void LoadDatabaseFile(const char* DatabaseFilename) {
if (GetParameter("Network output location").compare("none") != 0 && GetParameter("Network output location").length() > 0) {
if (GetParameter("os").compare("windows") == 0) {
system(("move "+GetDatabaseDirectory(GetParameter("database"),"output directory")+GetParameter("output folder")+" "+GetParameter("Network output location")).data());
} else {
system(("cp -r "+GetDatabaseDirectory(GetParameter("database"),"output directory")+GetParameter("output folder")+" "+GetParameter("Network output location")).data());
}
}
//Getting filename that all compound and reaction data will be saved into
string Filename(DatabaseFilename);
if (Filename.length() == 0) {
Filename = AskString("Input filename for database: ");
}
//Creating datastructure for all program data
Data* NewData = new Data(0);
NewData->ClearData("NAME",STRING);
NewData->AddData("NAME",RemoveExtension(RemovePath(Filename)).data(),STRING);
//Loading data from file
if (NewData->LoadSystem(Filename) == FAIL) {
delete NewData;
return;
}
//Performing a variety of tasks according to the parameters in the parameters files including KEGG lookup, reaction and compound printing etc.
NewData->PerformAllRequestedTasks();
// Test for Adjustment of DeltaGs for PH for COMPOUNDS
bool TestCpds = 0;
if (TestCpds){
double IonicS = 0.25;
FErrorFile() << "Std Transformed Gibbs Energy of Formation vs pH" << endl;
for (int i=0; i < NewData->FNumSpecies(); i++){
string CompoundID = NewData->GetSpecies(i)->GetData("DATABASE",STRING); // gets the cpdID
string Name = NewData->GetSpecies(i)->GetData("NAME",STRING); // gets the name of the cpd
Species* Temp = NewData->FindSpecies("DATABASE",CompoundID.data());
//if (CompoundID.compare("cpd00003") == 0 || CompoundID.compare("cpd00004") == 0 || CompoundID.compare("cpd00002") == 0) {
double AdjDeltaG5 = Temp->AdjustedDeltaG(IonicS,5,298.15);
double AdjDeltaG5_kJ = 4.184*AdjDeltaG5;
double AdjDeltaG6 = Temp->AdjustedDeltaG(IonicS,6,298.15);
double AdjDeltaG6_kJ = 4.184*AdjDeltaG6;
double AdjDeltaG7 = Temp->AdjustedDeltaG(IonicS,7,298.15);
double AdjDeltaG7_kJ = 4.184*AdjDeltaG7;
double AdjDeltaG8 = Temp->AdjustedDeltaG(IonicS,8,298.15);
double AdjDeltaG8_kJ = 4.184*AdjDeltaG8;
double AdjDeltaG9 = Temp->AdjustedDeltaG(IonicS,9,298.15);
double AdjDeltaG9_kJ = 4.184*AdjDeltaG9;
FErrorFile() << CompoundID << "\t" << AdjDeltaG5_kJ << "\t" << AdjDeltaG6_kJ << "\t" << AdjDeltaG7_kJ << "\t" << AdjDeltaG8_kJ << "\t" << AdjDeltaG9_kJ << endl;
//}
}
FlushErrorFile();
}
// Test for Adjustment of DeltaGs for IONIC STRENGTH for COMPOUNDS
bool TestCpdsIS = 0;
if (TestCpdsIS){
FErrorFile() << "Std Transformed Gibbs Energy of Formation vs Ionic Strength" << endl;
for (int i=0; i < NewData->FNumSpecies(); i++){
string CompoundID = NewData->GetSpecies(i)->GetData("DATABASE",STRING); // gets the cpdID
string Name = NewData->GetSpecies(i)->GetData("NAME",STRING); // gets the name of the cpd
Species* Temp = NewData->FindSpecies("DATABASE",CompoundID.data());
double AdjDeltaG_IS0 = Temp->AdjustedDeltaG(0,7,298.15);
double AdjDeltaG_IS0_kJ = 4.184*AdjDeltaG_IS0;
double AdjDeltaG_IS10 = Temp->AdjustedDeltaG(0.1,7,298.15);
double AdjDeltaG_IS10_kJ = 4.184*AdjDeltaG_IS10;
double AdjDeltaG_IS25 = Temp->AdjustedDeltaG(0.25,7,298.15);
double AdjDeltaG_IS25_kJ = 4.184*AdjDeltaG_IS25;
FErrorFile() << CompoundID << "\t" << AdjDeltaG_IS0_kJ << "\t" << AdjDeltaG_IS10_kJ << "\t" << AdjDeltaG_IS25_kJ << endl;
}
FlushErrorFile();
}
// Test for Adjustment of DeltaGs for pH for REACTIONS
bool TestRxns = 0;
if (TestRxns){
double IonicS = 0.25;
//double pH = 7;
FErrorFile() << "Std Transformed Gibbs Energy of Reaction (kJmol-1) vs pH" << endl;
for (int i=0; i < NewData->FNumReactions(); i++){
Reaction* Rxn = NewData->GetReaction(i);
string RxnID = Rxn->GetData("DATABASE",STRING);
string Name = Rxn->GetData("NAME",STRING);
double DG5 = Rxn->FEstDeltaG(5,IonicS)*4.184;
double DG6 = Rxn->FEstDeltaG(6,IonicS)*4.184;
double DG7 = Rxn->FEstDeltaG(7,IonicS)*4.184;
double DG8 = Rxn->FEstDeltaG(8,IonicS)*4.184;
double DG9 = Rxn->FEstDeltaG(9,IonicS)*4.184;
FErrorFile() << RxnID << "\t" << DG5 << "\t" << DG6 << "\t" << DG7 << "\t" << DG8 << "\t" << DG9 << endl;
}
FlushErrorFile();
}
// Test for Adjustment of DeltaGs for IONIC STRENGTH for REACTIONS
bool TestRxnsIS = 0;
if (TestRxnsIS){
FErrorFile() << "Std Transformed Gibbs Energy of Reaction (kJmol-1) vs Ionic Strength" << endl;
for (int i=0; i < NewData->FNumReactions(); i++){
Reaction* Rxn = NewData->GetReaction(i);
string RxnID = Rxn->GetData("DATABASE",STRING);
string Name = Rxn->GetData("NAME",STRING);
double DG_IS0 = Rxn->FEstDeltaG(7,0.25)*4.184;
double DG_IS10 = Rxn->FEstDeltaG(7,0.15)*4.184;
double DG_IS25 = Rxn->FEstDeltaG(7,0.25)*4.184;
FErrorFile() << RxnID << "\t" << DG_IS0 << "\t" << DG_IS10 << "\t" << DG_IS25 << endl;
}
// FlushErrorFile();
}
delete NewData;
};
