1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
|
// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Marcel Schumann $
// ----------------------------------------------------
#include <BALL/SCORING/COMPONENTS/electrostatic.h>
#include <BALL/SCORING/COMPONENTS/vanDerWaals.h>
#include <BALL/SCORING/COMMON/scoringFunction.h>
using namespace BALL;
Electrostatic::Electrostatic(Options& options, ForceFieldParameters& forcefield_parameters)
{
amber_nb_ = new AmberNonBonded;
amber_nb_->setup(options, forcefield_parameters);
do_calculations_ = 1;
setName("Electrostatics");
type_name_ = "ES";
}
Electrostatic::Electrostatic(VanDerWaals* vdw)
{
amber_nb_ = vdw->getAmberNonBonded();
do_calculations_ = 0;
ligand_intra_molecular_ = vdw->isLigandIntraMolecular();
setName("Electrostatics");
type_name_ = "ES";
}
Electrostatic::~Electrostatic()
{
if (do_calculations_) delete amber_nb_;
}
void Electrostatic::update(const vector<std::pair<Atom*, Atom*> >& pair_vector)
{
if (do_calculations_)
{
amber_nb_->update(pair_vector);
}
}
double Electrostatic::updateScore()
{
if (do_calculations_)
{
bool b = scoring_function_->storeInteractionsEnabled();
amber_nb_->enableStoreInteractions(b);
amber_nb_->updateEnergy();
}
score_ = amber_nb_->getElectrostaticEnergy();
//scaleScore();
// use threshold for unrealistically good amber-ES energies due to consideration of only point-charges
/// TODO: convert this to a value for each ligand atom == each grid cell
/// else thresholds will be different when using grid-based and non-grid-based scoring
//double threshold = scoring_function_->getNoLigandAtoms()*-10;
//if (score < threshold) score_ = threshold;
//if (score_ < -40) score_ = -40;
//return score_;
return getScaledScore();
}
AmberNonBonded* Electrostatic::getAmberNonBonded()
{
return amber_nb_;
}
|
