/usr/share/SBMLToolbox/AccessModel/Contents.m is in sbmltoolbox 4.1.0-2.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 | % toolbox\AccessModel
%
% The AccessModel folder contains a number of functions that derive
% information from the MATLAB_SBML structures.
%
%===================================================================
% array = DetermineSpeciesRoleInReaction(SBMLSpecies, SBMLReaction)
%===================================================================
% Takes
% 1. SBMLSpecies, an SBML species structure
% 2. SBMLReaction, an SBML reaction structure
% Returns
% 1. 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
% 1. array = 0 if the species is NOT part of the reaction
%
%================================================
% [names, values] = GetAllParameters(SBMLModel)
%================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all parameters
% (both global and embedded) within the model
% 2. an array of the values of each parameter
%
%=====================================================
% [names, values] = GetAllParametersUnique(SBMLModel)
%=====================================================
% Takes
% 1. SBMLModel, an SBML model structure
% Returns
% 1. 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
% 2. an array of the values of each parameter
%
%========================================
% names = GetCompartmentTypes(SBMLModel)
%========================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all compartmentTypes within the model
%
%==============================================
% [names, values] = GetCompartments(SBMLModel)
%==============================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all compartments within the model
% 2. an array of the size/volume values of each compartment
%
%==================================================
% [names, values] = GetGlobalParameters(SBMLModel)
%==================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of
% all global parameters within the model
% 2. an array of the values of each parameter
%
%======================================================================
% [parameters, algebraicRules] = GetParameterAlgebraicRules(SBMLModel)
%======================================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all parameters
% 2. 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
%
%=========================================================================
% [parameters, assignmentRules] = GetParameterAssignmentRules(SBMLModel)
%=========================================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all parameters
% 2. 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
% 1. SBMLReaction, an SBML Reaction structure
% Returns
% 1. an array of strings representing the identifiers of all parameters defined
% within the kinetic law of the reaction
% 2. an array of the values of each parameter
%
%================================================================
% [names, values] = GetParameterFromReactionUnique(SBMLReaction)
%================================================================
% Takes
% 1. SBMLReaction, an SBML Reaction structure
% Returns
% 1. an array of strings representing the identifiers of all parameters defined
% within the kinetic law of the reaction, with the reaction
% name appended
% 2. an array of the values of each parameter
%
%=============================================================
% [parameters, raterules] = GetParameterRateRules((SBMLModel)
%=============================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all parameters
% 2. 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
% 1. SBMLModel; an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all species
% 2. 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
%
%=======================================================
% [species, rateLaws] = GetRateLawsFromRules(SBMLModel)
%=======================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all species
% 2. 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
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all species within the model
% 2. an array of the initial concentration/amount values of each species
%
%=======================================================
% [names, values] = GetSpeciesAlgebraicRules(SBMLModel)
%=======================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all species
% 2. 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
%
%====================================================================
% [species, assignmentRules] = GetSpeciesAssignmentRules(SBMLModel)
%====================================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all species
% 2. 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
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. an array of strings representing the identifiers of all SpeciesTypes within the model
%
%=======================================================
% [matrix, species] = GetStoichiometryMatrix(SBMLModel)
%=======================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. the stoichiometry matrix produced from the reactions/species
% 2. an array of strings representing the identifiers of all species within the model
% (in the order in which the matrix deals with them)
%
%=======================================
% S = GetStoichiometrySparse(SBMLModel)
%=======================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. a sparse stoichiometry matrix produced from the reactions/species
%
%===================================================
% [names, values] = GetVaryingParameters(SBMLModel)
%===================================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
%
% 1. an array of strings representing the identifiers of any non-constant parameters
% within the model
% 2. an array of the values of each of these parameter
%
%======================================================
% num = IsSpeciesInReaction(SBMLSpecies, SBMLReaction)
%======================================================
% Takes
% 1. SBMLSpecies, an SBML Species structure
% 2. SBMLReaction, an SBML Reaction structure
% Returns
% 1. the number of times the species occurs within the reaction
%
%<!---------------------------------------------------------------------------
% 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.
%----------------------------------------------------------------------- -->
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