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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/selector.h>
#include <BALL/STRUCTURE/peptides.h>
#include <BALL/FORMAT/commandlineParser.h>
#include "version.h"
using namespace BALL;
int main(int argc, char* argv[])
{
// instantiate CommandlineParser object
CommandlineParser parpars("RemoveWater", "removes water from PDB file ", VERSION, String(__DATE__), "Preparation");
parpars.registerMandatoryInputFile("i", "input pdb file ");
parpars.registerMandatoryOutputFile("o", "output fasta file");
// the manual
String man = String("This tool removes water from a given pdb file.");
parpars.setToolManual(man);
parpars.setSupportedFormats("i", "pdb");
parpars.setSupportedFormats("o", "pdb");
// parse the command line
parpars.parse(argc, argv);
PDBFile in_file;
in_file.open(parpars.get("i"), std::ios::in);
if (!in_file)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << parpars.get("i") << " for input." << std::endl;
exit(2);
}
PDBFile out_file;
out_file.open(parpars.get("o"), std::ios::out);
if (!out_file)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << parpars.get("o") << " for output." << std::endl;
exit(2);
}
System system;
in_file >> system;
in_file.close();
// define the selector by Expression
Selector wat("residue(HOH) OR residue(WAT)");
// apply
system.apply(wat);
// remove
system.removeSelected();
system.deselect();
Log << wat.getNumberOfSelectedAtoms() << std::endl;
out_file << system;
out_file.close();
Log << "wrote file " << parpars.get("o") << std::endl;
return 0;
}
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