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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: partialChargeBase.C,v 1.2.28.1 2007-03-16 00:06:47 bertsch Exp $
//
#include <BALL/QSAR/partialChargeBase.h>
#include <BALL/QSAR/partialChargeProcessor.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/bondIterator.h>
#include <BALL/KERNEL/atomIterator.h>
#include <BALL/KERNEL/forEach.h>
#include <BALL/KERNEL/fragment.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/CONCEPT/timeStamp.h>
#include <utility>
using namespace std;
namespace BALL
{
PartialChargeBase::PartialChargeBase()
: Descriptor()
{
data_folder_ = "QSAR/";
}
PartialChargeBase::PartialChargeBase(const PartialChargeBase& pcb)
: Descriptor(pcb)
{
data_folder_ = "QSAR/";
}
PartialChargeBase::PartialChargeBase(const String& name)
: Descriptor(name)
{
data_folder_ = "QSAR/";
}
PartialChargeBase::PartialChargeBase(const String& name, const String& unit)
: Descriptor(name, unit)
{
data_folder_ = "QSAR/";
}
PartialChargeBase::~PartialChargeBase()
{
}
PartialChargeBase& PartialChargeBase::operator = (const PartialChargeBase& pcb)
{
setName(pcb.getName());
setUnit(pcb.getUnit());
data_folder_ = pcb.data_folder_;
return *this;
}
bool PartialChargeBase::isValid_(AtomContainer& ac)
{
static HashMap<Handle, PreciseTime> mod_times;
PreciseTime last_mod = ac.getModificationTime();
Handle mol_handle = ac.getHandle();
if (mod_times.has(mol_handle))
{
if (mod_times[mol_handle] == last_mod)
{
return true;
}
else
{
mod_times[mol_handle] = last_mod;
return false;
}
}
else
{
mod_times.insert(std::make_pair(mol_handle, last_mod));
return false;
}
}
void PartialChargeBase::computeAllDescriptors(AtomContainer& ac)
{
if (!isValid_(ac))
{
calculate_(ac);
}
}
void PartialChargeBase::setDataFolder(const char* folder)
{
data_folder_ = folder;
}
void PartialChargeBase::calculate_(AtomContainer& ac)
{
// sets partial charges;
PartialChargeProcessor pcp;
pcp.setDataFolder(data_folder_.c_str());
ac.apply(pcp);
//HashMap<Atom*, double>::Iterator it = charges.begin();
AtomIterator it = ac.beginAtom();
// assign the calculated values to the descriptors
double tot_pos(0), tot_neg(0), rel_pos(0), rel_neg(0), max_charge(0), min_charge(0);
for (it = ac.beginAtom(); it != ac.endAtom(); ++it)
{
double charge = it->getProperty("PEOEPartialCharge").getDouble();
if (charge > 0)
{
tot_pos += charge;
}
else
{
tot_neg += charge;
}
if (charge > max_charge)
{
max_charge = charge;
}
if (charge < min_charge)
{
min_charge = charge;
}
// set partial charge as atom property
}
// this might be paranoid, but you never know
if (max_charge > 0 && tot_pos > 0)
{
rel_pos = max_charge/tot_pos;
}
// this might be also paranoid, but you still never know
if (min_charge < 0 && tot_neg < 0)
{
rel_neg = min_charge/tot_neg;
}
ac.setProperty("TotalPositivePartialCharge", tot_pos);
ac.setProperty("TotalNegativePartialCharge", tot_neg);
ac.setProperty("RelPositivePartialCharge", rel_pos);
ac.setProperty("RelNegativePartialCharge", rel_neg);
}
} // namespace BALL
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