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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// A small program for adding hydrogens to a PDB file (which usually comes
// without hydrogen information) and minimizing all hydrogens by means of a
// StrangLBFGS minimizer.
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/selector.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/MOLMEC/AMBER/amber.h>
#include <BALL/MOLMEC/MINIMIZATION/conjugateGradient.h>
#include <BALL/MOLMEC/MINIMIZATION/steepestDescent.h>
#include <BALL/MOLMEC/MINIMIZATION/strangLBFGS.h>
#include <BALL/MOLMEC/MINIMIZATION/shiftedLVMM.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/SYSTEM/path.h>
using namespace std;
using namespace BALL;
int main(int argc, char** argv)
{
if ((argc < 3) || (argc > 4))
{
Log << "Usage:" << argv[0] << " <PDB infile> <PDB outfile> [<amber parameter file>]" << endl;
return 1;
}
Log << "Loading " << argv[1] << "..." << endl;
PDBFile infile(argv[1]);
if (!infile)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << argv[1] << " for input." << endl;
return 2;
}
System system;
infile >> system;
Log << "done." << endl;
Log << "Initializing FragmentDB..." << endl;
FragmentDB db("");
Log << "done." << endl;
Log << "Normalizing names..." << endl;
system.apply(db.normalize_names);
Log << "done." << endl;
Log << "Adding hydrogens..." << endl;
system.apply(db.add_hydrogens);
Log << " ...added " << db.add_hydrogens.getNumberOfInsertedAtoms()
<< " atoms" << endl;
Log << "done." << endl;
Log << "Building Bonds..." << endl;
system.apply(db.build_bonds);
Log << "done." << endl;
Log << "Applying ResidueChecker..." << endl << endl;
ResidueChecker check;
system.apply(check);
Log << "done." << endl;
Log << "Initializing force field..." << endl;
AmberFF amber_ff;
if (argc == 4)
{
Path path;
String tmp = path.find(argv[3]);
if (tmp == "") tmp = argv[3];
amber_ff.options.set(AmberFF::Option::FILENAME, tmp);
}
amber_ff.setup(system);
Log << "done." << endl;
Log << "Selecting H atoms..." << endl;
Selector h_select("element(H)");
system.apply(h_select);
Log << "done." << endl;
Log << "Starting minimizer: " << endl << endl;
// We choose the L-BFGS minimizer
/*
SteepestDescentMinimizer sdm(amber_ff);
sdm.setEnergyOutputFrequency(1);
sdm.minimize(1000);
*/
/*
ConjugateGradientMinimizer cgm(amber_ff);
cgm.setEnergyOutputFrequency(1);
cgm.minimize(1000);
*/
/*
ShiftedLVMMMinimizer sm(amber_ff);
sm.setEnergyOutputFrequency(1);
sm.minimize(1000);
*/
StrangLBFGSMinimizer bfgsm(amber_ff);
bfgsm.setEnergyOutputFrequency(1);
bfgsm.minimize(1000);
Log << "Writing " << argv[2] << "..." << endl;
PDBFile outfile(argv[2], std::ios::out);
outfile << system;
Log << "done." << endl;
return 0;
}
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