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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: surfaceBase.C,v 1.2.28.1 2007-03-16 00:06:50 bertsch Exp $
//
#include <BALL/QSAR/surfaceBase.h>
#include <BALL/QSAR/partialChargeDescriptors.h>
#include <BALL/QSAR/simpleDescriptors.h>
#include <BALL/KERNEL/atomIterator.h>
#include <BALL/KERNEL/fragment.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/CONCEPT/timeStamp.h>
#include <BALL/STRUCTURE/numericalSAS.h>
#define BALL_QSAR_SURFACEBASE_DEBUG
#undef BALL_QSAR_SURFACEBASE_DEBUG
using namespace std;
namespace BALL
{
SurfaceBase::SurfaceBase()
: Descriptor()
{
}
SurfaceBase::SurfaceBase(const SurfaceBase& sb)
: Descriptor(sb)
{
}
SurfaceBase::SurfaceBase(const String& name)
: Descriptor(name)
{
}
SurfaceBase::SurfaceBase(const String& name, const String& unit)
: Descriptor(name, unit)
{
}
SurfaceBase& SurfaceBase::operator = (const SurfaceBase& sb)
{
this->setName(sb.getName());
this->setUnit(sb.getUnit());
return *this;
}
SurfaceBase::~SurfaceBase()
{
}
bool SurfaceBase::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 SurfaceBase::computeAllDescriptors(AtomContainer& ac)
{
if (!isValid_(ac))
{
calculate_(ac);
}
}
void SurfaceBase::calculate_(AtomContainer& ac)
{
// first we must be shure that the PEOE charges are calculated
TotalPositivePartialCharge tppc;
ac.apply(tppc);
MolecularWeight mw;
ac.apply(mw);
// assign van der Waals radii for the SAS calculator
for (AtomIterator it = ac.beginAtom(); it != ac.endAtom(); ++it)
{
it->setRadius(it->getElement().getVanDerWaalsRadius());
}
// calc the areas for each atom
NumericalSAS sas;
sas.options.setInteger(NumericalSAS::Option::NUMBER_OF_POINTS, 400);
sas.options.setReal(NumericalSAS::Option::PROBE_RADIUS, 0.);
sas(ac);
HashMap<const Atom*, float> atom_areas = sas.getAtomAreas();
double tot_pos(0), tot_neg(0), tot_pos_pol(0), tot_neg_pol(0), tot_hyd(0), tot_pol(0), tot(0);
// add the atom areas
HashMap<const Atom*, float>::ConstIterator a_it(atom_areas.begin());
for (; a_it != atom_areas.end(); ++a_it)
{
float area = a_it->second;
double charge = a_it->first->getProperty("PEOEPartialCharge").getDouble();
// total positive polar van der Waals surface area
if (charge > 0.2) { tot_pos_pol += area; }
// total negative polar van der Waals surface area
if (charge < -0.2) { tot_neg_pol += area; }
// total polar van der Waals surface area
if (fabs(charge) > 0.2) { tot_pol += area; }
// total hydrophobic van der Waals surface area
if (fabs(charge) <= 0.2) { tot_hyd += area; }
// total positive van der Waals surface area
if (charge > 0) { tot_pos += area; }
// total negative van der Waals surface area
if (charge < 0) { tot_neg += area; }
// total van der Waals surface area
tot += area;
}
double vol = sas.getTotalVolume();
double rho(0);
if (vol != 0)
{
rho = ac.getProperty("MolecularWeight").getDouble()/vol;
}
ac.setProperty("PositiveVdWSurface", tot_pos);
ac.setProperty("NegativeVdWSurface", tot_neg);
ac.setProperty("PositivePolarVdWSurface", tot_pos_pol);
ac.setProperty("NegativePolarVdWSurface", tot_neg_pol);
ac.setProperty("HydrophobicVdWSurface", tot_hyd);
ac.setProperty("PolarVdWSurface", tot_pol);
ac.setProperty("VdWSurface", tot);
ac.setProperty("VdWVolume", vol);
ac.setProperty("Density", rho);
}
} // namespace BALL
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