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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// A small program for using the GAFF atomtyper
#include <BALL/KERNEL/system.h>
// #include <BALL/FORMAT/HINFile.h>
#include <BALL/MOLMEC/AMBER/GAFFTypeProcessor.h>
#include <BALL/STRUCTURE/assignBondOrderProcessor.h>
#include <BALL/FORMAT/molFileFactory.h>
#include <BALL/FORMAT/genericMolFile.h>
using namespace BALL;
using namespace std;
int main(int argc, char** argv)
{
if ((argc < 3 || argc > 4))
{
Log << "Usage:" << argv[0] << " <infile> <outfile> [GAFFTypes.dat]" << endl;
return 1;
}
Log << "Loading " << argv[1] << "..." << endl;
GenericMolFile* infile = MolFileFactory::open(argv[1]);
if (!infile)
{
Log.error() << "Could not determine filetype, aborting" << std::endl;
return 2;
}
if (!*infile)
{
std::cerr << "Invalid file, aborting" << std::endl;
return 2;
}
System system;
*infile >> system;
Log << "done." << endl;
AssignBondOrderProcessor abp;
system.apply(abp);
Options options;
options[GAFFTypeProcessor::Option::ATOMTYPE_FILENAME] = "atomtyping/GAFFTypes.dat";
if (argc > 3)
options[GAFFTypeProcessor::Option::ATOMTYPE_FILENAME] = String("Amber/")+argv[3];
GAFFTypeProcessor gt(options);
system.apply(gt);
for (AtomIterator at_it = system.beginAtom(); +at_it; ++at_it)
std::cout << "atom name: " << at_it->getName() << " atomtype " << at_it->getProperty("atomtype").getString() << std::endl;
Log << "Writing " << argv[2] << "..." << endl;
GenericMolFile* outfile = MolFileFactory::open(argv[2], std::ios::out);
if (!outfile)
{
std::cerr << "Could not determine filetype, aborting" << std::endl;
exit(-1);
}
if (!*outfile)
{
std::cerr << "Invalid file, aborting" << std::endl;
exit(-1);
}
*outfile << system;
Log << "done." << endl;
// Important: Cleanup
outfile->close();
delete outfile;
}
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