be set
Returns
- the SBML FBC FluxObjective structure with the new value for the fbc_coefficient attribute
SBMLFluxObjective = FluxObjective_setMetaid(SBMLFluxObjective, metaid)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
- metaid, a string representing the metaid to be set
Returns
- the SBML FBC FluxObjective structure with the new value for the metaid attribute
SBMLFluxObjective = FluxObjective_setReaction(SBMLFluxObjective, reaction)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
- reaction, a string representing the fbc_reaction to be set
Returns
- the SBML FBC FluxObjective structure with the new value for the fbc_reaction attribute
SBMLFluxObjective = FluxObjective_setSBOTerm(SBMLFluxObjective, sboTerm)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
- sboTerm, a number representing the sboTerm to be set
Returns
- the SBML FBC FluxObjective structure with the new value for the sboTerm attribute
SBMLFluxObjective = FluxObjective_unsetCoefficient(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the SBML FBC FluxObjective structure with the fbc_coefficient attribute unset
SBMLFluxObjective = FluxObjective_unsetMetaid(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the SBML FBC FluxObjective structure with the metaid attribute unset
SBMLFluxObjective = FluxObjective_unsetReaction(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the SBML FBC FluxObjective structure with the fbc_reaction attribute unset
SBMLFluxObjective = FluxObjective_unsetSBOTerm(SBMLFluxObjective)
Takes
- SBMLFluxObjective, an SBML FluxObjective structure
Returns
- the SBML FBC FluxObjective structure with the sboTerm attribute unset
SBMLToolbox-4.1.0/docs/fbc_package/structure-functions/fluxBound.html 0000644 0000000 0000000 00000015435 11660503634 024371 0 ustar root root FBC_PACKAGE\MATLAB_SBML_STRUCTURES\FLUXBOUND
The functions allow users to create and work with the SBML FBC FluxBound structure.
Function are:
FluxBound = FluxBound_create(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- a MATLAB_SBML FBC FluxBound structure of the appropriate level, version and pkgVersion
id = FluxBound_getId(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the value of the fbc_id attribute
metaid = FluxBound_getMetaid(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the value of the metaid attribute
operation = FluxBound_getOperation(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the value of the fbc_operation attribute
reaction = FluxBound_getReaction(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the value of the fbc_reaction attribute
sboTerm = FluxBound_getSBOTerm(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the value of the sboTerm attribute
value = FluxBound_getValue(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the value of the fbc_value attribute
id = FluxBound_isSetId(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- value =
- 1 if the fbc_id attribute is set
- 0 otherwise
metaid = FluxBound_isSetMetaid(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- value =
- 1 if the metaid attribute is set
- 0 otherwise
operation = FluxBound_isSetOperation(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- value =
- 1 if the fbc_operation attribute is set
- 0 otherwise
reaction = FluxBound_isSetReaction(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- value =
- 1 if the fbc_reaction attribute is set
- 0 otherwise
sboTerm = FluxBound_isSetSBOTerm(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- value =
- 1 if the sboTerm attribute is set
- 0 otherwise
value = FluxBound_isSetValue(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- value =
- 1 if the fbc_value attribute is set
- 0 otherwise
SBMLFluxBound = FluxBound_setId(SBMLFluxBound, id)
Takes
- SBMLFluxBound, an SBML FluxBound structure
- id, a string representing the fbc_id to be set
Returns
- the SBML FBC FluxBound structure with the new value for the fbc_id attribute
SBMLFluxBound = FluxBound_setMetaid(SBMLFluxBound, metaid)
Takes
- SBMLFluxBound, an SBML FluxBound structure
- metaid, a string representing the metaid to be set
Returns
- the SBML FBC FluxBound structure with the new value for the metaid attribute
SBMLFluxBound = FluxBound_setOperation(SBMLFluxBound, operation)
Takes
- SBMLFluxBound, an SBML FluxBound structure
- operation, a string representing the fbc_operation to be set
Returns
- the SBML FBC FluxBound structure with the new value for the fbc_operation attribute
SBMLFluxBound = FluxBound_setReaction(SBMLFluxBound, reaction)
Takes
- SBMLFluxBound, an SBML FluxBound structure
- reaction, a string representing the fbc_reaction to be set
Returns
- the SBML FBC FluxBound structure with the new value for the fbc_reaction attribute
SBMLFluxBound = FluxBound_setSBOTerm(SBMLFluxBound, sboTerm)
Takes
- SBMLFluxBound, an SBML FluxBound structure
- sboTerm, a number representing the sboTerm to be set
Returns
- the SBML FBC FluxBound structure with the new value for the sboTerm attribute
SBMLFluxBound = FluxBound_setValue(SBMLFluxBound, value)
Takes
- SBMLFluxBound, an SBML FluxBound structure
- value, a number representing the fbc_value to be set
Returns
- the SBML FBC FluxBound structure with the new value for the fbc_value attribute
SBMLFluxBound = FluxBound_unsetId(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the SBML FBC FluxBound structure with the fbc_id attribute unset
SBMLFluxBound = FluxBound_unsetMetaid(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the SBML FBC FluxBound structure with the metaid attribute unset
SBMLFluxBound = FluxBound_unsetOperation(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the SBML FBC FluxBound structure with the fbc_operation attribute unset
SBMLFluxBound = FluxBound_unsetReaction(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the SBML FBC FluxBound structure with the fbc_reaction attribute unset
SBMLFluxBound = FluxBound_unsetSBOTerm(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the SBML FBC FluxBound structure with the sboTerm attribute unset
SBMLFluxBound = FluxBound_unsetValue(SBMLFluxBound)
Takes
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the SBML FBC FluxBound structure with the fbc_value attribute unset
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The functions allow users to create and work with the FBC elements
and attributes of an SBML FBC Species structure.
Function are:
FBCSpecies = FBCSpecies_create(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- a MATLAB_SBML FBC FBCSpecies structure of the appropriate level, version and pkgVersion
charge = FBCSpecies_getCharge(SBMLFBCSpecies)
Takes
- SBMLFBCSpecies, an SBML FBCSpecies structure
Returns
- the value of the fbc_charge attribute
chemicalFormula = FBCSpecies_getChemicalFormula(SBMLFBCSpecies)
Takes
- SBMLFBCSpecies, an SBML FBCSpecies structure
Returns
- the value of the fbc_chemicalFormula attribute
charge = FBCSpecies_isSetCharge(SBMLFBCSpecies)
Takes
- SBMLFBCSpecies, an SBML FBCSpecies structure
Returns
- value =
- 1 if the fbc_charge attribute is set
- 0 otherwise
chemicalFormula = FBCSpecies_isSetChemicalFormula(SBMLFBCSpecies)
Takes
- SBMLFBCSpecies, an SBML FBCSpecies structure
Returns
- value =
- 1 if the fbc_chemicalFormula attribute is set
- 0 otherwise
SBMLFBCSpecies = FBCSpecies_setCharge(SBMLFBCSpecies, charge)
Takes
- SBMLFBCSpecies, an SBML FBCSpecies structure
- charge, a number representing the fbc_charge to be set
Returns
- the SBML FBC FBCSpecies structure with the new value for the fbc_charge attribute
SBMLFBCSpecies = FBCSpecies_setChemicalFormula(SBMLFBCSpecies, chemicalFormula)
Takes
- SBMLFBCSpecies, an SBML FBCSpecies structure
- chemicalFormula, a string representing the fbc_chemicalFormula to be set
Returns
- the SBML FBC FBCSpecies structure with the new value for the fbc_chemicalFormula attribute
SBMLFBCSpecies = FBCSpecies_unsetCharge(SBMLFBCSpecies)
Takes
- SBMLFBCSpecies, an SBML FBCSpecies structure
Returns
- the SBML FBC FBCSpecies structure with the fbc_charge attribute unset
SBMLFBCSpecies = FBCSpecies_unsetChemicalFormula(SBMLFBCSpecies)
Takes
- SBMLFBCSpecies, an SBML FBCSpecies structure
Returns
- the SBML FBC FBCSpecies structure with the fbc_chemicalFormula attribute unset
SBMLToolbox-4.1.0/docs/fbc_package/structure-functions/fBCModel.html 0000644 0000000 0000000 00000010534 11660503634 024031 0 ustar root root FBC_PACKAGE\MATLAB_SBML_STRUCTURES\FBCMODEL
The functions allow users to create and work with the FBC elements
and attributes of an SBML FBC Model structure.
Function are:
SBMLFBCModel = FBCModel_addFluxBound(SBMLFBCModel, SBMLFluxBound)
Takes
- SBMLFBCModel, an SBML FBCModel structure
- SBMLFluxBound, an SBML FluxBound structure
Returns
- the SBML FBCModel structure with the SBML FluxBound structure added
SBMLFBCModel = FBCModel_addObjective(SBMLFBCModel, SBMLObjective)
Takes
- SBMLFBCModel, an SBML FBCModel structure
- SBMLObjective, an SBML Objective structure
Returns
- the SBML FBCModel structure with the SBML Objective structure added
FBCModel = FBCModel_create(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- a MATLAB_SBML FBC FBCModel structure of the appropriate level, version and pkgVersion
SBMLFBCModel = FBCModel_createFluxBound(SBMLFBCModel)
Takes
- FBCModel, an SBML FBCModel structure
Returns
- the SBML FBCModel structure with a new SBML FluxBound structure added
SBMLFBCModel = FBCModel_createObjective(SBMLFBCModel)
Takes
- FBCModel, an SBML FBCModel structure
Returns
- the SBML FBCModel structure with a new SBML Objective structure added
activeObjective = FBCModel_getActiveObjective(SBMLFBCModel)
Takes
- SBMLFBCModel, an SBML FBCModel structure
Returns
- the value of the fbc_activeObjective attribute
fluxBound = FBCModel_getFluxBound(SBMLFBCModel, index)
Takes
- SBMLFBCModel, an SBML FBCModel structure
- index, an integer representing the index of SBML FluxBound structure
Returns
- the SBML FluxBound structure at the indexed position
fluxBound = FBCModel_getListOfFluxBounds(SBMLFBCModel)
Takes
- SBMLFBCModel, an SBML FBCModel structure
Returns
- an array of the fluxBound structures
objective = FBCModel_getListOfObjectives(SBMLFBCModel)
Takes
- SBMLFBCModel, an SBML FBCModel structure
Returns
- an array of the objective structures
num = FBCModel_getNumFluxBounds(SBMLFBCModel)
Takes
- SBMLFBCModel, an SBML FBCModel structure
Returns
- the number of SBML FluxBound structures present in the FBCModel
num = FBCModel_getNumObjectives(SBMLFBCModel)
Takes
- SBMLFBCModel, an SBML FBCModel structure
Returns
- the number of SBML Objective structures present in the FBCModel
objective = FBCModel_getObjective(SBMLFBCModel, index)
Takes
- SBMLFBCModel, an SBML FBCModel structure
- index, an integer representing the index of SBML Objective structure
Returns
- the SBML Objective structure at the indexed position
activeObjective = FBCModel_isSetActiveObjective(SBMLFBCModel)
Takes
- SBMLFBCModel, an SBML FBCModel structure
Returns
- value =
- 1 if the fbc_activeObjective attribute is set
- 0 otherwise
SBMLFBCModel = FBCModel_setActiveObjective(SBMLFBCModel, activeObjective)
Takes
- SBMLFBCModel, an SBML FBCModel structure
- activeObjective, a string representing the fbc_activeObjective to be set
Returns
- the SBML FBC FBCModel structure with the new value for the fbc_activeObjective attribute
SBMLFBCModel = FBCModel_unsetActiveObjective(SBMLFBCModel)
Takes
- SBMLFBCModel, an SBML FBCModel structure
Returns
- the SBML FBC FBCModel structure with the fbc_activeObjective attribute unset
SBMLToolbox-4.1.0/docs/fbc_package/structure/ 0000755 0000000 0000000 00000000000 11704572220 017513 5 ustar root root SBMLToolbox-4.1.0/docs/fbc_package/structure/objective.html 0000644 0000000 0000000 00000003004 11662153034 022351 0 ustar root root
Objective
typecode = SBML_FBC_OBJECTIVE
SBML Level 3 Version 1
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
fbc_id |
string |
fbc_type |
string |
| fbc_fluxObjective |
array of structures |
|
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FluxObjective
typecode = SBML_FBC_FLUXOBJECTIVE
SBML Level 3 Version 1
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
fbc_reaction |
string |
fbc_coefficient |
double |
isSetfbc_coefficient |
boolean |
|
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FluxBound
typecode = SBML_FBC_FLUXBOUND
SBML Level 3 Version 1
typecode |
as above |
metaid |
string |
notes |
string |
annotation |
string |
sboTerm |
integer |
fbc_id |
string |
fbc_reaction |
string |
fbc_operation |
string |
fbc_value |
double |
isSetfbc_value |
boolean |
|
SBMLToolbox-4.1.0/docs/fbc_package/structure/fbcspecies.html 0000644 0000000 0000000 00000005651 11665137076 022532 0 ustar root root
FBCSpecies
typecode = SBML_SPECIES
SBML Level 3 Version 1
|
typecode |
as above |
|
metaid |
string |
|
notes |
string |
|
annotation |
string |
|
sboTerm |
integer |
|
name |
string |
|
id |
string |
|
compartment |
string |
|
initialAmount |
double |
|
initialConcentration |
double |
|
substanceUnits |
string |
|
hasOnlySubstanceUnits |
boolean |
|
boundaryCondition |
boolean |
|
constant |
boolean |
|
isSetInitialAmount |
boolean |
|
isSetInitialConcentration |
boolean |
|
conversionFactor |
string |
| ∗ |
fbc_charge |
integer |
| ∗ |
isSetfbc_charge |
boolean |
| ∗ |
fbc_chemicalFormula |
string |
|
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FBCModel
typecode = SBML_MODEL
SBML Level 3 Version 1
|
typecode |
as above |
|
metaid |
string |
|
notes |
string |
|
annotation |
string |
|
SBML_level |
double |
|
SBML_version |
double |
|
name |
string |
|
id |
string |
|
sboTerm |
integer |
|
functionDefinition |
array of structures |
|
unitDefinition |
array of structures |
|
compartment |
array of structures |
| ‡ |
species |
array of structures |
|
parameter |
array of structures |
|
initialAssignment |
array of structures |
|
rule |
array of structures |
|
constraint |
array of structures |
|
reaction |
array of structures |
|
event |
array of structures |
|
substanceUnits |
string |
|
timeUnits |
string |
|
lengthUnits |
string |
|
areaUnits |
string |
|
volumeUnits |
string |
|
extentUnits |
string |
|
conversionFactor |
string |
| ∗ |
fbc_fluxBound |
array of structures |
| ∗ |
fbc_objective |
array of structures |
| ∗ |
fbc_activeObjective |
string |
|
SBMLToolbox-4.1.0/docs/fbc_package/fbcValidation.html 0000644 0000000 0000000 00000011616 11660503434 021115 0 ustar root root FBC_PACKAGE\VALIDATE_MATLAB_SBML_STRUCTURES
This folder contains tests that checks that the structure supplied as argument
is of the appropriate form to represent the intended element of an SBML model
that includes the fbc package.
Function are:
[valid, message] = isSBML_FBC_FluxBound(SBMLFBCFluxBound, level, version, pkgVersion)
Takes
- SBMLStructure, an SBML FBC FluxBound structure
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an FBC package version
Returns
- valid =
- 1, if the structure represents
a MATLAB_SBML FBC FluxBound structure of the appropriate
level, version and FBC version
- 0, otherwise
- a message explaining any failure
NOTE: The fields present in a MATLAB_SBML FBC FluxBound structure of the appropriate
level and version can be found using getFluxBoundFieldnames(level, version, pkgVersion)
[valid, message] = isSBML_FBC_FluxObjective(SBMLFBCFluxObjective, level, version, pkgVersion)
Takes
- SBMLStructure, an SBML FBC FluxObjective structure
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an FBC package version
Returns
- valid =
- 1, if the structure represents
a MATLAB_SBML FBC FluxObjective structure of the appropriate
level, version and FBC version
- 0, otherwise
- a message explaining any failure
NOTE: The fields present in a MATLAB_SBML FBC FluxObjective structure of the appropriate
level and version can be found using getFluxObjectiveFieldnames(level, version, pkgVersion)
[valid, message] = isSBML_FBC_Model(SBMLFBCModel, level, version, pkgVersion)
Takes
- SBMLStructure, an SBML FBC Model structure
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an FBC package version
Returns
- valid =
- 1, if the structure represents
a MATLAB_SBML FBC Model structure of the appropriate
level, version and FBC version
- 0, otherwise
- a message explaining any failure
NOTE: The fields present in a MATLAB_SBML FBC Model structure of the appropriate
level and version can be found using getModelFieldnames(level, version, pkgVersion)
[valid, message] = isSBML_FBC_Objective(SBMLFBCObjective, level, version, pkgVersion)
Takes
- SBMLStructure, an SBML FBC Objective structure
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an FBC package version
Returns
- valid =
- 1, if the structure represents
a MATLAB_SBML FBC Objective structure of the appropriate
level, version and FBC version
- 0, otherwise
- a message explaining any failure
NOTE: The fields present in a MATLAB_SBML FBC Objective structure of the appropriate
level and version can be found using getObjectiveFieldnames(level, version, pkgVersion)
[valid, message] = isSBML_FBC_Species(SBMLFBCSpecies, level, version, pkgVersion)
Takes
- SBMLStructure, an SBML FBC Species structure
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an FBC package version
Returns
- valid =
- 1, if the structure represents
a MATLAB_SBML FBC Species structure of the appropriate
level, version and FBC version
- 0, otherwise
- a message explaining any failure
NOTE: The fields present in a MATLAB_SBML FBC Species structure of the appropriate
level and version can be found using getSpeciesFieldnames(level, version, pkgVersion)
[valid, message] = isValidFBC(SBMLStruct, level, version, pkgVersion)
Takes
- SBMLStruct, an SBML structure
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing the FBC package version
Returns
- valid =
- 1, if the structure represents
a MATLAB_SBML FBC structure of the appropriate
level and version
- 0, otherwise
- a message explaining any failure
NOTE: The fields present in a MATLAB_SBML structure of the appropriate
level and version can be found using getFieldnames(typecode, level, version)
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These functions return the fieldnames and default values for the MATLAB_SBML FBC structures.
Function are:
[values] = getFBCModelDefaultValues(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of default values for teh FBC attributes SBML Model structure of the given level and version
NOTE: The corresponding fields present in an SBML FBC Model structure can be found using
the function getFBCModelFieldnames
[fieldnames, num] = getFBCModelFieldnames(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of fieldnames for an SBML FBCModel structure of the given level and version
- the number of fieldnames
[values] = getFBCSpeciesDefaultValues(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of default values for teh FBC attributes SBML Species structure of the given level and version
NOTE: The corresponding fields present in an SBML FBC Species structure can be found using
the function getFBCSpeciesFieldnames
[fieldnames, num] = getFBCSpeciesFieldnames(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of fieldnames for an SBML FBCSpecies structure of the given level and version
- the number of fieldnames
[values] = getFluxBoundsDefaultValues(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of default values for an SBML FluxBound structure of the given level and version
NOTE: The corresponding fields present in an SBML FluxBound structure can be found using
the function getFluxBoundFieldnames
[fieldnames, num] = getFluxBoundFieldnames(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of fieldnames for an SBML FluxBound structure of the given level and version
- the number of fieldnames
[values] = getFluxObjectivesDefaultValues(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of default values for an SBML FluxObjective structure of the given level and version
NOTE: The corresponding fields present in an SBML FluxObjective structure can be found using
the function getFluxObjectiveFieldnames
[fieldnames, num] = getFluxObjectiveFieldnames(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of fieldnames for an SBML FluxObjective structure of the given level and version
- the number of fieldnames
[values] = getObjectiveDefaultValues(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of default values for an SBML Objective structure of the given level and version
NOTE: The corresponding fields present in an SBML Objective structure can be found using
the function getObjectiveFieldnames
[fieldnames, num] = getObjectiveFieldnames(level, version, pkgVersion)
Takes
- level, an integer representing an SBML level
- version, an integer representing an SBML version
- pkgVersion, an integer representing an SBML package version
Returns
- an array of fieldnames for an SBML Objective structure of the given level and version
- the number of fieldnames
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Functions for using the SBML L3V1 fbc package.
Function are:
fbcEnabled = isBindingFbcEnabled()
Returns
- fbcEnabled =
- 1 if the executables are enabled with fbc support
- 0 otherwise
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CONVENIENCE
The Convenience folder contains a number of convenience functions for checking information or manipulating math expressions.
Function are:
y = CheckValidUnitKind(kind)
Takes
- kind, a string representing a unit kind
Returns
- y =
- 1 if the string represents a valid unit kind
- 0 otherwise
NOTE: This is identical to the function isValidUnitKind
newArray = LoseWhiteSpace(charArray)
Takes
- charArray, an array of characters
Returns
- the array with any white space removed
EXAMPLE:
newArray = LoseWhiteSpace(' exa mp le')
newArray = 'example'
pairs = PairBrackets(expression)
Takes
- expression, a string representation of a math expression
Returns
- an array of the indices of each pair of brackets ordered from
the opening bracket index
EXAMPLE:
pairs = PairBrackets('(a+((b*c)/(a+b)))')
pairs =
1 17
4 16
5 9
11 15
output = Rearrange(expression, name)
Takes
- expression, a string representation of a math expression
- name, a string representing the name of a variable
Returns
- the expression rearranged in terms of the variable
EXAMPLE:
output = Rearrange('X + Y - Z', 'X')
output = '-Y+Z'
newArray = RemoveDuplicates(array)
Takes
- array, any array
Returns
- the array with any duplicate entries removed
EXAMPLE:
newArray = RemoveDuplicates([2, 3, 4, 3, 2, 5])
newArray = [2, 3, 4, 5]
value = Substitute(expression, SBMLModel)
Takes
- expression, a string representation of a math expression
- SBMLModel, an SBML Model structure
Returns
- the value of the expression when all variables within the model have
been substituted
EXAMPLE:
Consider m to be an SBMLModel containing a species with
id = 'g' and initialConcentration = '3'
value = Substitute('g*2', m)
value = 6
newExpression = SubstituteConstants(expression, SBMLModel)
Takes
- expression, a string representation of a math expression
- SBMLModel, an SBML Model structure
Returns
- the string representation of the expression when all constants within the
model have been substituted
EXAMPLE:
Consider m to be an SBMLModel containing a parameter
with id = 'g', constant = '1' and value = 3'
newExpression = SubstituteConstants('2 * g * S1', SBMLModel)
newExpression = '2 * 3 * S1'
newExpression = SubstituteFunction(expression, SBMLFunctionDefinition)
Takes
- expression, a string representation of a math expression
- SBMLFunctionDefinition, an SBML FunctionDefinition structure
Returns
- newExpression
- the string representation of the expression when any instances of the
functionDefinition have been substituted
- an empty string if the functiondefinition is not in the original
expression
EXAMPLE:
Consider fD to be an SBMLFunctionDefinition
with id = 'g' and math = 'lambda(x,x+0.5)'
formula = SubstituteFormula('g(y)', fD)
formula = 'y+0.5'
formula = SubstituteFormula('h(y)', fD)
formula = ''
y = isIntegralNumber(number)
Takes
- number, any number
Returns
- y =
- 1 if the number represents an integer
- 0 otherwise
EXAMPLE:
y = isIntegralNumber(int32(3))
y = 1
y = isIntegralNumber(double(3.2))
y = 0
y = isIntegralNumber(double(3))
y = 1
NOTE: The inbuilt 'isinteger' function only returns true if the number
has been declared as having an integer type, whereas the default type for numbers
in MATLAB is double. This function will return '1' if the number
represents an integer.
y = isValidUnitKind(kind)
Takes
- kind, a string representing a unit kind
returns
- y =
- 1 if the string represents a valid unit kind
- 0 otherwise
NOTE: This is identical to the function CheckValidUnitKind
index = matchFunctionName(expression, name)
Takes
- expression, a string representation of a math expression
- name, a string representing the name of a function
Returns
- the index of the starting point of 'name' in the 'expression'
EXAMPLE:
index = matchFunctionName('f*g', 'g')
index = []
index = matchFunctionName('add(d,g_1)', 'add')
index = 0
index = matchFunctionName('add(add(a,b), c)', 'add')
index = [1, 5]
NOTE: This differs from the 'strfind' function in that it checks
that the name is used as a function call.
index = matchName(expression, name)
Takes
- expression, a string representation of a math expression
- name, a string representing the name of a variable
Returns
- the index of the starting point of 'name' in the 'expression'
EXAMPLE:
index = matchName('f*g', 'g')
index = 3
index = matchName('f*g_1', 'g')
index = []
index = matchName('f*g(a,g)', 'g')
index = 7
NOTE: This differs from the 'strfind' function in that it checks
that the name is used as a variable.
value = piecewise(value1, test, value2)
Takes
- value1, the value to return if the test is true
- test, a boolean test that will return true or false
- value2, the value to return if the test is false
Returns
- value =
- value1, if test returns true
- value2, if test returns false
EXAMPLE:
value = piecewise(3, 1<2, 4)
value = 3
value = piecewise(3, 1>2, 4)
value = 4
NOTE: This function provides the functionality of the MathML 'piecewise' function.
y = testmember(value, array)
Takes
- value, any number/string
- array, an array of objects
Returns
- y =
- 1 if value is a member of the array
- 0 otherwise
NOTE: this function is necessary for octave to emulate the MATLAB
functionality of the 'ismember' function
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ACCESSMODEL
The AccessModel folder contains a number of functions that derive information from the MATLAB_SBML structures.
Function are:
array = DetermineSpeciesRoleInReaction(SBMLSpecies, SBMLReaction)
Takes
- SBMLSpecies, an SBML species structure
- SBMLReaction, an SBML reaction structure
Returns
- an array with five elements
[isProduct, isReactant, isModifier,
positionInProductList, positionInReactantList] indicating
whether the species is a product, reactant or modifier and recording
the position in the list of products/reactants
or
- array = 0 if the species is NOT part of the reaction
EXAMPLE:
y = DetermineSpeciesRoleInReaction(s, r)
= 0 if s is not in r
= [1, 0, 0, 2, 0] if s is product number 2 in rb
= [0, 1, 0, 0, 1] if s is reactant number 1 in r
= [0, 0, 1, 0, 0] if s is a modifier in r
= [1, 1, 0, 1, 2] if s is product number 1 and reactant number 2 in r
[names, values] = GetAllParameters(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all parameters
(both global and embedded) within the model
- an array of the values of each parameter
NOTE: the value returned will be (in order)
- determined from assignmentRules/initialAssignments where appropriate
- the attribute 'value' for the given parameter
- NaN, if the value is not specified in any way within the model
[names, values] = GetAllParametersUnique(SBMLModel)
Takes
- SBMLModel, an SBML model structure
Returns
- an array of strings representing the identifiers of all parameters
(both global and embedded) within the model.
Note: reaction names are appended to the names of parameters
declared within a reaction
- an array of the values of each parameter
NOTE: the value returned will be (in order)
- determined from assignmentRules/initialAssignments where appropriate
- the attribute 'value' for the given parameter
- NaN, if the value is not specified in any way within the model
EXAMPLE:
model has 1 parameter k1
and reaction R1 that lists a local parameter k1
[names, values] = GetAllParametersUnique(model)
names = [k1, k1_R1]
values = [2, 1.5]
names = GetCompartmentTypes(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all compartmentTypes within the model
[names, values] = GetCompartments(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all compartments within the model
- an array of the size/volume values of each compartment
NOTE: the value returned will be (in order)
- determined from assignmentRules/initialAssignments where appropriate
- the attribute 'size' ('volume' in L1) for the given compartment
- NaN, if the value is not specified in any way within the model
[names, values] = GetGlobalParameters(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of
all global parameters within the model
- an array of the values of each parameter
NOTE: the value returned will be (in order)
- determined from assignmentRules/initialAssignments where appropriate
- the attribute 'value' for the given parameter
- NaN, if the value is not specified in any way within the model
[parameters, algebraicRules] = GetParameterAlgebraicRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all parameters
an array of
- the character representation of each algebraic
rule the parameter appears in
- '0' if the particular parameter is not in an algebraic rule
EXAMPLE:
model has 3 parameters (k1, k2, k3)
and 2 algebraic rules with formula 'k2+7' and 'k2-k3'
[parameters, algebraicRules] = GetParameterAlgebraicRules(model)
parameters = ['k1', 'k2', 'k3']
algebraicRules = {'0', ['k2+7', 'k2-k3'], ['k2-k3']}
[parameters, assignmentRules] = GetParameterAssignmentRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all parameters
an array of
- the character representation of the assignment rule used to
assign value to a given parameter
- '0' if the parameter is not assigned by a rule
[names, values] = GetParameterFromReaction(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- an array of strings representing the identifiers of all parameters defined
within the kinetic law of the reaction
- an array of the values of each parameter
[names, values] = GetParameterFromReactionUnique(SBMLReaction)
Takes
- SBMLReaction, an SBML Reaction structure
Returns
- an array of strings representing the identifiers of all parameters defined
within the kinetic law of the reaction, with the reaction
name appended
- an array of the values of each parameter
EXAMPLE:
reaction with id R1 has 2 parameters k1 and k2
[names, values] = GetParameterFromReactionUnique(reaction)
names = [k1_R1, k2_R1]
values = [2, 1.5]
[parameters, raterules] = GetParameterRateRules((SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all parameters
an array of
- the character representation of the rate rule used to
assign value to a given parameter
- '0' if the parameter is not assigned by a rule
[species, rateLaws] = GetRateLawsFromReactions(SBMLModel)
Takes
- SBMLModel; an SBML Model structure
Returns
- an array of strings representing the identifiers of all species
an array of
- the character representation of the rate law established from any reactions
that determines the particular species
- '0' if the particular species is not a reactant/product in any reaction
EXAMPLE:
model has 4 species (s1, s2, s3, s4)
and 2 reactions; s1 -> s2 with kineticLaw 'k1*s1'
s2 -> s3 with kineticLaw 'k2*s2'
[species, rateLaws] = GetRateLawsFromReactions(model)
species = ['s1', 's2', 's3', 's4']
rateLaws = {'-k1*s1', 'k1*s1-k2*s2', 'k2*s2', '0'}
[species, rateLaws] = GetRateLawsFromRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all species
an array of
- the character representation of the rateRule that determines
the particular species
- '0' if the particular species is not assigned by a rateRule
[names, values] = GetSpecies(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all species within the model
- an array of the initial concentration/amount values of each species
NOTE: the value returned will be (in order)
- determined from assignmentRules/initialAssignments where appropriate
- the attribute 'initialAmount' or 'initialConcentration' for the given parameter
- NaN, if the value is not specified in any way within the model
[names, values] = GetSpeciesAlgebraicRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all species
an array of
- the character representation of each algebraic
rule the species appears in
- '0' if the particular species is not in an algebraic rule
EXAMPLE:
model has 3 species (s1, s2, s3)
and 2 algebraic rules with formula 's2+7' and 's2-s3'
[species, algebraicRules] = GetSpeciesAlgebraicRules(model)
species = ['s1', 's2', 's3']
algebraicRules = {'0', ['s2+7', 's2-s3'], ['k2-k3']}
[species, assignmentRules] = GetSpeciesAssignmentRules(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all species
an array of
- the character representation of the assignment rule used to
assign value to a given species
- '0' if the species is not assigned by a rule
names = GetSpeciesTypes(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of all SpeciesTypes within the model
[matrix, species] = GetStoichiometryMatrix(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- the stoichiometry matrix produced from the reactions/species
- an array of strings representing the identifiers of all species within the model
(in the order in which the matrix deals with them)
EXAMPLE:
model has 5 species (s1, s2, s3, s4, s5)
and 3 reactions: s1 -> s2
s3 -> s5
2s1 -> s5
[matrix, species] = GetRateLawsFromReactions(model)
matrix = -1 0 -2
1 0 0
0 -1 0
0 1 1
species = ['s1', 's2', 's3', 's5']
(species s4 does not play a role in any reaction)
S = GetStoichiometrySparse(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- a sparse stoichiometry matrix produced from the reactions/species
NOTE: This function was contributed by: Arsen Batagov (2006)
[names, values] = GetVaryingParameters(SBMLModel)
Takes
- SBMLModel, an SBML Model structure
Returns
- an array of strings representing the identifiers of any non-constant parameters
within the model
- an array of the values of each of these parameter
NOTE: the value returned will be (in order)
- determined from assignmentRules/initialAssignments where appropriate
- the attribute 'value' for the given parameter
- NaN; if the value is not specified in any way within the model
num = IsSpeciesInReaction(SBMLSpecies, SBMLReaction)
Takes
- SBMLSpecies, an SBML Species structure
- SBMLReaction, an SBML Reaction structure
Returns
- the number of times the species occurs within the reaction
SBMLToolbox-4.1.0/COPYING.txt 0000644 0000000 0000000 00000063647 11540617602 014211 0 ustar root root
GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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GNU LESSER GENERAL PUBLIC LICENSE
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That's all there is to it!
|
SBMLToolbox-4.1.0/AUTHORS.txt 0000644 0000000 0000000 00000000750 11626644524 014220 0 ustar root root SBMLToolbox has been primarily developed by
Sarah Keating
with contributions from (in alphabetical order)
Arsen Batagov, Ben Bornstein, Will Bryant, Bill Denney,
Andrew Finney, Thomas Grotkjær, Mike Hucka, Pieter Pareit,
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and others in the SBML community.
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