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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/STRUCTURE/analyticalSES.h>
#include <BALL/KERNEL/atom.h>
#include <BALL/KERNEL/atomContainer.h>
namespace BALL
{
extern int connolly_ (int number_of_atoms, double *coordinates, double *radius,
double *volume, double *area, double probe, double exclude, double* atom_areas);
float calculateSESArea(const AtomContainer& fragment, float probe_radius)
{
// extract all atoms: iterate over all composites and
// check whether they are Atoms
vector<const Atom*> atoms;
AtomConstIterator it = fragment.beginAtom();
for (; +it; ++it)
{
if (it->getRadius() > 0.0)
{
atoms.push_back(&*it);
}
}
// if no atoms are found, return zero
if (atoms.empty())
{
return 0;
}
// create the field required by nsc and fill it with the atom coordinates
double* coordinates = new double[atoms.size() * 3];
double* radii = new double[atoms.size()];
double* atom_areas = new double[atoms.size()];
for (Size i = 0; i < atoms.size(); i++)
{
float tmp[3];
atoms[i]->getPosition().get(tmp);
coordinates[i * 3] = tmp[0];
coordinates[i * 3 + 1] = tmp[1];
coordinates[i * 3 + 2] = tmp[2];
radii[i] = atoms[i]->getRadius();
}
double area;
double volume;
int number_of_atoms = (int)atoms.size();
// int connolly_ (int number_of_atoms, double *coordinates, double *radius,
// double *volume, double *area, double probe, double exclude, double* atom_areas);
// call connolly_
connolly_(number_of_atoms, coordinates, radii,
&volume, &area, probe_radius, 0.0, atom_areas);
// free the input fields
delete [] coordinates;
delete [] radii;
delete [] atom_areas;
return area;
}
float calculateSESAtomAreas
(const AtomContainer& fragment, HashMap<const Atom*,float>& atom_areas, float probe_radius)
{
// extract all atoms: iterate over all composites and
// check whether they are Atoms
vector<const Atom*> atoms;
AtomConstIterator it = fragment.beginAtom();
for (; +it; ++it)
{
if (it->getRadius() > 0.0)
{
atoms.push_back(&*it);
}
}
// if no atoms are found, return zero
if (atoms.empty())
{
return 0;
}
// create the field required by nsc and fill it with the atom coordinates
double* coordinates = new double[atoms.size() * 3];
double* radii = new double[atoms.size()];
double* tmp_atom_areas = new double[atoms.size()];
for (Size i = 0; i < atoms.size(); i++)
{
float tmp[3];
atoms[i]->getPosition().get(tmp);
coordinates[i * 3] = tmp[0];
coordinates[i * 3 + 1] = tmp[1];
coordinates[i * 3 + 2] = tmp[2];
radii[i] = atoms[i]->getRadius();
}
double area;
double volume;
int number_of_atoms = (int)atoms.size();
// call connolly_
connolly_(number_of_atoms, coordinates, radii,
&volume, &area, probe_radius, 0.0, tmp_atom_areas);
// extract the atom areas and store them in the hash map
atom_areas.clear();
for (Position i = 0; i < atoms.size(); ++i)
{
atom_areas.insert(std::pair<const Atom*, float>(atoms[i], tmp_atom_areas[i]));
}
// free the input fields
delete [] coordinates;
delete [] radii;
delete [] tmp_atom_areas;
return area;
}
float calculateSESVolume
(const AtomContainer& fragment, float probe_radius)
{
// extract all atoms: iterate over all composites and
// check whether they are Atoms
vector<const Atom*> atoms;
AtomConstIterator it = fragment.beginAtom();
for (; +it; ++it)
{
if (it->getRadius() > 0.0)
{
atoms.push_back(&*it);
}
}
// if no atoms are found, return zero
if (atoms.empty())
{
return 0;
}
// create the field required by nsc and fill it with the atom coordinates
double* coordinates = new double[atoms.size() * 3];
double* radii = new double[atoms.size()];
double* tmp_atom_areas = new double[atoms.size()];
for (Size i = 0; i < atoms.size(); i++)
{
float tmp[3];
atoms[i]->getPosition().get(tmp);
coordinates[i * 3] = tmp[0];
coordinates[i * 3 + 1] = tmp[1];
coordinates[i * 3 + 2] = tmp[2];
radii[i] = atoms[i]->getRadius();
}
double area;
double volume;
int number_of_atoms = (int)atoms.size();
// call connolly_
connolly_(number_of_atoms, coordinates, radii,
&volume, &area, probe_radius, 0.0, tmp_atom_areas);
// free the input fields
delete [] coordinates;
delete [] radii;
delete [] tmp_atom_areas;
return volume;
}
} // namespace BALL
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