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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: reconstruct_fragment.C,v 1.7 2004/05/27 18:13:08 oliver Exp $
//
// A little helper program that tries to reconstruct broken fragments in a
// molecule. This program assumes that there is only *one* chain in the
// file.
//
// Usage: reconstruct_fragemnt reference_fragment_name res_id infile outfile
#include <BALL/common.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/STRUCTURE/reconstructFragmentProcessor.h>
#include <BALL/FORMAT/PDBFile.h>
using namespace BALL;
using namespace std;
int main(int argc, char** argv)
{
if ((argc != 5) && (argc != 3))
{
Log.info() << "Usage:" << endl;
Log.info() << argv[0] << " infile.pdb outfile.pdb" << "\n" << endl;
Log.info() << " or\n" << endl;
Log.info() << argv[0] << " fragment-name residue-id infile.pdb outfile.pdb"
<< endl;
return(1);
}
bool automatic = true;
String reference_fragment_name;
String res_id;
String infile_name;
String outfile_name;
if (argc == 5)
{
automatic = false;
reference_fragment_name = argv[1];
res_id = argv[2];
infile_name = argv[3];
outfile_name = argv[4];
}
else
{
infile_name = argv[1];
outfile_name = argv[2];
}
System system;
PDBFile infile(infile_name);
infile >> system;
infile.close();
FragmentDB db("");
system.apply(db.normalize_names);
if (automatic)
{
ReconstructFragmentProcessor proc(db);
system.apply(proc);
system.apply(db.build_bonds);
}
else
{
ResidueIterator res_it = system.beginResidue();
while (res_it->getID() != res_id)
{
++res_it;
}
if (!res_it.isValid())
{
cerr << "Didn't find res_id " << res_id << " in system" << endl;
}
const Fragment& ref = *db.getFragment(reference_fragment_name);
list<Atom*> atoms = ReconstructFragmentProcessor::reconstructFragment(*res_it, ref);
Log.info() << " added " << atoms.size() << " atoms" << std::endl;
Size bonds = db.build_bonds.buildFragmentBonds(*res_it, ref);
Log.info() << " added " << bonds << " bonds" << std::endl;
}
ResidueChecker check(db);
system.apply(check);
PDBFile outfile(outfile_name, ios::out);
outfile << system;
outfile.close();
}
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