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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/STRUCTURE/surfaceProcessor.h>
namespace BALL
{
SurfaceProcessor::SurfaceProcessor()
: UnaryProcessor<Atom>(),
radius_offset_(0.0),
vdw_factor_(1.0),
surface_type_(SurfaceProcessor::SOLVENT_EXCLUDED_SURFACE),
surface_(),
spheres_(),
density_(4.5),
probe_radius_(1.5)
{
}
bool SurfaceProcessor::start()
{
spheres_.clear();
return true;
}
Processor::Result SurfaceProcessor::operator () (Atom& atom)
{
TVector3<double> position((double)atom.getPosition().x,
(double)atom.getPosition().y,
(double)atom.getPosition().z);
if (atom.getElement() != Element::UNKNOWN && atom.getElement().getVanDerWaalsRadius() > 0.0)
{
spheres_.push_back(TSphere3<double>(position, vdw_factor_ * atom.getElement().getVanDerWaalsRadius() + radius_offset_));
}
else
{
spheres_.push_back(TSphere3<double>(position, radius_offset_ + vdw_factor_));
}
return Processor::CONTINUE;
}
bool SurfaceProcessor::finish()
{
if (spheres_.empty())
{
Log.error() << "empty surface" << std::endl;
return true;
}
ReducedSurface* reduced_surface = new ReducedSurface(spheres_, probe_radius_);
reduced_surface->compute();
if (surface_type_ == SurfaceProcessor::SOLVENT_EXCLUDED_SURFACE)
{
SolventExcludedSurface* ses = new SolventExcludedSurface(reduced_surface);
ses->compute();
double diff = (probe_radius_ < 1.5 ? 0.01 : -0.01);
Size i = 0;
bool ok = false;
while (!ok && (i < 10))
{
i++;
ok = ses->check();
if (!ok)
{
delete ses;
delete reduced_surface;
probe_radius_ += diff;
reduced_surface = new ReducedSurface(spheres_, probe_radius_);
reduced_surface->compute();
ses = new SolventExcludedSurface(reduced_surface);
ses->compute();
}
}
if (ok)
{
TriangulatedSES* surface = new TriangulatedSES(ses, density_);
surface->compute();
surface->exportSurface(surface_);
delete surface;
}
delete ses;
}
else
{
SolventAccessibleSurface* sas = new SolventAccessibleSurface(reduced_surface);
sas->compute();
TriangulatedSAS* surface = new TriangulatedSAS(sas, density_);
surface->compute();
surface->exportSurface(surface_);
delete surface;
delete sas;
}
delete reduced_surface;
return true;
}
} // namespace
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