/usr/share/SBMLToolbox/AccessModel/GetParameterRateRules.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 [Parameter, RateRules] = GetParameterRateRules(SBMLModel)
% [parameters, raterules] = GetParameterRateRules((SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. an array of strings representing the identifiers of all parameters
% 2. an array of
%
% - the character representation of the rate rule used to
% assign value to a given parameter
% - '0' if the parameter is not assigned by a rule
%<!---------------------------------------------------------------------------
% 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('GetParameterRateRules(SBMLModel)\n%s', 'input must be an SBMLModel structure');
end;
%--------------------------------------------------------------
% get information from the model
Parameter = GetGlobalParameters(SBMLModel);
NumberParameter = length(SBMLModel.parameter);
AssignRules = Model_getListOfRateRules(SBMLModel);
NumAssignRules = Model_getNumRateRules(SBMLModel);
% for each Parameter loop through each rule and determine whether the Parameter
% takes part and in what capacity
for i = 1:NumberParameter
output = '';
% if Parameter is constant in level 2
% concentration cannot be changed by a rule
if (SBMLModel.SBML_level > 1)
constant = SBMLModel.parameter(i).constant;
else
constant = -1;
end;
if (constant == 1)
output = '0';
else
if (NumAssignRules > 0)
%determine which rules it occurs within
RuleNo = Parameter_isAssignedByRateRule(SBMLModel.parameter(i), AssignRules);
if (RuleNo > 0)
output = AssignRules(RuleNo).formula;
end;
end;
end; % if constant
% finished looking for this Parameter
% record rate law and loop to next Parameter
% rate = 0 if no law found
if (isempty(output))
RateRules{i} = '0';
else
RateRules{i} = output;
end;
end; % for NumParameter
|