/usr/share/SBMLToolbox/AccessModel/GetParameterFromReactionUnique.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 | function varargout = GetParameterFromReactionUnique(SBMLReaction)
% [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
%
% *EXAMPLE:*
%
% reaction with id R1 has 2 parameters k1 and k2
%
% [names, values] = GetParameterFromReactionUnique(reaction)
%
% names = [k1_R1, k2_R1]
% values = [2, 1.5]
%
%<!---------------------------------------------------------------------------
% 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 reaction and determine level
if (~isValid(SBMLReaction))
error('GetParameterFromReaction(SBMLReaction)\n%s', 'input must be an SBMLReaction structure');
end;
Level = GetLevel(SBMLReaction);
%------------------------------------------------------------
% determine the name of the reaction
if (Level == 1)
Reaction_name = SBMLReaction.name;
else
if (isempty(SBMLReaction.id))
Reaction_name = SBMLReaction.name;
else
Reaction_name = SBMLReaction.id;
end;
end;
%------------------------------------------------------------
% determine the number of parameters within the reaction
% catch case with no kinetic law
if (isempty(SBMLReaction.kineticLaw))
NumParams = 0;
else
if (Level < 3)
NumParams = length(SBMLReaction.kineticLaw.parameter);
else
NumParams = length(SBMLReaction.kineticLaw.localParameter);
end;
end;
%------------------------------------------------------------
% loop through the list of parameters
for i = 1:NumParams
%determine the name or id of the parameter
if (Level == 1)
name = SBMLReaction.kineticLaw.parameter(i).name;
elseif (Level == 2)
if (isempty(SBMLReaction.kineticLaw.parameter(i).id))
name = SBMLReaction.kineticLaw.parameter(i).name;
else
name = SBMLReaction.kineticLaw.parameter(i).id;
end;
else
name = SBMLReaction.kineticLaw.localParameter(i).id;
end;
% append the reaction name
name = strcat(name, '_', Reaction_name);
% save into an array of character names
CharArray{i} = name;
% put the value into the array
if (Level < 3)
Values(i) = SBMLReaction.kineticLaw.parameter(i).value;
else
Values(i) = SBMLReaction.kineticLaw.localParameter(i).value;
end;
end;
%--------------------------------------------------------------------------
% assign output
if (NumParams ~= 0)
varargout{1} = CharArray;
varargout{2} = Values;
else
varargout{1} = [];
varargout{2} = [];
end;
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