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// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Marcel Schumann $
// ----------------------------------------------------
#include <BALL/SCORING/COMPONENTS/polarity.h>
#include <BALL/SCORING/COMPONENTS/fresnoTypes.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/SYSTEM/timer.h>
using namespace std;
using namespace BALL;
const double Polarity::POL_ES_THRESHOLD = 0.2;
const double Polarity::LIP_ES_THRESHOLD = 0.1;
Polarity::Polarity(ScoringFunction& sf)
: ScoringComponent(sf)
{
setName("Polarity");
type_name_ = "pol";
receptor_fresno_types_ = 0;
ligand_fresno_types_ = 0;
gridable_ = false;
atom_pairwise_ = 0;
setup();
}
Polarity::Polarity(const Polarity& bp)
: ScoringComponent(bp)
{
setName("Polarity");
type_name_ = "pol";
receptor_fresno_types_ = 0;
ligand_fresno_types_ = 0;
gridable_ = false;
atom_pairwise_ = 0;
setup();
}
Polarity::~Polarity()
{
delete receptor_fresno_types_;
delete ligand_fresno_types_;
}
void Polarity::clear()
{
}
bool Polarity::setup()
{
ScoringFunction* sf = getScoringFunction();
if (sf == 0)
{
Log.error() << "Polarity::setup(): "
<< "component not bound to force field." << endl;
return false;
}
delete receptor_fresno_types_;
receptor_fresno_types_ = new FresnoTypes(getScoringFunction()->getReceptor());
setupLigand();
return true;
}
void Polarity::setupLigand()
{
delete ligand_fresno_types_;
ligand_fresno_types_ = new FresnoTypes(getScoringFunction()->getLigand());
}
Size Polarity::getType_(const Atom* atom)
{
HashMap<const Atom*, Size>::const_iterator it = receptor_fresno_types_->getTypeMap()->find(atom);
if (it != receptor_fresno_types_->getTypeMap()->end())
{
return it->second;
}
it = ligand_fresno_types_->getTypeMap()->find(atom);
if (it != ligand_fresno_types_->getTypeMap()->end())
{
return it->second;
}
return FresnoTypes::UNKNOWN;
}
void Polarity::update(const std::vector<std::pair<Atom*, Atom*> >& /* pair_vector */)
{
// nothing to be done here ...
}
bool Polarity::isPolar_(const Atom* atom)
{
// if atom is polar, it should (besides the correct Fresno type) also have a significant charge
if (fabs(atom->getCharge()) < POL_ES_THRESHOLD) return false;
int type = getType_(atom);
return (type == FresnoTypes::POLAR) || (type == FresnoTypes::HBOND_ACCEPTOR)
|| (type == FresnoTypes::HBOND_DONOR) || (type == FresnoTypes::HBOND_ACCEPTOR_DONOR)
|| (type == FresnoTypes::HBOND_HYDROGEN);
}
bool Polarity::isLipophilic_(const Atom* atom)
{
// if atom is lipophilic, it should (besides the correct Fresno type) also have no significant charge
if (fabs(atom->getCharge()) > LIP_ES_THRESHOLD) return false;
int type = getType_(atom);
return type == FresnoTypes::LIPOPHILIC;
}
bool Polarity::isBackboneAtom_(const Atom* atom)
{
return atom->getName() == "O" || atom->getName() == "N"
|| atom->getName() == "H" || atom->getName() == "C";
}
double Polarity::updateScore()
{
score_ = 0.0;
//float val = 0.0;
//float distance;
//float R1;
//float R2;
const HashGrid3<Atom*>* hashgrid = scoring_function_->getHashGrid();
int radius = 1;
Size no_neighbor_cells = (Size)pow((double)(radius*2+1), 3); // radius of 1 cell == > 3 cells on each axis
double total_sum = 0;
AtomPairVector::const_iterator it;
for (AtomIterator it = scoring_function_->getLigand()->beginAtom(); +it; it++)
{
int no_positive_contacts = 0;
int no_negative_contacts = 0;
bool ligandatom_is_lipophilic = isLipophilic_(&*it);
if (!ligandatom_is_lipophilic)
{
continue;
}
const HashGridBox3<Atom*>* box = hashgrid->getBox(it->getPosition());
// ligand atom lies outside of grid
if (!box) continue;
Position pos_x, pos_y, pos_z;
hashgrid->getIndices(*box, pos_x, pos_y, pos_z);
// indices in HashGrid, where the search for interacting target atoms should begin ( != position of ligand atom)
int i = ((int)pos_x)-radius; if (i < 0){i = 0; }
int j0 = ((int)pos_y)-radius; if (j0 < 0){j0 = 0; }
int k0 = ((int)pos_z)-radius; if (k0 < 0){k0 = 0; }
int x_size = (int)hashgrid->getSizeX();
int y_size = (int)hashgrid->getSizeY();
int z_size = (int)hashgrid->getSizeZ();
for (; i <= ((int)pos_x)+radius && i < x_size; i++)
{
for (int j = j0; j <= ((int)pos_y)+radius && j < y_size; j++)
{
for (int k = k0; k <= ((int)pos_z)+radius && k < z_size; k++)
{
const HashGridBox3<Atom*>* box = hashgrid->getBox(i, j, k);
if (!box->isEmpty())
{
double cell_score = 0;
for (HashGridBox3 < Atom* > ::ConstDataIterator d_it = box->beginData(); d_it != box->endData(); d_it++)
{
if (isBackboneAtom_(*d_it)) continue;
bool rec_polar = isPolar_(*d_it);
bool rec_lipophilic = 0;
if (!rec_polar) rec_lipophilic = isLipophilic_(*d_it);
if (!rec_polar && ! rec_lipophilic) continue;
double distance = ((*d_it)->getPosition()-it->getPosition()).getLength();
if (distance > (*d_it)->getElement().getVanDerWaalsRadius()+it->getElement().getVanDerWaalsRadius()+1.5) continue;
double val;
if (distance > 1) val = 1/distance;
else val = 1;
// lipophilic--lipophilic interaction; else polar rec. -- lipophilic ligand atom
if (rec_lipophilic)
{
val *= -1;
}
cell_score += val;
total_sum += val;
if (scoring_function_->storeInteractionsEnabled())
{
val = scaleScore(val);
it->addInteraction(*d_it, "pol", val);
(*d_it)->addInteraction(&*it, "pol", val);
}
}
if (cell_score < -0.1) no_positive_contacts++;
else if (cell_score > 0.1) no_negative_contacts++;
}
// if there is no neighboring receptor atom, there will be water ...
// else if(i!=pos_x||j!=pos_y||k!=pos_z)
// {
// if(ligandatom_is_lipophilic)
// {
// no_negative_contacts++;
// double scaled_atom_score = 1.0/no_neighbor_cells;
// scaleScore(scaled_atom_score);
// total_sum += scaled_atom_score;
// it->addInteraction("pol",scaled_atom_score);
// }
// }
}
}
}
score_ += (no_negative_contacts-no_positive_contacts)/((double)no_neighbor_cells);
//cout<<it->getFullName()<<" : "<<no_negative_contacts<<", "<<no_positive_contacts<<" "<<(no_negative_contacts-no_positive_contacts)/((double)no_neighbor_cells)<<endl;
}
// scaleScore();
// cout<<"polarity: total sum="<<total_sum<<endl;
// cout<<"polarity: score="<<score_<<endl;
// return score_;
return getScaledScore();
}
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