/usr/share/SBMLToolbox/AccessModel/IsSpeciesInReaction.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 y = IsSpeciesInReaction(SBMLSpecies, SBMLReaction)
% 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
% Filename : IsSpeciesInReaction.m
% Description : IsSpeciesInReaction(SBMLSpecies, SBMLReaction)takes a SBML species and reaction
% and determines where the species takes part in the reaction
% Author(s) : SBML Development Group <sbml-team@caltech.edu>
% Organization: University of Hertfordshire STRC
% Created : 2004-02-02
% Revision : $Id: IsSpeciesInReaction.m 15207 2012-01-10 18:07:47Z mhucka $
% Source : $Source $
%
%<!---------------------------------------------------------------------------
% 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 that input is valid
if (~isValid(SBMLSpecies))
error('IsSpeciesInReaction(SBMLSpecies, SBMLReaction)\n%s', 'first input must be an SBML Species structure');
end;
if(~isValid(SBMLReaction))
error('IsSpeciesInReaction(SBMLSpecies, SBMLReaction)\n%s', 'second input must be an SBML Reaction structure');
end;
SBMLLevel = GetLevel(SBMLSpecies);
%--------------------------------------------------------------------------
% determine the name of the species
% this will match to the speciesreference within the reaction
if (SBMLLevel == 1)
name = SBMLSpecies.name;
else
if (isempty(SBMLSpecies.id))
name = SBMLSpecies.name;
else
name = SBMLSpecies.id;
end;
end;
%--------------------------------------------------------------------------
%determine number of each type of species included within this reaction
NumProducts = length(SBMLReaction.product);
NumReactants = length(SBMLReaction.reactant);
if (SBMLLevel > 1)
NumModifiers = length(SBMLReaction.modifier);
else
NumModifiers = 0;
end;
%-------------------------------------------------------------------------
% find species in this reaction
y = 0;
for c = 1:NumProducts
if (strcmp(name, SBMLReaction.product(c).species))
y = y + 1;
end;
end;
for c = 1:NumReactants
if (strcmp(name, SBMLReaction.reactant(c).species))
y = y + 1;
end;
end;
for c = 1:NumModifiers
if (strcmp(name, SBMLReaction.modifier(c).species))
y = y + 1;
end;
end;
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