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// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Marcel Schumann $
// ----------------------------------------------------
#include <BALL/SCORING/COMPONENTS/fragmentationalSolvation.h>
#include <BALL/KERNEL/PTE.h>
#include <map>
using namespace BALL;
using namespace std;
FragmentationalSolvation::FragmentationalSolvation(ScoringFunction& sf)
: Solvation(sf)
{
setName("FragmentationalSolvation");
atom_pairwise_ = 0;
type_name_ = "fragSolv";
}
void FragmentationalSolvation::update(const AtomPairVector& /*pair_vector*/)
{
}
double FragmentationalSolvation::updateScore()
{
score_ = 0;
const HashGrid3<Atom*>* hashgrid = 0;
bool use_selection = scoring_function_->getLigand()->containsSelection();
HashGrid3<Atom*>* nonconst_hashgrid = 0;
if (!isLigandIntraMolecular())
{
hashgrid = scoring_function_->getHashGrid();
nonconst_hashgrid = const_cast<HashGrid3<Atom*>* >(hashgrid);
// Add contribution of ligand atoms to desolvation of ligand
for(AtomIterator atom_it=scoring_function_->getLigand()->beginAtom(); !atom_it.isEnd(); atom_it++)
{
Vector3 cell = getAtomCell(&*atom_it,hashgrid);
if(cell[0]>=0)
{
nonconst_hashgrid->insert((Position)cell[0],(Position)cell[1],(Position)cell[2],&*atom_it);
}
}
}
else
{
double resolution = 3.0;
Vector3 center = scoring_function_->getLigandCenter();
// no of cells on each axis for a resolution of 3 Angstroem
int size = (int)(ceil(scoring_function_->getLigandRadius()*2/resolution)+1);
hashgrid = scoring_function_->initializeHashGrid(scoring_function_->getLigand(), center, resolution, size);
}
for (AtomIterator atom_it = scoring_function_->getLigand()->beginAtom(); !atom_it.isEnd(); atom_it++)
{
if (use_selection && !atom_it->isSelected())
{
continue;
}
// get the fraction of the volume surrounding the current ligand atom that is occupied by receptor atoms
double desolv_frac = getDesolvatedFraction(&*atom_it, hashgrid);
String element = atom_it->getElement().getSymbol();
map<String, double>::iterator it = solvation_parameters.find(element);
if (it == solvation_parameters.end())
{
throw BALL::Exception::GeneralException(__FILE__, __LINE__, "FragmentationalSolvation::updateScore() error", "No solvation parameter for element "+element+" found!");
}
double par = it->second;
it = solvation_volumes.find(element);
if (it == solvation_volumes.end())
{
throw BALL::Exception::GeneralException(__FILE__, __LINE__, "FragmentationalSolvation::updateScore() error", "No solvation volume for element "+element+" found!");
}
double atom_score = par*it->second*desolv_frac;
if (scoring_function_->storeInteractionsEnabled())
{
//double scaled_atom_score = atom_score;
//scaled_atom_score = scaleScore(scaled_atom_score);
//atom_it->addInteraction("fragSolv", scaled_atom_score);
atom_it->addInteraction("fragSolv", scaleScore(atom_score));
}
score_ += atom_score;
}
if(!isLigandIntraMolecular())
{
// remove ligand atoms for hashgrid
for(AtomIterator atom_it=scoring_function_->getLigand()->beginAtom(); !atom_it.isEnd(); atom_it++)
{
Vector3 cell = getAtomCell(&*atom_it,hashgrid);
if(cell[0]>=0)
{
nonconst_hashgrid->remove((Position)cell[0],(Position)cell[1],(Position)cell[2],&*atom_it);
}
}
}
else
{
delete hashgrid;
}
/*
scaleScore();
return score_;
*/
return getScaledScore();
}
double FragmentationalSolvation::getDesolvatedFraction(const Atom* atom, const HashGrid3<Atom*>* hashgrid)
{
int x_size = (int)hashgrid->getSizeX();
int y_size = (int)hashgrid->getSizeY();
int z_size = (int)hashgrid->getSizeZ();
Vector3 lig_atom_cell = (atom->getPosition() - hashgrid->getOrigin());
lig_atom_cell[0] /= hashgrid->getUnit()[0];
lig_atom_cell[1] /= hashgrid->getUnit()[1];
lig_atom_cell[2] /= hashgrid->getUnit()[2];
// no desolvation of ligand atom if this atom is outside of grid
if (lig_atom_cell[0] < 0 || lig_atom_cell[0] > x_size || lig_atom_cell[1] < 0 || lig_atom_cell[1] > y_size || lig_atom_cell[2] < 0 || lig_atom_cell[2] > z_size )
{
return 0;
}
if (hashgrid->getUnit()[0] > 4 || hashgrid->getUnit()[0] < 3 )
{
throw BALL::Exception::GeneralException(__FILE__, __LINE__, "FragmentationalSolvation error", "The ScoringFunction's hashgrid resolution must be between 3 and 4 Angstroem in order to use FragmentationalSolvation!");
}
Size radius = 1;
// indices in HashGrid, where the search for interacting target atoms should begin ( != position of ligand atom)
int i = static_cast < int > (lig_atom_cell[0]-radius); if (i < 0){i = 0; }
int j0 = static_cast < int > (lig_atom_cell[1]-radius); if (j0 < 0){j0 = 0; }
int k0 = static_cast < int > (lig_atom_cell[2]-radius); if (k0 < 0){k0 = 0; }
Size occupied_cells = 0;
for (; i <= lig_atom_cell[0]+radius && i < x_size; i++)
{
for (int j = j0; j <= lig_atom_cell[1]+radius && j < y_size; j++)
{
for (int k = k0; k <= lig_atom_cell[2]+radius && k < z_size; k++)
{
const HashGridBox3<Atom*>* box = hashgrid->getBox(i, j, k);
if (!box->isEmpty())
{
// count only if Box contains not only the Atom whose desolvated volume-fraction is to be estimated
HashGridBox3<Atom*>::ConstDataIterator d_it = box->beginData();
if (*d_it != atom || ++d_it != box->endData())
{
occupied_cells++;
}
}
}
}
}
double no_neighbor_cell = pow((double)(radius*2+1), 3); // radius of 1 cell == > 3 cells on each axis
return occupied_cells/no_neighbor_cell;
}
Vector3 FragmentationalSolvation::getAtomCell(Atom* atom, const HashGrid3<Atom*>* hashgrid)
{
Vector3 cell(-1, -1, -1);
int x_size = (int)hashgrid->getSizeX();
int y_size = (int)hashgrid->getSizeY();
int z_size = (int)hashgrid->getSizeZ();
cell = (atom->getPosition() - hashgrid->getOrigin());
cell[0] /= hashgrid->getUnit()[0];
cell[1] /= hashgrid->getUnit()[1];
cell[2] /= hashgrid->getUnit()[2];
if (cell[0] < 0 || cell[0] > x_size || cell[1] < 0 || cell[1] > y_size || cell[2] < 0 || cell[2] > z_size )
{
return Vector3(-1, -1, -1);
}
return cell;
}
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