/usr/share/SBMLToolbox/AccessModel/GetSpeciesAlgebraicRules.m is in sbmltoolbox 4.1.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | function [Species, AlgebraicRules] = GetSpeciesAlgebraicRules(SBMLModel)
% [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
%
% *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']}
%
%
%
%<!---------------------------------------------------------------------------
% 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.
%----------------------------------------------------------------------- -->
% check input is an SBML model
if (~isValidSBML_Model(SBMLModel))
error('GetSpeciesAlgebraicRules(SBMLModel)\n%s', 'input must be an SBMLModel structure');
end;
%--------------------------------------------------------------
% get information from the model
Species = GetSpecies(SBMLModel);
NumberSpecies = length(SBMLModel.species);
Rules = Model_getListOfAlgebraicRules(SBMLModel);
NumRules = Model_getNumAlgebraicRules(SBMLModel);
for i = 1:NumberSpecies
output = '';
if (NumRules > 0)
%determine which rules it occurs within
RuleNo = Species_isInAlgebraicRule(SBMLModel.species(i), Rules);
for j = 1:length(RuleNo)
if (RuleNo(j) > 0)
output{j} = Rules(RuleNo(j)).formula;
end;
end;
end;
% finished looking for this species
% record rate law and loop to next species
% rate = 0 if no law found
if (isempty(output))
AlgebraicRules{i} = '0';
else
AlgebraicRules{i} = output;
end;
end; % for NumSpecies
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