/usr/share/SBMLToolbox/AccessModel/DetermineSpeciesRoleInReaction.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 | function y = DetermineSpeciesRoleInReaction(SBMLSpecies, SBMLReaction)
% 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
%
%
% *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
%<!---------------------------------------------------------------------------
% 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.
%----------------------------------------------------------------------- -->
if ~isValid(SBMLSpecies)
error('DetermineSpeciesRoleInReaction(SBMLSpecies, SBMLReaction)\n%s', ...
'first input must be an SBML Species structure');
elseif ~isValid(SBMLReaction)
error('DetermineSpeciesRoleInReaction(SBMLSpecies, SBMLReaction)\n%s', ...
'second input must be an SBML Reaction structure');
end;
Number = IsSpeciesInReaction(SBMLSpecies, SBMLReaction);
if (Number == 0)
y = 0;
return;
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;
reactionName = SBMLReaction.name;
else
if (isempty(SBMLSpecies.id))
name = SBMLSpecies.name;
else
name = SBMLSpecies.id;
end;
if (isempty(SBMLReaction.id))
reactionName = SBMLReaction.name;
else
reactionName = SBMLReaction.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
% zero all flags
ProductNo = 0;
ReactantNo = 0;
ModifierNo = 0;
ReactantPosition = 0;
ProductPosition = 0;
%look for reference to this species
for c = 1:NumProducts
if (strcmp(name, SBMLReaction.product(c).species))
ProductNo = ProductNo + 1;
ProductPosition(ProductNo) = c;
end;
end;
for c = 1:NumReactants
if (strcmp(name, SBMLReaction.reactant(c).species))
ReactantNo = ReactantNo + 1;
ReactantPosition(ReactantNo) = c;
end;
end;
for c = 1:NumModifiers
if (strcmp(name, SBMLReaction.modifier(c).species))
ModifierNo = ModifierNo + 1;
end;
end;
%--------------------------------------------------------------------------
% assign output
if ((ReactantNo > 1) || (ProductNo > 1))
error('DetermineSpeciesRoleInReaction(SBMLSpecies, SBMLReaction)\nspecies %s %s %s\n%s', name,'occurs more than once as a reactant/product in reaction', reactionName, 'this code does not deal with that situation');
end;
y = [ProductNo, ReactantNo, ModifierNo, ProductPosition, ReactantPosition];
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