/usr/share/SBMLToolbox/Convenience/SubstituteConstants.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 | function subsFormula = SubstituteConstants(OriginalFormula, SBMLModel)
% newExpression = SubstituteConstants(expression, SBMLModel)
%
% Takes
%
% 1. expression, a string representation of a math expression
% 2. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. the string representation of the expression when all constants within the
% model have been substituted
%
% *EXAMPLE:*
%
% Consider m to be an SBMLModel containing a parameter
% with id = 'g', constant = '1' and value = 3'
%
% newExpression = SubstituteConstants('2 * g * S1', SBMLModel)
%
% newExpression = '2 * 3 * S1'
%
%<!---------------------------------------------------------------------------
% 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 arguments are appropriate
if (~ischar(OriginalFormula))
error('SubstituteConstants(OriginalFormula, SBMLModel)\n%s', 'first argument must be a character array representing a formula');
elseif (~isValidSBML_Model(SBMLModel))
error('SubstituteConstants(OriginalFormula, SBMLModel)\n%s', 'second argument must be an SBML model structure');
end;
subsFormula = OriginalFormula;
[Comp, comp_values] = GetCompartments(SBMLModel);
for i=1:length(SBMLModel.compartment)
if (SBMLModel.SBML_level == 1)
if (~isnan(comp_values(i)))
subsFormula = strrep(subsFormula, SBMLModel.compartment(i).name, sprintf('%g', comp_values(i)));
end;
elseif (SBMLModel.compartment(i).constant == 1)
if (~isnan(comp_values(i)))
subsFormula = strrep(subsFormula, SBMLModel.compartment(i).id, sprintf('%g', comp_values(i)));
end;
end;
end;
[Param, param_values] = GetGlobalParameters(SBMLModel);
for i=1:length(SBMLModel.parameter)
if (SBMLModel.SBML_level == 1)
if (~isnan(param_values(i)))
subsFormula = strrep(subsFormula, SBMLModel.parameter(i).name, sprintf('%g', param_values(i)));
end;
elseif (SBMLModel.parameter(i).constant == 1)
if (~isnan(param_values(i)))
subsFormula = strrep(subsFormula, SBMLModel.parameter(i).id, sprintf('%g', param_values(i)));
end;
end;
end;
[Species, species_values] = GetSpecies(SBMLModel);
for i=1:length(SBMLModel.species)
if (SBMLModel.SBML_level > 1 && SBMLModel.species(i).constant == 1)
if (~isnan(species_values(i)))
subsFormula = strrep(subsFormula, SBMLModel.species(i).id, sprintf('%g', species_values(i)));
end;
end;
end;
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