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// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Marcel Schumann $
// ----------------------------------------------------
#include <BALL/SCORING/FUNCTIONS/gridedMM.h>
#include <BALL/SCORING/COMPONENTS/advElectrostatic.h>
#include <BALL/SCORING/COMPONENTS/aromaticRingStacking.h>
#include <BALL/SCORING/COMPONENTS/solvation.h>
#include <BALL/SCORING/COMPONENTS/fragmentationalSolvation.h>
#include <BALL/SCORING/COMPONENTS/vanDerWaals.h>
#include <BALL/SCORING/COMPONENTS/hydrogenBond.h>
#include <BALL/SCORING/COMPONENTS/rotationalEntropy.h>
#include <BALL/SCORING/COMPONENTS/lipophilic.h>
using namespace BALL;
GridedMM::GridedMM(AtomContainer& receptor, AtomContainer& ligand, Options& options)
: DiffGridBasedScoring(receptor, ligand, options)
{
setup();
}
GridedMM::GridedMM(AtomContainer& receptor, Vector3& hashgrid_origin, Options& options)
: DiffGridBasedScoring(receptor, hashgrid_origin, options)
{
setup();
}
void GridedMM::setup()
{
setName("GridedMM");
AdvancedElectrostatic* es = new AdvancedElectrostatic(this, options_, forcefield_parameters_);
es->setCoefficient(0.01);
es->setScoringFunction(*this);
scoring_components_.push_back(es);
VanDerWaals* vdw = new VanDerWaals(es);
vdw->setCoefficient(0.1);
vdw->setScoringFunction(*this);
scoring_components_.push_back(vdw);
FragmentationalSolvation* solv = new FragmentationalSolvation(*this);
solv->setCoefficient(19.823265);
scoring_components_.push_back(solv);
// HydrogenBond for h-bonds between receptor-hydrogens and ligand-acceptors.
// The scores for this component will be precalculated and stored in the grid.
HydrogenBond* hb = new HydrogenBond(*this, HydrogenBond::RECEPTOR_HYDROGENS);
hb->selectBaseFunction("fermi");
hb->setCoefficient(3);
hb->setup();
hb->setName("HB_rh");
scoring_components_.push_back(hb);
// HydrogenBond for h-bonds between ligand-hydrogens and receptor-acceptors.
// The scores for this component cannot be precalculated and are calculated on-the-fly during docking.
HydrogenBond* hb2 = new HydrogenBond(*this, HydrogenBond::LIGAND_HYDROGENS);
hb2->selectBaseFunction("fermi");
hb2->setCoefficient(3);
hb2->setup();
hb2->setName("HB_lh");
scoring_components_.push_back(hb2);
//RotationalEntropy will not be precalculated, thus we can use normalization
//add ( = penalize) 1kJ/mol for each rotatable bond exceeding 14
RotationalEntropy* re = new RotationalEntropy(*this);
re->setNormalizationParameters(1, 14);
re->setCoefficient(1);
scoring_components_.push_back(re);
/*
// The following two components are used to penalize bad ligand conformations.
// The score for a good conformation is scaled down according to option 'conformation_scale'.
Electrostatic* lig_es = new Electrostatic(options_, forcefield_parameters_);
lig_es->setLigandIntraMolecular(true);
lig_es->setName("ES_lig");
lig_es->setCoefficient(0.1);
lig_es->setScoringFunction(*this);
scoring_components_.push_back(lig_es);
VanDerWaals* lig_vdw = new VanDerWaals(lig_es);
lig_es->setLigandIntraMolecular(true);
lig_vdw->setName("vdW_lig");
lig_vdw->setCoefficient(0.1);
lig_vdw->setScoringFunction(*this);
scoring_components_.push_back(lig_vdw);
*/
}
BALL::AtomTypes& GridedMM::getAtomTypes()
{
return forcefield_parameters_.getAtomTypes();
}
// used during grid-calculation in order to fetch the ES-score
double GridedMM::getES()
{
double es_score = 0;
for (vector<ScoringComponent*> ::iterator it = scoring_components_.begin(); it != scoring_components_.end(); ++it)
{
Electrostatic* es = dynamic_cast<Electrostatic*>(*it);
if (!(*it)->isLigandIntraMolecular() && (*it)->isEnabled() && es != NULL)
{
es_score += es->getScaledScore();
}
}
return es_score;
}
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