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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/molFileFactory.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/MOLMEC/AMBER/amber.h>
#include <BALL/MOLMEC/MINIMIZATION/conjugateGradient.h>
#include <BALL/MOLMEC/COMMON/assignTypes.h>
#include <BALL/KERNEL/selector.h>
#include <BALL/STRUCTURE/defaultProcessors.h>
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include "version.h"
using namespace BALL;
using namespace std;
int main(int argc, char* argv[])
{
CommandlineParser parpars("AddMissingAtoms", "add missing atoms to protein structures", VERSION, String(__DATE__), "Preparation");
parpars.registerMandatoryInputFile("i", "input file");
parpars.registerMandatoryOutputFile("o", "output file");
parpars.setSupportedFormats("i","pdb");
parpars.setSupportedFormats("o","pdb,drf");
parpars.registerFlag("opt_hyd", "optimize the positions of hydrogens", false);
String manual = "AddMissingAtoms tool allows you to missing atoms, i.e. hydrogens to a protein structure.\n\n Optional parameter is the optimize_hydrogens flag (-opt_hyd), which uses the AMBER force field to run a quick energy minization for all hydrogen atoms.\n\nOutput of this tool is one pdb-file containing the input protein structure with added atoms.";
parpars.setToolManual(manual);
parpars.parse(argc, argv);
PDBFile input(parpars.get("i"), ios::in);
//GenericMolFile* input = MolFileFactory::open(parpars.get("i"), ios::in);
//PDBFile* pdb_input = dynamic_cast<PDBFile*>(input);
if (!input)
{
Log.error() << "Cannot open PDB input file " << parpars.get("i") << endl;
return 2;
}
System S;
input >> S;
input.close();
FragmentDB fragdb("");
Log.disableOutput();
S.apply(fragdb.normalize_names);
S.apply(fragdb.add_hydrogens);
S.apply(fragdb.build_bonds);
Log.enableOutput();
if (parpars.has("opt_hyd") && parpars.get("opt_hyd").toBool())
{
AmberFF FF;
// we then select all hydrogens (element(H))
// using a specialized processor (Selector)
S.deselect();
FF.setup(S);
Selector selector("element(H)");
S.apply(selector);
// now we create a minimizer object that uses a conjugate
// gradient algorithm to optimize the atom positions
ConjugateGradientMinimizer minimizer;
// calculate the total energy of the system
float initial_energy = FF.updateEnergy();
Log << "initial energy: " << initial_energy << " kJ/mol" << endl;
// initialize the minimizer and perform (up to)
// 1000 optimization steps
minimizer.setup(FF);
minimizer.setEnergyOutputFrequency(1);
minimizer.minimize(50);
// calculate the terminal energy and print it
float terminal_energy = FF.getEnergy();
Log << "energy before/after minimization: " << initial_energy << "/" << terminal_energy << " kJ/mol" << endl;
}
// write the optimized structure to a file whose
// name is given as the second command line argument
String outfile_name = String(parpars.get("o"));
PDBFile outfile(outfile_name, ios::out);
outfile << S;
outfile.close();
Log << "wrote file " << outfile_name << endl;
}
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