///////////////////////////////////////////////////////////////////////////////
// Run calculations.
///////////////////////////////////////////////////////////////////////////////
void efn2Interface::run() {
// Create a variable that handles errors.
int error = 0;
/*
* Use the constructor for RNA that specifies a filename.
* Specify type = 1 (CT file).
* isRNA identifies whether the strand is RNA (true) or DNA (false).
*
* After construction of the strand data structure, create the error checker which monitors for errors.
* Throughout, the error status of the calculation is checked with a variant of the isErrorStatus method, which returns 0 if no error occurred.
* The calculation proceeds as long as error = 0.
*/
cout << "Initializing nucleic acids..." << flush;
RNA* strand = new RNA( ctFile.c_str(), 1, isRNA );
ErrorChecker<RNA>* checker = new ErrorChecker<RNA>( strand );
error = checker->isErrorStatus();
if( error == 0 ) { cout << "done." << endl; }
/*
* Check the strand for pseudoknots by looking through each structure with the ContainsPseudoknot method.
* efn2 cannot handle pseudoknots, so if the strand contains pseudoknots, this is considered an error.
*/
if( error == 0 ) {
structures = strand->GetStructureNumber();
for( int i = 1; i <= structures; i++ ) {
if( strand->ContainsPseudoknot( i ) ) {
cerr << "Nucleic acids contain pseudoknots; cannot proceed." << endl;
error = -1;
}
}
}
/*
* Set the temperature using the SetTemperature method.
* Only set the temperature if a given temperature doesn't equal the default.
* If the temperature does need to be set, use the error checker's isErrorStatus method to check for errors.
*/
if( ( error == 0 ) && ( temperature != 310.15 ) ) {
// Show a message saying that the temperature is being set.
cout << "Setting temperature..." << flush;
// Set the temperature and check for errors.
int tempError = strand->SetTemperature( temperature );
error = checker->isErrorStatus( tempError );
// If no error occurred, print a message saying that temperature is set.
if( error == 0 ) { cout << "done." << endl; }
}
/*
* Read SHAPE constraints, if applicable.
* When reading SHAPE constraints, use the ReadSHAPE method.
* After constraints are read, use the error checker's isErrorStatus method to check for errors.
*/
if( error == 0 && SHAPEFile != "" ) {
// Show a message saying that SHAPE constraints are being read.
cout << "Applying SHAPE constraints..." << flush;
// Initialize the single stranded SHAPE slope and intercept.
// For now, these are hard-coded as 0.
double slopeSingle = 0;
double interceptSingle = 0;
// Read SHAPE constraints and check for errors.
int constraintError = strand->ReadSHAPE( SHAPEFile.c_str(), slope, intercept, slopeSingle, interceptSingle );
error = checker->isErrorStatus( constraintError );
// If no error occurred, print a message saying that SHAPE constraints are set.
if( error == 0 ) { cout << "done." << endl; }
}
/*
* Do the efn2 calculation.
* If the user wants a simple output file, get free energies for each structure using the CalculateFreeEnergy method.
* If the user wants a thermodynamic details file, write the file with the WriteThemodynamicDetails method.
*/
if( error == 0 ) {
// Write a thermodynamic details file, if asked.
if( writeTherm ) {
// Show a message saying that the details file is being written.
cout << "Writing thermodynamic details file..." << flush;
// Write the thermodynamic details file and check for errors.
int thermError = strand->WriteThermodynamicDetails( outFile.c_str() );
error = checker->isErrorStatus( thermError );
// Print a message saying that the details file has been written.
if( error == 0 ) { cout << "done." << endl; }
}
// Write a simple list file, if asked.
else {
// Show a message saying that the list file is being written.
cout << "Writing free energy list file..." << flush;
// For each structure, calculate its energy and push it into the energies vector.
// Changed this 5-14-2013, no longer pushes into a vector. Instead use calculatefreeenergy method from RNA class.
// This is so it works with openMP -- vector would be filled out of order when loop runs in parallel and the indexing would be messed up.
// If an error occurs, set it.
//vector<double> energies;
strand->CalculateFreeEnergy( 1 , simple ); //calculate the free energy of the first structure first (this is to make it play well with openMP)
#ifdef SMP
#pragma omp parallel for
#endif
for( int i = 2; i <= structures; i++ ) {
strand->CalculateFreeEnergy( i , simple ); //now calculate the free energy of the remaining structures
error = checker->isErrorStatus();
//if( error == 0 ) { energies.push_back( energy ); }
//else break;
}
// If all free energies were calculated correctly, write the output file.
if( error == 0 ) {
ofstream out( outFile.c_str() );
for( int i = 1; i <= structures; i++ ) {
int index = i - 1;
out << "Structure: " << i << " Energy = " << fixed << setprecision( 1 ) << strand->GetFreeEnergy(i) << endl; //changed to GetFreeEnergy instead of writing the energies vector
}
out.close();
}
// Print a message saying that the list file has been written.
if( error == 0 ) { cout << "done." << endl; }
// If the output should be piped to standard output, then pipe it.
if( ( error == 0 ) && ( stdPrint ) ) {
cout << endl << "Generated output file: " << outFile << endl << endl;
for( int i = 1; i <= structures; i++ ) {
cout << "Structure: " << i << " Energy = " << fixed << setprecision( 1 ) << strand->GetFreeEnergy(i) << endl;
}
cout << endl;
}
}
}
// Delete the error checker and data structure.
delete checker;
delete strand;
// Print confirmation of run finishing.
if( error == 0 ) { cout << calcType << " complete." << endl; }
else { cerr << calcType << " complete with errors." << endl; }
}
