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revision 1.4, Fri Jul 27 13:38:09 2007 UTC revision 1.6, Wed Nov 12 18:29:31 2008 UTC
# Line 30  Line 30 
30  print STDERR "Creating SBML model for genome $genome_id\n" if($debug);  print STDERR "Creating SBML model for genome $genome_id\n" if($debug);
31  print STDERR "\tStage 1 - Loading Scenarios, model inputs and biomass\n" if($debug);  print STDERR "\tStage 1 - Loading Scenarios, model inputs and biomass\n" if($debug);
32  my @scenarios = @{Scenario->get_genome_scenarios($genome_id,1)};  my @scenarios = @{Scenario->get_genome_scenarios($genome_id,1)};
33  my $filebase = $fig->model_directory($genome_id)."/Analysis/";  my $filebase = $fig->scenario_directory($genome_id)."/Analysis/";
34    
35  my %input_cpds;  my %input_cpds;
36  open(INPUTS,$filebase."inputs.txt")  open(INPUTS,$filebase."inputs.txt")
# Line 147  Line 147 
147      }      }
148  }  }
149    
150    #the ATP Synthase hack reaction
151    $core_metabolites{"C00009"} = 1;
152    $core_metabolites{"C00001"} = 1;
153    $core_metabolites{"C00008"} = 1;
154    $core_metabolites{"C00002"} = 1;
155    $reaction_reversible{"ATPSYN"} = 0;
156    $reaction_to_substrates{"ATPSYN"} = {};
157    $reaction_to_products{"ATPSYN"} = {};
158    $reaction_to_substrates{"ATPSYN"}->{"C00008"} = 1;
159    $reaction_to_substrates{"ATPSYN"}->{"C00009"} = 1;
160    $reaction_to_products{"ATPSYN"}->{"C00001"} = 1;
161    $reaction_to_products{"ATPSYN"}->{"C00002"} = 1;
162    $reaction_notes{"ATPSYN"} = {};
163    $reaction_notes{"ATPSYN"}->{"Manual Reaction:This fixes problems because we lack electron transport reactions."} = 1;
164    #end hack
165    
166  print STDERR "\tStage 1 - Complete\n" if($debug);  print STDERR "\tStage 1 - Complete\n" if($debug);
167    
168  print STDERR "\tStage 2 - Write SBML file\n" if($debug);  print STDERR "\tStage 2 - Write SBML file\n" if($debug);

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