/usr/share/SBMLToolbox/AccessModel/GetRateLawsFromRules.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 94 95 96 97 98 99 100 101 102 | function [Species, RateLaws] = GetRateLawsFromRules(SBMLModel)
% [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
%<!---------------------------------------------------------------------------
% 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('GetRateLawsFromRules(SBMLModel)\n%s', 'input must be an SBMLModel structure');
end;
%--------------------------------------------------------------
% get information from the model
Species = GetSpecies(SBMLModel);
NumberSpecies = length(SBMLModel.species);
RateRules = Model_getListOfRateRules(SBMLModel);
NumRateRules = Model_getNumRateRules(SBMLModel);
% for each species loop through each reaction and determine whether the species
% takes part and in what capacity
for i = 1:NumberSpecies
output = '';
% if species is constant in level 2
% concentration cannot be changed by a rate rule
boundary = SBMLModel.species(i).boundaryCondition;
if (SBMLModel.SBML_level > 1)
constant = SBMLModel.species(i).constant;
else
constant = -1;
end;
if (constant == 1)
output = '0';
else
%determine which rules it occurs within
j = 0;
while (j <NumRateRules)
if ((strcmp(Species(i), RateRules(j+1).variable)) | (strcmp(Species(i), RateRules(j+1).species)))
output = RateRules(j+1).formula;
break;
else
j = j + 1;
end;
end; % while NumRateRules
end; % if constant
% finished looking for this species
% record rate law and loop to next species
% rate = 0 if no law found
if (isempty(output))
RateLaws{i} = '0';
else
RateLaws{i} = output;
end;
end; % for NumSpecies
if NumberSpecies == 0
RateLaws = {};
end;
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