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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/common.h>
#include <BALL/KERNEL/system.h>
#include <BALL/FORMAT/INIFile.h>
#include <BALL/FORMAT/HINFile.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/SYSTEM/path.h>
#include <BALL/MOLMEC/COMMON/radiusRuleProcessor.h>
#include <BALL/STRUCTURE/fragmentDB.h>
using namespace BALL;
using namespace std;
int main(int argc, char** argv)
{
if (argc != 4)
{
Log.info() << "Need 3 arguments: <INIFile> <input.pdb> <output.hin>" << endl;
Log.info() << "Note: exemplary rules can be found in BALL/data/solvation/PARSE.rul." << endl;
return(1);
}
Path path;
String filename = path.find(argv[1]);
if (filename == "")
{
cerr << "Could not find rule file " << argv[1] << std::endl;
return(1);
}
INIFile charge_rules(filename);
charge_rules.read();
RadiusRuleProcessor proc(charge_rules, "RadiusRules");
PDBFile infile(argv[2]);
if (!infile)
{
// if file does not exist: complain and abort
Log.error() << "error opening " << argv[2] << " for input." << endl;
return 2;
}
System system;
infile >> system;
infile.close();
Log << "Initializing FragmentDB..." << endl;
FragmentDB db("");
Log << " done." << endl;
Log << "Normalizing names..." << endl;
system.apply(db.normalize_names);
Log << " done." << endl;
Log << "Building Bonds..." << endl;
system.apply(db.build_bonds);
Log << " done." << endl;
Log << "Applying RadiusRuleProcessor..." << endl;
system.apply(proc);
Log << " done." << endl;
Log << "Checking results..." << endl;
// PARANOIA
ResidueConstIterator res_it = system.beginResidue();
for (; +res_it; ++res_it)
{
AtomConstIterator it = res_it->beginAtom();
for (; +it; ++it)
{
float c = it->getCharge();
if (fabs(c) > 4.0f)
{
Log.warn() << "WARNING: atom " << it->getFullName() << ":"
<< res_it->getID() << " has suspect charge " << c << endl;
}
}
}
Log << " done." << endl;
HINFile outfile(argv[3], std::ios::out);
outfile << system;
outfile.close();
Log << "Outputfile " << argv[3] << " written." << endl;
}
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