/
FbaLPWriter.m
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FbaLPWriter.m
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%FbaLPWriter
% Formats metabolic model in stm format.
%
% Author: Jonathan Karr, jkarr@stanford.edu
% Affiliation: Covert Lab, Department of Bioengineering, Stanford University
% Last updaetd 2/3/2011
classdef FbaLPWriter
methods (Static)
function write(sim, dirName)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
p = sim.process('Metabolism');
%SBML-COBRA
p.formulateFBA([], [], false);
FbaLPWriter.write_cobra_matlab(sim, [dirName filesep 'metabolism.full.mmol-gDCW-h.sbml'], 'mmol/gDCW/h');
FbaLPWriter.write_sbml(sim, [dirName filesep 'metabolism.full.mmol-gDCW-h.sbml'], 'mmol/gDCW/h');
%LP
p.formulateFBA([], [], false);
FbaLPWriter.write_lpsolve_lp(sim, [dirName filesep 'metabolism.full.mmol-gDCW-h.lp'], 'mmol/gDCW/h');
FbaLPWriter.write_cplex_lp(sim, [dirName filesep 'metabolism.full.mmol-gDCW-h.lpt'], 'mmol/gDCW/h');
FbaLPWriter.write_gurobi_lp(sim, [dirName filesep 'metabolism.full.mmol-gDCW-h.gurobi.lp'], 'mmol/gDCW/h');
%lindo
p.formulateFBA([], [], false);
FbaLPWriter.write_lindo(sim, [dirName filesep 'metabolism.full.molecules-cell-s.ltx'], 'molecules/cell/s');
FbaLPWriter.write_lindo(sim, [dirName filesep 'metabolism.full.mmol-gDCW-h.ltx'], 'mmol/gDCW/h');
p.formulateFBA([], [], true);
FbaLPWriter.write_lindo(sim, [dirName filesep 'metabolism.reduced.molecules-cell-s.ltx'], 'molecules/cell/s');
FbaLPWriter.write_lindo(sim, [dirName filesep 'metabolism.reduced.mmol-gDCW-h.ltx'], 'mmol/gDCW/h');
%fba3
p.formulateFBA([], [], false);
FbaLPWriter.write_fba3_stoichiometry(sim, [dirName filesep 'metabolism.full.stm'], 'mmol/gDCW/h');
p.formulateFBA([], [], true);
FbaLPWriter.write_fba3_stoichiometry(sim, [dirName filesep 'metabolism.reduced.stm'], 'mmol/gDCW/h');
FbaLPWriter.write_fba3_deletion(sim, [dirName filesep 'metabolismDeletions.txt']);
end
%SBML format for use with COBRA toolbox
%- http://lpsolve.sourceforge.net/5.5/lp-format.htm
function write_sbml(sim, fileName, units)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
import edu.stanford.covert.util.ConstantUtil;
%parse unit option
%growth (molecules/cell/s) = growth (mmol/gDCW/h) * biomass scale / flux scale
if nargin < 3
units = 'molecules/cell/s';
elseif ~ismember(units, {'mmol/gDCW/h', 'molecules/cell/s'})
throw(MException('FbaLPWriter:error', 'Invalid units'))
end
[model, compartmentIDs, compartmentNames] = FbaLPWriter.make_cobra_model(sim, units);
writeCbModel(model, 'sbml', fileName, compartmentIDs, compartmentNames);
movefile([fileName '.xml'], fileName);
end
%MATLAB struct format for use with COBRA toolbox
%- http://lpsolve.sourceforge.net/5.5/lp-format.htm
function write_cobra_matlab(sim, fileName, units)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
import edu.stanford.covert.util.ConstantUtil;
%growth (molecules/cell/s) = growth (mmol/gDCW/h) * biomass scale / flux scale
if nargin < 3
units = 'mmol/gDCW/h';
elseif ~ismember(units, {'mmol/gDCW/h', 'molecules/cell/s'})
throw(MException('FbaLPWriter:error', 'Invalid units'))
end
if ~strcmp(substr(fileName, -4, 4), '.mat')
fileName = [fileName '.mat'];
end
metabolism_full_mmol_gDCW_h = FbaLPWriter.make_cobra_model(sim, units);
save(fileName, 'metabolism_full_mmol_gDCW_h');
end
%MATLAB struct format for use with COBRA toolbox
%- http://lpsolve.sourceforge.net/5.5/lp-format.htm
function [model, compartmentIDs, compartmentNames] = make_cobra_model(sim, units)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
import edu.stanford.covert.util.ConstantUtil;
%parse unit option
%growth (molecules/cell/s) = growth (mmol/gDCW/h) * biomass scale / flux scale
if nargin < 2
units = 'molecules/cell/s';
elseif ~ismember(units, {'mmol/gDCW/h', 'molecules/cell/s'})
throw(MException('FbaLPWriter:error', 'Invalid units'))
end
%references
p = sim.process('Metabolism');
%IDs, names
[compartmentIDs, compartmentNames, substrateIDs, ~, substrateNames, reactionIDs, ~, reactionNames] = ...
edu.stanford.covert.cell.sim.util.FbaLPWriter.calcIDs(sim, true);
compartmentIDs = [compartmentIDs; 'none'];
compartmentNames = [compartmentNames; 'None'];
idx = 0;
for i = 1:numel(substrateIDs)
if isempty(substrateIDs{i}) || strcmp(substrateIDs{i}, '[none]')
idx = idx + 1;
substrateIDs{i} = sprintf('Constraint_%03d[none]', idx);
substrateNames{i} = sprintf('Constraint %d', idx);
end
end
%scale units
[fbaReactionStoichiometryMatrix, fluxBounds, fbaObjective] = FbaLPWriter.scaleNetwork(sim, units, ConstantUtil.realmax);
enzGeneComp = p.enzymeGeneComposition();
tmp = any(enzGeneComp, 2);
geneIDs = p.gene.wholeCellModelIDs(tmp);
rxnGeneMat = (p.fbaReactionCatalysisMatrix * enzGeneComp(tmp, :)') ~= 0;
grRules = cell(size(reactionIDs));
for i = 1:numel(reactionIDs)
grRules{i} = strjoin(' and ', geneIDs{rxnGeneMat(i, :)});
end
model = struct();
model.description = 'Mycoplasma genitalium metabolic sub-model';
model.rxns = reactionIDs;
model.mets = substrateIDs;
model.S = fbaReactionStoichiometryMatrix;
model.lb = fluxBounds(:, 1);
model.ub = fluxBounds(:, 2);
model.rev = fluxBounds(:, 1) < 0 & fluxBounds(:, 2) > 0;
model.c = fbaObjective;
model.rxnNames = reactionNames;
model.metNames = substrateNames;
model.grRules = grRules;
model.genes = geneIDs;
end
%LP format
%- http://lpsolve.sourceforge.net/5.5/lp-format.htm
function write_lpsolve_lp(sim, fileName, units)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
import edu.stanford.covert.util.ConstantUtil;
%parse unit option
%growth (molecules/cell/s) = growth (mmol/gDCW/h) * biomass scale / flux scale
if nargin < 3
units = 'molecules/cell/s';
elseif ~ismember(units, {'mmol/gDCW/h', 'molecules/cell/s'})
throw(MException('FbaLPWriter:error', 'Invalid units'))
end
%references
p = sim.process('Metabolism');
%numbers
nSubstrates = size(p.fbaReactionStoichiometryMatrix, 1);
nReactions = size(p.fbaReactionStoichiometryMatrix, 2);
%IDs, names
[compartmentIDs, compartmentNames, substrateIDs, ~, substrateNames, reactionIDs, ~, reactionNames] = ...
edu.stanford.covert.cell.sim.util.FbaLPWriter.calcIDs(sim);
%scale units
[fbaReactionStoichiometryMatrix, fluxBounds, fbaObjective] = FbaLPWriter.scaleNetwork(sim, units, ConstantUtil.realmax);
%initialize
str = [];
%header
str = [str sprintf('/*\n')];
str = [str sprintf('%s\n', 'Mycoplasma genitalium metabolism')];
str = [str sprintf('Generated %s by edu.stanford.covert.cell.sim.util.FbaLPWriter\n', datestr(now, 31))];
str = [str sprintf('*/\n\n')];
%objective
if strcmp(units, 'mmol/gDCW/h')
str = [str sprintf('// Maximize (mmol/gDCW)\n')];
else
str = [str sprintf('// Maximize (molecules/cell)\n')];
end
idxs = find(fbaObjective);
tmp = cellfun(@(id, coeff) sprintf('%e %s', coeff, id), reactionIDs(idxs), num2cell(fbaObjective(idxs)), 'UniformOutput', false);
str = [str sprintf('max: %s;\n', strjoin(' + ', tmp{:}))];
str = [str sprintf('\n')];
%Constraints
str = [str sprintf('// Metabolites with compartments\n')];
for i = 1:numel(compartmentIDs);
str = [str sprintf('// - %s: %s\n', compartmentIDs{i}, compartmentNames{i})];
end
for i = 1:nSubstrates
idxs = find(fbaReactionStoichiometryMatrix(i, :));
if isempty(idxs)
continue;
end
tmp = cell(size(idxs));
for j = 1:numel(idxs)
if fbaReactionStoichiometryMatrix(i, idxs(j)) == ceil(fbaReactionStoichiometryMatrix(i, idxs(j)))
tmp{j} = sprintf('%d %s', fbaReactionStoichiometryMatrix(i, idxs(j)), reactionIDs{idxs(j)});
else
tmp{j} = sprintf('%e %s', fbaReactionStoichiometryMatrix(i, idxs(j)), reactionIDs{idxs(j)});
end
end
str = [str sprintf('%s: %s = 0;\n', substrateIDs{i}, strjoin(' + ', tmp{:}))];
end
str = [str sprintf('\n')];
%Bounds
if strcmp(units, 'mmol/gDCW/h')
str = [str sprintf('// Bounds (mmol/gDCW/h)\n')];
else
str = [str sprintf('// Bounds (1/cell/s)\n')];
end
for i = 1:nReactions
if fluxBounds(i, 1) == ceil(fluxBounds(i, 1))
lower = sprintf('%d <= ', fluxBounds(i, 1));
else
lower = sprintf('%e <= ', fluxBounds(i, 1));
end
if fluxBounds(i, 2) == ceil(fluxBounds(i, 2))
upper = sprintf(' <= %d', fluxBounds(i, 2));
else
upper = sprintf(' <= %e', fluxBounds(i, 2));
end
if fluxBounds(i, 1) == fluxBounds(i, 2)
if fluxBounds(i, 1) == ceil(fluxBounds(i, 1))
str = [str sprintf('%s = %d;\n', reactionIDs{i}, fluxBounds(i, 1))];
else
str = [str sprintf('%s = %e;\n', reactionIDs{i}, fluxBounds(i, 1))];
end
else
if ~isempty(lower) || ~isempty(upper)
str = [str sprintf('%s%s%s;\n', lower, reactionIDs{i}, upper)];
end
end
end
str = [str sprintf('\n')];
%define variables
%str = [str sprintf('// Declare reactions\n')];
%str = [str sprintf('free %s;\n', strjoin(', ', reactionIDs{:}))];
%write file
fid = fopen(fileName, 'w');
fwrite(fid, str);
fclose(fid);
end
%LP format
%- http://lpsolve.sourceforge.net/5.5/CPLEX-format.htm
%- http://www2.isye.gatech.edu/~wcook/qsopt/hlp/ff_lp_format.htm
function write_cplex_lp(sim, fileName, units)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
import edu.stanford.covert.util.ConstantUtil;
%parse unit option
%growth (molecules/cell/s) = growth (mmol/gDCW/h) * biomass scale / flux scale
if nargin < 3
units = 'molecules/cell/s';
elseif ~ismember(units, {'mmol/gDCW/h', 'molecules/cell/s'})
throw(MException('FbaLPWriter:error', 'Invalid units'))
end
%references
p = sim.process('Metabolism');
%numbers
nSubstrates = size(p.fbaReactionStoichiometryMatrix, 1);
nReactions = size(p.fbaReactionStoichiometryMatrix, 2);
%IDs, names
[compartmentIDs, compartmentNames, substrateIDs, ~, ~, reactionIDs, ~, ~] = ...
edu.stanford.covert.cell.sim.util.FbaLPWriter.calcIDs(sim);
%scale units
[fbaReactionStoichiometryMatrix, fluxBounds, fbaObjective] = FbaLPWriter.scaleNetwork(sim, units, ConstantUtil.realmax);
%initialize
str = [];
%header
str = [str sprintf('\\ %s\n', 'Mycoplasma genitalium metabolism')];
str = [str sprintf('\\ Generated %s by edu.stanford.covert.cell.sim.util.FbaLPWriter\n\n', datestr(now, 31))];
%objective
str = [str sprintf('Maximize\n')];
if strcmp(units, 'mmol/gDCW/h')
str = [str sprintf('\\ mmol/gDCW\n')];
else
str = [str sprintf('\\ molecules/cell\n')];
end
idxs = find(fbaObjective);
tmp = cellfun(@(id, coeff) sprintf('%e %s', coeff, id), reactionIDs(idxs), num2cell(fbaObjective(idxs)), 'UniformOutput', false);
str = [str strrep(sprintf(' obj: %s\n', strjoin(' + ', tmp{:})), ' + -', ' -')];
%Constraints
str = [str sprintf('Subject To\n')];
str = [str sprintf('\\ Metabolites\n')];
str = [str sprintf('\\ Compartments\n')];
for i = 1:numel(compartmentIDs);
str = [str sprintf('\\ - %s: %s\n', compartmentIDs{i}, compartmentNames{i})];
end
for i = 1:nSubstrates
idxs = find(fbaReactionStoichiometryMatrix(i, :));
if isempty(idxs)
continue;
end
tmp = cell(size(idxs));
for j = 1:numel(idxs)
if fbaReactionStoichiometryMatrix(i, idxs(j)) == ceil(fbaReactionStoichiometryMatrix(i, idxs(j)))
tmp{j} = sprintf('%d %s', fbaReactionStoichiometryMatrix(i, idxs(j)), reactionIDs{idxs(j)});
else
tmp{j} = sprintf('%e %s', fbaReactionStoichiometryMatrix(i, idxs(j)), reactionIDs{idxs(j)});
end
end
str = [str strrep(sprintf(' %s: %s = 0\n', substrateIDs{i}, strjoin(' + ', tmp{:})), ' + -', ' -')];
end
%Bounds
str = [str sprintf('Bounds\n')];
if strcmp(units, 'mmol/gDCW/h')
str = [str sprintf('\\ mmol/gDCW/h\n')];
else
str = [str sprintf('\\ 1/cell/s\n')];
end
for i = 1:nReactions
if fluxBounds(i, 1) == ceil(fluxBounds(i, 1))
lower = sprintf('%d', fluxBounds(i, 1));
else
lower = sprintf('%e', fluxBounds(i, 1));
end
if fluxBounds(i, 2) == ceil(fluxBounds(i, 2))
upper = sprintf('%d', fluxBounds(i, 2));
else
upper = sprintf('%e', fluxBounds(i, 2));
end
if fluxBounds(i, 1) == fluxBounds(i, 2)
str = [str sprintf(' %s = %s\n', reactionIDs{i}, lower)];
else
if ~isempty(lower)
str = [str sprintf(' %s >= %s\n', reactionIDs{i}, lower)];
end
if ~isempty(upper)
str = [str sprintf(' %s <= %s\n', reactionIDs{i}, upper)];
end
end
end
%End
str = [str sprintf('End\n')];
%write file
fid = fopen(fileName, 'w');
fwrite(fid, str);
fclose(fid);
end
%LP format
%- http://www.gurobi.com/documentation/5.5/reference-manual/node902
%- http://www2.isye.gatech.edu/~wcook/qsopt/hlp/ff_lp_format.htm
function write_gurobi_lp(sim, fileName, units)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
import edu.stanford.covert.util.ConstantUtil;
%parse unit option
%growth (molecules/cell/s) = growth (mmol/gDCW/h) * biomass scale / flux scale
if nargin < 3
units = 'molecules/cell/s';
elseif ~ismember(units, {'mmol/gDCW/h', 'molecules/cell/s'})
throw(MException('FbaLPWriter:error', 'Invalid units'))
end
%references
p = sim.process('Metabolism');
%numbers
nSubstrates = size(p.fbaReactionStoichiometryMatrix, 1);
nReactions = size(p.fbaReactionStoichiometryMatrix, 2);
%IDs, names
[compartmentIDs, compartmentNames, substrateIDs, ~, ~, reactionIDs, ~, ~] = ...
edu.stanford.covert.cell.sim.util.FbaLPWriter.calcIDs(sim);
%scale units
[fbaReactionStoichiometryMatrix, fluxBounds, fbaObjective] = FbaLPWriter.scaleNetwork(sim, units, ConstantUtil.realmax);
%initialize
str = [];
%header
str = [str sprintf('\\ %s\n', 'Mycoplasma genitalium metabolism')];
str = [str sprintf('\\ Generated %s by edu.stanford.covert.cell.sim.util.FbaLPWriter\n\n', datestr(now, 31))];
%objective
str = [str sprintf('Maximize\n')];
if strcmp(units, 'mmol/gDCW/h')
str = [str sprintf('\\ mmol/gDCW\n')];
else
str = [str sprintf('\\ molecules/cell\n')];
end
idxs = find(fbaObjective);
tmp = cellfun(@(id, coeff) sprintf('%e %s', coeff, id), reactionIDs(idxs), num2cell(fbaObjective(idxs)), 'UniformOutput', false);
str = [str strrep(sprintf(' obj: %s\n', strjoin(' + ', tmp{:})), ' + -', ' -')];
%Constraints
str = [str sprintf('Subject To\n')];
str = [str sprintf('\\ Metabolites\n')];
str = [str sprintf('\\ Compartments\n')];
for i = 1:numel(compartmentIDs);
str = [str sprintf('\\ - %s: %s\n', compartmentIDs{i}, compartmentNames{i})];
end
for i = 1:nSubstrates
idxs = find(fbaReactionStoichiometryMatrix(i, :));
if isempty(idxs)
continue;
end
tmp = cell(size(idxs));
for j = 1:numel(idxs)
if fbaReactionStoichiometryMatrix(i, idxs(j)) == ceil(fbaReactionStoichiometryMatrix(i, idxs(j)))
tmp{j} = sprintf('%d %s', fbaReactionStoichiometryMatrix(i, idxs(j)), reactionIDs{idxs(j)});
else
tmp{j} = sprintf('%e %s', fbaReactionStoichiometryMatrix(i, idxs(j)), reactionIDs{idxs(j)});
end
end
str = [str strrep(sprintf(' %s: %s = 0\n', substrateIDs{i}, strjoin(' + ', tmp{:})), ' + -', ' -')];
end
%Bounds
str = [str sprintf('Bounds\n')];
if strcmp(units, 'mmol/gDCW/h')
str = [str sprintf('\\ mmol/gDCW/h\n')];
else
str = [str sprintf('\\ 1/cell/s\n')];
end
for i = 1:nReactions
if fluxBounds(i, 1) == ceil(fluxBounds(i, 1))
lower = sprintf('%d', fluxBounds(i, 1));
else
lower = sprintf('%e', fluxBounds(i, 1));
end
if fluxBounds(i, 2) == ceil(fluxBounds(i, 2))
upper = sprintf('%d', fluxBounds(i, 2));
else
upper = sprintf('%e', fluxBounds(i, 2));
end
if fluxBounds(i, 1) == fluxBounds(i, 2)
str = [str sprintf('%s = %s\n', reactionIDs{i}, upper)];
else
str = [str sprintf('%s <= %s <= %s\n', lower, reactionIDs{i}, upper)];
end
end
%End
str = [str sprintf('End\n')];
%write file
fid = fopen(fileName, 'w');
fwrite(fid, str);
fclose(fid);
end
function write_lindo(sim, fileName, units)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
import edu.stanford.covert.util.ConstantUtil;
%parse unit option
%growth (molecules/cell/s) = growth (mmol/gDCW/h) * biomass scale / flux scale
if nargin < 3
units = 'molecules/cell/s';
elseif ~ismember(units, {'mmol/gDCW/h', 'molecules/cell/s'})
throw(MException('FbaLPWriter:error', 'Invalid units'))
end
%references
p = sim.process('Metabolism');
%numbers
nSubstrates = size(p.fbaReactionStoichiometryMatrix, 1);
nReactions = size(p.fbaReactionStoichiometryMatrix, 2);
%IDs, names
[compartmentIDs, compartmentNames, substrateIDs, ~, substrateNames, reactionIDs, ~, reactionNames] = ...
edu.stanford.covert.cell.sim.util.FbaLPWriter.calcIDs(sim);
%scale units
[fbaReactionStoichiometryMatrix, fluxBounds, fbaObjective] = FbaLPWriter.scaleNetwork(sim, units, ConstantUtil.realmax);
%initialize
str = [];
%header
str = [str sprintf('! Autogenerated %s by edu.stanford.covert.cell.sim.util.FbaLPWriter\n', datestr(now, 31))];
str = [str sprintf('TITLE %s\n\n', 'Metabolism')];
if strcmp(units, 'mmol/gDCW/h')
str = [str sprintf('! Objective function (mmol/gDCW)\n')];
else
str = [str sprintf('! Objective function (molecules/cell)\n')];
end
str = [str sprintf('MAXIMIZE\n')];
idxs = find(fbaObjective);
for i = 1:numel(idxs)
str = [str sprintf('\t%e %s\n', fbaObjective(idxs(i)), reactionIDs{idxs(i)})];
end
str = [str sprintf('\n')];
str = [str sprintf('! Reactions\nSUBJECT TO\n')];
for i = 1:nSubstrates
rxnIdxs = find(p.fbaReactionStoichiometryMatrix(i, :));
if isempty(rxnIdxs)
continue;
end
constraint = [];
for j = 1:numel(rxnIdxs)
coeff = fbaReactionStoichiometryMatrix(i, rxnIdxs(j));
if coeff == floor(coeff)
constraint = [constraint sprintf('%d %s ', coeff, reactionIDs{rxnIdxs(j)})];
else
constraint = [constraint sprintf('%e %s ', coeff, reactionIDs{rxnIdxs(j)})];
end
end
str = [str sprintf(' %s) %s= 0 ! %s\n', substrateIDs{i}, constraint, substrateNames{i})];
end
str = [str sprintf('\nEND\n\n')];
if strcmp(units, 'mmol/gDCW/h')
str = [str sprintf('! Reaction Bounds (mmol/gDCW/h)\n')];
else
str = [str sprintf('! Reaction Bounds (1/cell/s)\n')];
end
for i = 1:nReactions
enzIdx = find(p.fbaReactionCatalysisMatrix(i, :));
if fluxBounds(i, 1) == floor(fluxBounds(i, 1))
lb = sprintf('%d', fluxBounds(i, 1));
else
lb = sprintf('%d', fluxBounds(i, 1));
end
if fluxBounds(i, 2) == floor(fluxBounds(i, 2))
ub = sprintf('%d', fluxBounds(i, 2));
else
ub = sprintf('%d', fluxBounds(i, 2));
end
if ~isempty(enzIdx)
str = [str sprintf('SLB %s %s ! %s (%s)\n', reactionIDs{i}, lb, reactionNames{i}, p.enzymeWholeCellModelIDs{enzIdx})];
str = [str sprintf('SUB %s %s ! %s (%s)\n', reactionIDs{i}, ub, reactionNames{i}, p.enzymeWholeCellModelIDs{enzIdx})];
else
str = [str sprintf('SLB %s %s ! %s\n', reactionIDs{i}, lb, reactionNames{i})];
str = [str sprintf('SUB %s %s ! %s\n', reactionIDs{i}, ub, reactionNames{i})];
end
end
str = [str sprintf('\n')];
str = [str sprintf('! Compartments\n')];
for i = 1:numel(compartmentIDs);
str = [str sprintf('! %s\t%s\n', compartmentIDs{i}, compartmentNames{i})];
end
fid = fopen(fileName, 'w');
fwrite(fid, str);
fclose(fid);
end
function write_fba3_stoichiometry(sim, fileName, units)
import edu.stanford.covert.cell.sim.util.FbaLPWriter;
import edu.stanford.covert.util.ConstantUtil;
%references
p = sim.process('Metabolism');
%numbers
nSubstrates = size(p.reactionStoichiometryMatrix, 1);
nCompartments = size(p.reactionStoichiometryMatrix, 3);
%ids
[compartmentIDs, compartmentNames, ~, substrateIDs, substrateNames, ~, reactionIDs, reactionNames, reversible] = ...
edu.stanford.covert.cell.sim.util.FbaLPWriter.calcIDs(sim);
%scale units
[fbaSMat, fluxBounds, fbaObj] = FbaLPWriter.scaleNetwork(sim, units, 1000);
fbaObj = fbaObj * 10^max(0, -floor(log10(min(abs(fbaObj(fbaObj ~= 0))))));
%initialize
str = [];
%header
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('// Metabolic network //\n')];
str = [str sprintf('// Autogenerated %s by edu.stanford.covert.cell.sim.util.FbaLPWriter //\n', datestr(now, 31))];
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('\n')];
str = [str sprintf('\n')];
%compartments
idWidth = max(cellfun(@length, compartmentIDs));
nameWidth = max(cellfun(@length, compartmentNames));
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('// Compartments %s //\n', repmat(' ', 1, idWidth + nameWidth + 3 - numel('Compartments')))];
for i = 1:nCompartments
str = [str sprintf('// %s\t%s //\n', ...
[compartmentIDs{i} repmat(' ', 1, idWidth - numel(compartmentIDs{i}))], ...
[compartmentNames{i} repmat(' ', 1, nameWidth - numel(compartmentNames{i}))])];
end
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('\n')];
str = [str sprintf('\n')];
%substrates
idWidth = max(cellfun(@length, substrateIDs));
nameWidth = max(cellfun(@length, substrateNames));
[subIdxs, ~] = ind2sub([nSubstrates, nCompartments], p.substrateIndexs_fba);
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('// Substrates %s //\n', repmat(' ', 1, idWidth + nameWidth +5 - length('Substrates')))];
str = [str sprintf('// %s //\n', repmat(' ', 1, idWidth + nameWidth + 6))];
str = [str sprintf('// \tMetabolites %s //\n', repmat(' ', 1, idWidth + nameWidth +4 - length('Metabolites')))];
for i = 1:size(p.substrateMetaboliteLocalIndexs, 1)
idx = p.fbaSubstrateIndexs_substrates(p.substrateMetaboliteLocalIndexs(i) == subIdxs);
if isempty(idx)
continue;
elseif numel(idx)==1
id = substrateIDs{idx};
else
idx = idx(1);
id = substrateIDs{idx}(1:end-1);
end
name = substrateNames{idx};
str = [str sprintf('// \t\t%s\t%s //\n', ...
[id repmat(' ', 1, idWidth - numel(id))], ...
[name repmat(' ', 1, nameWidth - numel(name))])]; %#ok<*AGROW>
end
str = [str sprintf('// %s //\n', repmat(' ', 1, idWidth + nameWidth + 6))];
str = [str sprintf('// \tProtein Monomers %s //\n', repmat(' ', 1, idWidth + nameWidth +4 - length('Protein Monomers')))];
for i = 1:size(p.substrateMonomerLocalIndexs, 1)
idx = p.fbaSubstrateIndexs_substrates(p.substrateMonomerLocalIndexs(i) == subIdxs);
if isempty(idx)
continue;
elseif numel(idx)==1
id = substrateIDs{idx};
else
idx = idx(1);
id = substrateIDs{idx}(1:end-1);
end
name = substrateNames{idx};
str = [str sprintf('// \t\t%s\t%s //\n', ...
[id repmat(' ', 1, idWidth - numel(id))], ...
[name repmat(' ', 1, nameWidth - numel(name))])]; %#ok<*AGROW>
end
str = [str sprintf('// %s //\n', repmat(' ', 1, idWidth + nameWidth + 6))];
str = [str sprintf('// \tProtein Complexs %s //\n', repmat(' ', 1, idWidth + nameWidth +4 - length('Protein Complexs')))];
for i = 1:size(p.substrateComplexLocalIndexs, 1)
idx = p.fbaSubstrateIndexs_substrates(p.substrateComplexLocalIndexs(i) == subIdxs);
if isempty(idx)
continue;
elseif numel(idx)==1
id = substrateIDs{idx};
else
idx = idx(1);
id = substrateIDs{idx}(1:end-1);
end
name = substrateNames{idx};
str = [str sprintf('// \t\t%s\t%s //\n', ...
[id repmat(' ', 1, idWidth - numel(id))], ...
[name repmat(' ', 1, nameWidth - numel(name))])]; %#ok<*AGROW>
end
str = [str sprintf('// %s //\n', repmat(' ', 1, idWidth + nameWidth + 6))];
str = [str sprintf('// \tInternal exchange constraints %s //\n', repmat(' ', 1, idWidth + nameWidth +4 - length('Internal exchange constraints')))];
for i = 1:size(p.fbaSubstrateIndexs_metaboliteInternalExchangeConstraints, 1)
idx = p.fbaSubstrateIndexs_metaboliteInternalExchangeConstraints(i);
if isempty(idx)
continue;
elseif numel(idx)==1
id = substrateIDs{idx};
else
idx = idx(1);
id = substrateIDs{idx}(1:end-1);
end
name = substrateNames{idx};
str = [str sprintf('// \t\t%s\t%s //\n', ...
[id repmat(' ', 1, idWidth - numel(id))], ...
[name repmat(' ', 1, nameWidth - numel(name))])]; %#ok<*AGROW>
end
str = [str sprintf('// %s //\n', repmat(' ', 1, idWidth + nameWidth + 6))];
str = [str sprintf('// \tPseudospecies %s //\n', repmat(' ', 1, idWidth + nameWidth +4 - length('Pseudospecies')))];
str = [str sprintf('// \t\t%s\t%s //\n', ...
['Biomass' repmat(' ', 1, idWidth - numel('Biomass'))], ...
['Biomass' repmat(' ', 1, nameWidth - numel('Biomass'))])]; %#ok<*AGROW>
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('\n')];
str = [str sprintf('\n')];
%reactions
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('// Reactions //\n')];
str = [str sprintf('\n')];
%biomass production in mmol/gDCW
str = [str sprintf('// \tBiomass production //\n')];
biomassScaleFactor = 100;
idx = p.fbaReactionIndexs_biomassProduction;
stoichiometry = [];
stoichiometry2 = [];
scIdxs = p.fbaSubstrateIndexs_substrates(fbaSMat(p.fbaSubstrateIndexs_substrates, idx) < 0);
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%f %s ', repmat('+', 1, val >= 0), val * biomassScaleFactor, substrateIDs{scIdxs(j)})];
stoichiometry2 = [stoichiometry2 sprintf('// %17.6f %s%s //\n', ...
val, ...
substrateIDs{scIdxs(j)}, ...
repmat(' ', 1, idWidth-numel(substrateIDs{scIdxs(j)})))];
end
scIdxs = p.fbaSubstrateIndexs_substrates(fbaSMat(p.fbaSubstrateIndexs_substrates, idx) > 0);
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%f %s ', repmat('+', 1, val >= 0), val * biomassScaleFactor, substrateIDs{scIdxs(j)})];
stoichiometry2 = [stoichiometry2 sprintf('// %17.6f %s%s //\n', ...
val, ...
substrateIDs{scIdxs(j)}, ...
repmat(' ', 1, idWidth-numel(substrateIDs{scIdxs(j)})))];
end
stoichiometry = stoichiometry(1:end-1);
str = [str stoichiometry2];
str = [str sprintf('\n')];
str = [str sprintf('// Biomass production in mmol/gDCW //\n')];
spaces = find(stoichiometry == ' ');
spaces = [spaces(2:2:end) length(stoichiometry)+1];
nSplits = ceil((length(spaces)-1)/10);
splits = [0 spaces(ceil((1:nSplits)/nSplits * length(spaces)))];
assertEqual(splits, unique(splits));
growthStoichiometry = [];
for j = 1:nSplits
str = [str sprintf('%s +%d SbBmss%02d 0 SbGrth%02d // Sub growth - %d //\n', stoichiometry(splits(j)+1:splits(j+1)-1), biomassScaleFactor, j, j, j)];
growthStoichiometry = [growthStoichiometry sprintf('-1 SbBmss%02d ', j)];
end
str = [str sprintf('%s +1 Biomass 0 %s // %s //\n', growthStoichiometry(1:end-1), reactionIDs{idx}, reactionNames{idx})];
str = [str sprintf('\n')];
str = [str sprintf('// \tMetabolic Reactions //\n')];
for i = 1:numel(p.reactionIndexs_chemical)
idx = p.fbaReactionIndexs_metabolicConversion(p.reactionIndexs_chemical(i) == p.reactionIndexs_fba);
if isempty(idx)
continue;
end
stoichiometry = [];
scIdxs = find(fbaSMat(:, idx) < 0);
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%d %s ', repmat('+', 1, val>=0), val, substrateIDs{scIdxs(j)})];
end
scIdxs = find(fbaSMat(:, idx) > 0);
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%d %s ', repmat('+', 1, val>=0), val, substrateIDs{scIdxs(j)})];
end
eIdx = find(p.fbaReactionCatalysisMatrix(idx, :));
if ~isempty(eIdx)
enzymeID = p.enzymeWholeCellModelIDs{eIdx};
enzymeName = p.enzymeNames{eIdx};
str = [str sprintf('%s0 %s // %s (%s, %s) //\n', stoichiometry, reactionIDs{idx}, reactionNames{idx}, enzymeID, enzymeName)];
else
str = [str sprintf('%s0 %s // %s //\n', stoichiometry, reactionIDs{idx}, reactionNames{idx})];
end
end
str = [str sprintf('\n')];
str = [str sprintf('// \tTransport Reactions //\n')];
for i = 1:numel(p.reactionIndexs_transport)
idx = p.fbaReactionIndexs_metabolicConversion(p.reactionIndexs_transport(i) == p.reactionIndexs_fba);
if isempty(idx)
continue;
end
stoichiometry = [];
scIdxs = find(fbaSMat(:, idx) < 0);
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%d %s ', repmat('+', 1, val>=0), val, substrateIDs{scIdxs(j)})];
end
scIdxs = find(fbaSMat(:, idx) > 0);
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%d %s ', repmat('+', 1, val>=0), val, substrateIDs{scIdxs(j)})];
end
eIdx = find(p.fbaReactionCatalysisMatrix(idx, :));
if ~isempty(eIdx)
enzymeID = p.enzymeWholeCellModelIDs{eIdx};
enzymeName = p.enzymeNames{eIdx};
str = [str sprintf('%s0 %s // %s (%s, %s) //\n', stoichiometry, reactionIDs{idx}, reactionNames{idx}, enzymeID, enzymeName)];
else
str = [str sprintf('%s0 %s // %s //\n', stoichiometry, reactionIDs{idx}, reactionNames{idx})];
end
end
str = [str sprintf('\n')];
str = [str sprintf('// \tMetabolite External Exchange Reactions //\n')];
for i = 1:numel(p.fbaReactionIndexs_metaboliteExternalExchange)
idx = p.fbaReactionIndexs_metaboliteExternalExchange(i);
scIdxs = find(fbaSMat(:, idx));
stoichiometry = [];
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%d %s ', repmat('+', 1, val>=0), val, substrateIDs{scIdxs(j)})];
end
str = [str sprintf('%s0 %s // %s //\n', stoichiometry, reactionIDs{idx}, reactionNames{idx})];
end
str = [str sprintf('\n')];
str = [str sprintf('// \tMetabolite Internal Exchange Reactions //\n')];
for i = 1:numel(p.fbaReactionIndexs_metaboliteInternalExchange)
idx = p.fbaReactionIndexs_metaboliteInternalExchange(i);
if isempty(idx)
continue;
end
stoichiometry = [];
scIdxs = find(fbaSMat(:, idx) < 0);
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%d %s ', repmat('+', 1, val>=0), val, substrateIDs{scIdxs(j)})];
end
scIdxs = find(fbaSMat(:, idx) > 0);
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%d %s ', repmat('+', 1, val>=0), val, substrateIDs{scIdxs(j)})];
end
eIdx = find(p.fbaReactionCatalysisMatrix(idx, :));
if ~isempty(eIdx)
enzymeID = p.enzymeWholeCellModelIDs{eIdx};
enzymeName = p.enzymeNames{eIdx};
str = [str sprintf('%s0 %s // %s (%s, %s) //\n', stoichiometry, reactionIDs{idx}, reactionNames{idx}, enzymeID, enzymeName)];
else
str = [str sprintf('%s0 %s // %s //\n', stoichiometry, reactionIDs{idx}, reactionNames{idx})];
end
end
str = [str sprintf('\n')];
str = [str sprintf('// \tBiomass Exchange Reactions //\n')];
idx = p.fbaReactionIndexs_biomassExchange;
scIdxs = find(fbaSMat(:, idx));
stoichiometry = [];
for j = 1:numel(scIdxs)
val = fbaSMat(scIdxs(j), idx);
stoichiometry = [stoichiometry sprintf('%s%d %s ', repmat('+', 1, val>=0), val, substrateIDs{scIdxs(j)})];
end
str = [str sprintf('%s0 %s // %s //\n', stoichiometry, reactionIDs{idx}, reactionNames{idx})];
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('\n')];
str = [str sprintf('\n')];
%objective
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('// Objective //\n')];
str = [str sprintf('0.0 end\n')];
str = [str sprintf('\n')];
str = [str sprintf('end E 0\n')];
str = [str sprintf('max\n')];
idxs = find(fbaObj);
for i = 1:numel(idxs)
str = [str sprintf('%.6f %s\n', fbaObj(idxs(i)), reactionIDs{idxs(i)})];
end
str = [str sprintf('0 end\n')];
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('\n')];
str = [str sprintf('\n')];
%reaction bounds
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
str = [str sprintf('// Reaction Bounds (mmol/gDCW/h) //\n')];
for i = 1:size(fluxBounds, 1)
if ceil(fluxBounds(i, 1)) == fluxBounds(i, 1)
loStr = sprintf('%d', fluxBounds(i, 1));
else
loStr = sprintf('%.6f', fluxBounds(i, 1));
end
if ceil(fluxBounds(i, 2)) == fluxBounds(i, 2)
hiStr = sprintf('%d', fluxBounds(i, 2));
else
hiStr = sprintf('%.6f', fluxBounds(i, 2));
end
str = [str sprintf('%s %s %s\n', loStr, reactionIDs{i}, hiStr)];
% if reversible(i) && (fbaReactionBounds(i, 1) ~= -1000 || fbaReactionBounds(i, 2) ~= 1000)
% str = [str sprintf('%.6f %s %.6f\n', fbaReactionBounds(i, 1), reactionIDs{i}, fbaReactionBounds(i, 2))];
% elseif ~reversible(i) && (fbaReactionBounds(i, 1) ~= 0 || fbaReactionBounds(i, 2) ~= 1000)
% str = [str sprintf('%.6f %s %.6f\n', fbaReactionBounds(i, 1), reactionIDs{i}, fbaReactionBounds(i, 2))];
% end
end
str = [str sprintf('\n')];
str = [str sprintf('// End of reaction Bounds //\n')];
str = [str sprintf('0 end 0\n')];
str = [str sprintf('// %s //\n', repmat('*', 1, 120))];
fid = fopen(fileName, 'w');
fwrite(fid, str);
fclose(fid);
end
function write_fba3_deletion(sim, fileName)
[~, ~, ~, ~, ~, ~, reactionIDs] = edu.stanford.covert.cell.sim.util.FbaLPWriter.calcIDs(sim);
for i = 1:numel(reactionIDs)
reactionIDs{i} = regexprep(reactionIDs{i}, 'R$', '');
reactionIDs{i} = regexprep(reactionIDs{i}, '\d+$', '');
end
%initialize file
str = [];
%genes - reactions
m = sim.process('Metabolism');
geneEnzComp = m.enzymeGeneComposition ~= 0;
geneSubComp = m.substrateGeneComposition ~= 0;
[sIdxs, ~] = ind2sub([size(m.reactionStoichiometryMatrix, 1) size(m.reactionStoichiometryMatrix, 3)], m.substrateIndexs_fba);
for i = 1:numel(sim.gene.wholeCellModelIDs)
enzIdxs = find(geneEnzComp(i, :));
subIdxs = find(geneSubComp(i, :));
if isempty(enzIdxs) && isempty(subIdxs)
continue;
end
fbaSubIdxs = m.fbaSubstrateIndexs_substrates(ismember(sIdxs, subIdxs));
rxnIdxs = any(m.fbaReactionCatalysisMatrix(:, enzIdxs), 2) | any(m.fbaReactionStoichiometryMatrix(fbaSubIdxs, :), 1)';
rxnIDs = unique(reactionIDs(rxnIdxs));
for j = 1:7:numel(rxnIDs)
tmpRxnIDs = rxnIDs(j:min(j+6, end));
str = [str sprintf('%d\t%sg\t%s\n', numel(tmpRxnIDs)+1, strrep(sim.gene.wholeCellModelIDs{i},'_',''), strjoin(' ', tmpRxnIDs{:}))];
end
end
%terminator
str = [str sprintf('\n999 end\n')];
%write file
fid = fopen(fileName, 'w');
fwrite(fid, str);
fclose(fid);
end
function [sMat, bounds, obj] = scaleNetwork(sim, units, maxFlux)
import edu.stanford.covert.util.ConstantUtil;
p = sim.process('Metabolism');
mass = sim.state('Mass');
sMat = p.fbaReactionStoichiometryMatrix;
bounds = p.calcFluxBounds(p.substrates, p.enzymes, p.fbaReactionBounds, p.fbaEnzymeBounds);
obj = p.fbaObjective;
if strcmp(units, 'mmol/gDCW/h')
%biomass composition
biomassScaleFactor = 1 / (1e-3 * ConstantUtil.nAvogadro) / mass.cellInitialDryWeight;
sMat(:, p.fbaReactionIndexs_biomassProduction) = ...
sMat(:, p.fbaReactionIndexs_biomassProduction) * biomassScaleFactor;
sMat(p.fbaSubstrateIndexs_biomass, p.fbaReactionIndexs_biomassProduction) = 1;