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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: pierottiCavFreeEnergyProcessor.C,v 1.10 2002/02/27 12:24:06 sturm Exp $
#include <BALL/SOLVATION/pierottiCavFreeEnergyProcessor.h>
#include <BALL/STRUCTURE/numericalSAS.h>
using namespace std;
namespace BALL
{
const char* PierottiCavFreeEnergyProcessor::Option::VERBOSITY = "verbosity";
const char* PierottiCavFreeEnergyProcessor::Option::SOLVENT_NUMBER_DENSITY
= "solvent_number_density";
const char* PierottiCavFreeEnergyProcessor::Option::PRESSURE = "pressure";
const char* PierottiCavFreeEnergyProcessor::Option::ABSOLUTE_TEMPERATURE
= "absolute_temperature";
const char* PierottiCavFreeEnergyProcessor::Option::PROBE_RADIUS
= "probe_radius";
const int PierottiCavFreeEnergyProcessor::Default::VERBOSITY = 0;
const float PierottiCavFreeEnergyProcessor::Default::SOLVENT_NUMBER_DENSITY
= 3.33253e-2;
const float PierottiCavFreeEnergyProcessor::Default::PRESSURE = 1.01325e5;
const float PierottiCavFreeEnergyProcessor::Default::ABSOLUTE_TEMPERATURE
= 298.0;
const float PierottiCavFreeEnergyProcessor::Default::PROBE_RADIUS = 1.385;
PierottiCavFreeEnergyProcessor::PierottiCavFreeEnergyProcessor()
{
setDefaultOptions();
valid_ = true;
}
PierottiCavFreeEnergyProcessor::PierottiCavFreeEnergyProcessor
(const PierottiCavFreeEnergyProcessor& proc)
: EnergyProcessor(proc)
{
}
PierottiCavFreeEnergyProcessor::~PierottiCavFreeEnergyProcessor()
{
clear();
valid_ = false;
}
void PierottiCavFreeEnergyProcessor::clear()
{
setDefaultOptions();
valid_ = true;
}
const PierottiCavFreeEnergyProcessor& PierottiCavFreeEnergyProcessor::operator = (const PierottiCavFreeEnergyProcessor& proc)
{
valid_=proc.valid_;
energy_=proc.energy_;
fragment_=proc.fragment_;
return *this;
}
bool PierottiCavFreeEnergyProcessor::operator == (const PierottiCavFreeEnergyProcessor& proc) const
{
bool result;
if ((fragment_ == 0) && (proc.fragment_ == 0))
{
result = ((energy_ == proc.energy_) && (valid_ == proc.valid_));
}
else
{
if ((fragment_ == 0) || (proc.fragment_ == 0))
{
result = false;
}
else
{
result = ((*fragment_ == *proc.fragment_)
&& (energy_ == proc.energy_)
&& (valid_ == proc.valid_));
}
}
return result;
}
bool PierottiCavFreeEnergyProcessor::finish()
{
// first check for user settings
int verbosity = (int) options.getInteger(Option::VERBOSITY);
// rho is the number density of the solvent (i. e. water) [1/m^3]
double rho = options.getReal(Option::SOLVENT_NUMBER_DENSITY) * 1e30;
// the pressure [ Pa ]
double P = options.getReal(Option::PRESSURE);
// the temperature
double T = options.getReal(Option::ABSOLUTE_TEMPERATURE);
// the solvent radius [ A ]
double solvent_radius = options.getReal(Option::PROBE_RADIUS);
if (verbosity > 0)
{
Log.info() << "Using a probe radius of " << solvent_radius << " A" <<
endl;
}
// now compute some constant terms (names as in Pierotti, Chem. Rev.
// 76(6):717--726, 1976)
double s1 = 2 * solvent_radius * 1e-10; // [ m ]
double s1_3 = s1 * s1 * s1; // [ m^3 ]
double y = Constants::PI * s1_3 * (rho/6); // [ 1 ]
double y_frac = y/(1-y); //
double NkT = Constants::AVOGADRO * Constants::BOLTZMANN * T; // [ J/mol ]
if (verbosity > 0)
{
Log.info() << "y = " << y << endl;
Log.info() << "y_frac = " << y_frac << endl;
}
NumericalSAS sas_computer;
sas_computer.options[NumericalSAS::Option::PROBE_RADIUS ] = solvent_radius;
sas_computer.options[NumericalSAS::Option::COMPUTE_VOLUME] = false;
sas_computer(*fragment_);
HashMap<const Atom*,float> atom_areas = sas_computer.getAtomAreas();
// R is the relation between solute radius and solvent radius [ 1 ]
double R;
// deltaGspher is the cavitatonal energy of a spherical solute [ J/mol ]
double deltaGspher;
// deltaGcav is the cavitatonal energy of the molecule [ J/mol ]
double deltaGcav = 0;
HashMap<const Atom*,float>::Iterator it = atom_areas.begin();
for (; it != atom_areas.end(); ++it)
{
R = 2 * it->first->getRadius() * 1e-10 / s1;
/* the following code implements the Pierotti '76 variant, considering
* relations of radii */
deltaGspher = -log(1.0 - y)
+ 3.0 * y_frac * R
+ ( 3.0 * y_frac + 4.5 * y_frac * y_frac ) * ( R * R )
+ y * P / ( rho * NkT ) * ( R * R * R );
deltaGspher *= NkT;
R = it->first->getRadius() * 1e-10 + s1 / 2.0;
deltaGcav += it->second * 1e-20 /
( 4 * Constants::PI * R * R ) * deltaGspher;
}
// return energy in units of kJ/mol
energy_ = deltaGcav/1000;
return 1;
}
void PierottiCavFreeEnergyProcessor::setDefaultOptions()
{
options.setDefaultInteger(Option::VERBOSITY, Default::VERBOSITY);
options.setDefaultReal(Option::SOLVENT_NUMBER_DENSITY,
Default::SOLVENT_NUMBER_DENSITY);
options.setDefaultReal(Option::ABSOLUTE_TEMPERATURE,
Default::ABSOLUTE_TEMPERATURE);
options.setDefaultReal(Option::PRESSURE, Default::PRESSURE);
options.setDefaultReal(Option::PROBE_RADIUS, Default::PROBE_RADIUS);
}
} // namespace BALL
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