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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: ramachandran.C,v 1.9 2004/05/27 19:49:58 oliver Exp $
//
//============================================================================
// BALL - Ramachandran plot example
//============================================================================
// this example reads a PDB file and calculates the backbone torsion angles
// Phi and Psi that are needed to create ramachandran plots.
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/FORMAT/PDBFile.h>
using namespace BALL;
using namespace std;
int main(int argc, char** argv)
{
if (argc != 2)
{
Log.error() << argv[0] << " <pdb file>" << endl;
return 1;
}
// open the first PDB file
PDBFile pdb(argv[1]);
if (pdb.bad())
{
// if the file could not be opened, print error message and exit
Log.error() << "cannot open PBD file " << argv[1] << endl;
return 2;
}
// read the contents of the file A into a system
System S;
pdb >> S;
pdb.close();
// normalize the atom names (torsion angles are identified
// via the atom names)
Log.info() << "normalizing names..." << endl;
FragmentDB db("");
S.apply(db.normalize_names);
// now, iterate over all residues
ResidueIterator res_it = S.beginResidue();
for (;+res_it; ++res_it)
{
// torsion angle phi does not exist for N terminal residues
if (res_it->hasTorsionPhi())
{
// calculate the torsion angle and print its value in degree
Angle phi = res_it->getTorsionPhi();
cout << "phi(" << res_it->getName() << res_it->getID() << ") = " << phi.toDegree() << endl;
}
// torsion angle psi does not exist for C terminal residues
if (res_it->hasTorsionPsi())
{
// calculate the torsion angle and print its value in degree
Angle psi = res_it->getTorsionPsi();
cout << "psi(" << res_it->getName() << res_it->getID() << ") = " << psi.toDegree() << endl;
}
}
// done
return 0;
}
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