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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/molFileFactory.h>
#include <BALL/FORMAT/genericMolFile.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/KERNEL/molecule.h>
#include "version.h"
using namespace BALL;
using namespace std;
int main(int argc, char* argv[])
{
CommandlineParser par("PartialChargesCopy", "transfer part. charges between files", VERSION, String(__DATE__), "Preparation");
par.registerMandatoryInputFile("i", "input molecule file");
par.registerMandatoryInputFile("chr", "file containing the same molecules as the input file, but with (different) partial charges");
par.registerMandatoryOutputFile("o", "output file");
String man = "This tool copies partial charges from a given file to the conformations read from a different file.\nThis can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.";
par.setToolManual(man);
par.setSupportedFormats("i",MolFileFactory::getSupportedFormats());
par.setSupportedFormats("chr","mol2,drf");
par.setSupportedFormats("o","mol2,drf");
par.parse(argc, argv);
GenericMolFile* input = MolFileFactory::open(par.get("i"));
GenericMolFile* charges = MolFileFactory::open(par.get("chr"));
GenericMolFile* output = MolFileFactory::open(par.get("o"), ios::out, input);
int mol_no = 0;
Molecule* charged_mol = charges->read();
Molecule* mol = input->read();
for (; mol && charged_mol; mol = input->read(), charged_mol = charges->read())
{
AtomIterator it1 = mol->beginAtom();
AtomIterator it2 = charged_mol->beginAtom();
for (; +it1 && +it2; it1++, it2++)
{
it1->setCharge(it2->getCharge());
}
if (+it1 || +it2)
{
cerr << "Error: unequal number of atoms !!"<<endl;
exit(1);
}
*output << *mol;
mol_no++;
delete mol;
}
if (mol || charged_mol)
{
cerr <<"Error: unequal number of molecules !!"<<endl;
exit(1);
}
Log.level(20)<<"\rwrote "<<mol_no<<" molecules."<<endl;
delete input;
delete output;
delete charges;
}
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