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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: slickEnergy.C,v 1.4 2006/05/21 18:15:29 anker Exp $
#include <BALL/SCORING/FUNCTIONS/slickEnergy.h>
#include <BALL/SCORING/COMPONENTS/CHPISlick.h>
#include <BALL/SCORING/COMPONENTS/hydrogenBondSlick.h>
#include <BALL/SCORING/COMPONENTS/vanDerWaalsSlick.h>
#include <BALL/SCORING/COMPONENTS/nonpolarSolvation.h>
#include <BALL/SCORING/COMPONENTS/polarSolvation.h>
#include <BALL/SYSTEM/path.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/standardPredicates.h>
#include <BALL/KERNEL/bondIterator.h>
#include <BALL/KERNEL/forEach.h>
#include <BALL/MOLMEC/PARAMETER/templates.h>
namespace BALL
{
const char* SLICKEnergy::Option::CONST = "const";
const char* SLICKEnergy::Option::HB = "hb_coefficient";
const char* SLICKEnergy::Option::VDW = "vdw_coefficient";
const char* SLICKEnergy::Option::CHPI = "chpi_coefficient";
const char* SLICKEnergy::Option::NONPOLAR = "nonpolar_coefficient";
const char* SLICKEnergy::Option::POLAR = "polar_coefficient";
// Parameters for the new function containing HB contributions.
// Calibration for the complete set. [anker 2006/02/24]
// Calibration set: 1j4u 5cna 1gic 1qdo 1qdc 1ona 1dgl 1axz 1ax0 1ax1
// 1ax2 2bqp 1bqp 1qf3 2pel 1ehh 1en2 1k7u
// const float SLICKEnergy::Default::CONST = -2.70722038;
// const float SLICKEnergy::Default::HB = -1.31258320;
// const float SLICKEnergy::Default::CHPI = -0.74188312;
// const float SLICKEnergy::Default::VDW = 0.02207132;
// const float SLICKEnergy::Default::NONPOLAR = 0.49981964;
// const float SLICKEnergy::Default::POLAR = -0.12498055;
// Parameters for the whole calibration set, this time with Bondi
// observed mean radii in the nonpolar term and the log-softened VDW
// component
// [anker 2006/04/26]
// const float SLICKEnergy::Default::CONST = -5.23774531;
// const float SLICKEnergy::Default::HB = -0.09077441;
// const float SLICKEnergy::Default::CHPI = -0.50244683;
// const float SLICKEnergy::Default::VDW = 0.01559796;
// const float SLICKEnergy::Default::NONPOLAR = 0.36638941;
// const float SLICKEnergy::Default::POLAR = -0.10725374;
// Recalibrated after finding inconsistencies
// [anker 2008-Dec-15]
const float SLICKEnergy::Default::CONST = -5.303867;
const float SLICKEnergy::Default::HB = 0.160806;
const float SLICKEnergy::Default::CHPI = -0.655133;
const float SLICKEnergy::Default::VDW = 0.006934;
const float SLICKEnergy::Default::NONPOLAR = 0.406553;
const float SLICKEnergy::Default::POLAR = -0.099546;
SLICKEnergy::SLICKEnergy()
: ScoringFunction()
{
}
SLICKEnergy::SLICKEnergy(Molecule& protein, Molecule& ligand,
Options& new_options)
: ScoringFunction(protein, ligand, new_options)
{
setup();
}
SLICKEnergy::SLICKEnergy(const SLICKEnergy& slick)
: ScoringFunction(slick)
{
}
SLICKEnergy::~SLICKEnergy()
{
clear();
}
void SLICKEnergy::clear()
{
ScoringFunction::clear();
}
bool SLICKEnergy::setup()
{
setName("SLICKEnergy");
options_.set(NonpolarSolvation::Option::NONPOLAR_METHOD, NonpolarSolvation::CALCULATION__PCM);
options_.setInteger(PolarSolvation::Option::POLAR_METHOD, PolarSolvation::CALCULATION__FULL_CYCLE_FOCUSED);
options_.setInteger(VanDerWaalsSlick::Option::VDW_METHOD, VanDerWaalsSlick::CALCULATION__SOFTENED_LJ_POTENTIAL_LOG);
options_.setReal(VanDerWaalsSlick::Option::VDW_SOFTENING_LIMIT, 5.0f);
float CONST = options_.setDefaultReal(SLICKEnergy::Option::CONST, SLICKEnergy::Default::CONST);
setIntercept(CONST);
// register all components of the force field
registerComponents_();
// check whether we know which molecule is the protein and which is the
// ligand in this complex. In case we don't know, we have to guess.
// This can be wrong if we got two PDB files which will both be tagged
// as protein.
if ((getReceptor() == 0) || (getLigand() == 0))
{
Log.error() << "I don't know what the protein and the ligand is."
<< std::endl;
return false;
}
return true ;
}
const SLICKEnergy& SLICKEnergy::operator = (const SLICKEnergy& slick)
{
// avoid self assignment
if (&slick != this)
{
ScoringFunction::operator = (slick);
}
return *this;
}
double SLICKEnergy::getHydrogenBondScore() const
{
const ScoringComponent* component = getComponent("SLICK HydrogenBond");
if (component != 0)
{
return component->getRawScore();
}
else
{
return 0;
}
}
double SLICKEnergy::getCHPIScore() const
{
const ScoringComponent* component = getComponent("CHPISlick");
if (component != 0)
{
return component->getRawScore();
}
else
{
return 0;
}
}
double SLICKEnergy::getVDWScore() const
{
const ScoringComponent* component = getComponent("vanDerWaalsSlick");
if (component != 0)
{
return component->getRawScore();
}
else
{
return 0;
}
}
double SLICKEnergy::getPolarSolvationScore() const
{
const ScoringComponent* component = getComponent("Polar Solvation");
if (component != 0)
{
return component->getRawScore();
}
else
{
return 0;
}
}
double SLICKEnergy::getNonpolarSolvationScore() const
{
const ScoringComponent* component = getComponent("Nonpolar Solvation");
if (component != 0)
{
return component->getRawScore();
}
else
{
return 0;
}
}
void SLICKEnergy::registerComponents_()
{
float coeff_CHPI = options_.setDefaultReal(SLICKEnergy::Option::CHPI, SLICKEnergy::Default::CHPI);
float coeff_HB = options_.setDefaultReal(SLICKEnergy::Option::HB, SLICKEnergy::Default::HB);
float coeff_VDW = options_.setDefaultReal(SLICKEnergy::Option::VDW, SLICKEnergy::Default::VDW);
float coeff_NPS = options_.setDefaultReal(SLICKEnergy::Option::NONPOLAR, SLICKEnergy::Default::NONPOLAR);
float coeff_PS = options_.setDefaultReal(SLICKEnergy::Option::POLAR, SLICKEnergy::Default::POLAR);
CHPISlick* chpi = new CHPISlick(*this);
chpi->setCoefficient(coeff_CHPI);
chpi->setup();
chpi->setNormalizationParameters(0.0, 0.0);
insertComponent(chpi);
HydrogenBondSlick* hb = new HydrogenBondSlick(*this);
hb->setCoefficient(coeff_HB);
hb->setup();
hb->setNormalizationParameters(0.0, 0.0);
insertComponent(hb);
VanDerWaalsSlick* vdws = new VanDerWaalsSlick(*this);
vdws->setCoefficient(coeff_VDW);
vdws->setup();
vdws->setNormalizationParameters(0.0, 0.0);
insertComponent(vdws);
PolarSolvation* ps = new PolarSolvation(*this);
ps->setCoefficient(coeff_PS);
ps->setup();
ps->setNormalizationParameters(0.0, 0.0);
insertComponent(ps);
NonpolarSolvation* nps = new NonpolarSolvation(*this);
nps->setCoefficient(coeff_NPS);
nps->setup();
nps->setNormalizationParameters(0.0, 0.0);
insertComponent(nps);
}
} // namespace BALL
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