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// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Marcel Schumann $
// ----------------------------------------------------
#include <BALL/SCORING/COMPONENTS/solvation.h>
#include <BALL/KERNEL/PTE.h>
using namespace BALL;
using namespace std;
Solvation::Solvation(ScoringFunction& sf)
: ScoringComponent(sf)
{
setName("Solvation");
// Parameters taken from Autodock4, AD4_PARM99.dat
solvation_parameters["H"] = 0.00051;
solvation_parameters["N"] = -0.00162;
solvation_parameters["C"] = -0.00143;
solvation_parameters["O"] = -0.00251;
solvation_parameters["S"] = -0.00214;
solvation_parameters["Cl"] = -0.00110;
solvation_parameters["Ca"] = -0.00110;
solvation_parameters["Mn"] = -0.00110;
solvation_parameters["Mg"] = -0.00110;
solvation_parameters["Fe"] = -0.00110;
solvation_parameters["Zn"] = -0.00110;
solvation_parameters["Br"] = -0.00110;
solvation_parameters["I"] = -0.00110;
solvation_parameters["F"] = -0.00110;
solvation_parameters["Cs"] = -0.00110;
solvation_parameters["P"] = -0.00110;
solvation_volumes["H"] = 0.9;
solvation_volumes["N"] = 25.42;
solvation_volumes["C"] = 29.10;
solvation_volumes["O"] = 19.20;
solvation_volumes["S"] = 33.51;
solvation_volumes["Cl"] = 30.96;
solvation_volumes["Ca"] = 21.06;
solvation_volumes["Mn"] = 2.1400; // from AD4_parameters.dat
solvation_volumes["Mg"] = 2.09;
solvation_volumes["Fe"] = 1.8400; // from AD4_parameters.dat
solvation_volumes["Zn"] = 5.58;
solvation_volumes["Br"] = 45.83;
solvation_volumes["I"] = 54.36;
solvation_volumes["F"] = 22.45;
solvation_volumes["Cs"] = 163.91;
solvation_volumes["P"] = 38.79;
type_name_ = "solv";
}
void Solvation::update(const AtomPairVector& pair_vector)
{
pair_vector_ = pair_vector;
}
double Solvation::updateScore()
{
score_ = 0;
for (AtomPairVector::iterator it = pair_vector_.begin(); it != pair_vector_.end(); it++)
{
const Atom* atom_i = it->first;
const Atom* atom_j = it->second;
double distance = atom_i->getPosition().getDistance(atom_j->getPosition());
String element_i = atom_i->getElement().getSymbol();
map<String, double>::iterator search_it = solvation_parameters.find(element_i);
if (search_it == solvation_parameters.end())
{
throw BALL::Exception::GeneralException(__FILE__, __LINE__, "Solvation::updateScore() error", "No solvation parameter for element "+element_i+" found!");
}
double par_i = search_it->second;
String element_j = atom_j->getElement().getSymbol();
search_it = solvation_volumes.find(element_j);
if (search_it == solvation_volumes.end())
{
throw BALL::Exception::GeneralException(__FILE__, __LINE__, "Solvation::updateScore() error", "No solvation volume for element "+element_j+" found!");
}
double vol_j = search_it->second;
score_ += par_i*vol_j*exp((-distance*distance)/(2*3.5*3.5));
}
/*
scaleScore();
return score_;
*/
return getScaledScore();
}
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