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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: PDBChecker.C,v 1.6 2004/05/27 19:49:57 oliver Exp $
//
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/STRUCTURE/defaultProcessors.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/STRUCTURE/fragmentDB.h>
using namespace BALL;
using namespace std;
int main(int argc, char** argv)
{
// print a suage message, if called with the wrong number
// of arguments
if (argc != 2)
{
Log.error() << argv[0] << " <pdbfile>" << endl;
Log.error() << " checks the PDB file for consistency." << endl;
return 1;
}
// create a System and read the contents of the PDB file
System S;
PDBFile pdb_file(argv[1]);
if (pdb_file.bad())
{
Log.error() << "cannot open file " << argv[1] << endl;
return 2;
}
pdb_file >> S;
pdb_file.close();
// create a fragment database
// The fragment database contains information on
// all amino acids: structure, names, bond distances, and so on.
FragmentDB db("");
// normalize the names
// This processor converts the atom names from several naming
// conventions to the standard PDB names
S.apply(db.normalize_names);
// build bonds
// Since PDB files normally do not contain bond information
// we have to reconstruct the bonds from the templates in
// the fragment database
S.apply(db.build_bonds);
// now we create a ResidueChecker object and apply it
// This object checks all residues it is given and
// prints warnings to Log if
// - bond distances deviate from their usual values
// - non integral charges of a residues (does not apply here)
// - missing or superfluous atoms in a residue
ResidueChecker check(db);
S.apply(check);
// done.
return 0;
}
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