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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: surfaceModel.C,v 1.13.18.2 2007/04/12 12:04:06 amoll Exp $
//
#include <BALL/VIEW/MODELS/surfaceModel.h>
#include <BALL/VIEW/PRIMITIVES/mesh.h>
#include <BALL/VIEW/KERNEL/common.h>
#include <BALL/KERNEL/atomContainer.h>
#include <BALL/KERNEL/forEach.h>
using namespace std;
namespace BALL
{
namespace VIEW
{
AddSurfaceModel::AddSurfaceModel()
: ModelProcessor(),
type_(SurfaceProcessor::SOLVENT_EXCLUDED_SURFACE),
probe_radius_(1.5)
{
}
AddSurfaceModel::AddSurfaceModel(const AddSurfaceModel& add_surface)
: ModelProcessor(add_surface),
type_(add_surface.type_),
probe_radius_(add_surface.probe_radius_)
{
}
AddSurfaceModel::~AddSurfaceModel()
{
#ifdef BALL_VIEW_DEBUG
Log.info() << "Destructing object " << (void *)this
<< " of class " << RTTI::getName<AddSurfaceModel>() << std::endl;
#endif
}
void AddSurfaceModel::clear()
{
ModelProcessor::clear();
type_ = SurfaceProcessor::SOLVENT_EXCLUDED_SURFACE;
}
Processor::Result AddSurfaceModel::operator () (Composite& composite)
{
if (RTTI::isKindOf<AtomContainer>(&composite))
{
AtomIterator it;
BALL_FOREACH_ATOM(*(AtomContainer*) &composite, it)
{
atoms_.insert((Atom*) &*it);
}
return Processor::CONTINUE;
}
if (!RTTI::isKindOf<Atom>(&composite)) return Processor::CONTINUE;
atoms_.insert((Atom*) &composite);
return Processor::CONTINUE;
}
void AddSurfaceModel::dump(std::ostream& s, Size depth) const
{
BALL_DUMP_STREAM_PREFIX(s);
BALL_DUMP_DEPTH(s, depth);
BALL_DUMP_HEADER(s, this, this);
ModelProcessor::dump(s, depth + 1);
BALL_DUMP_STREAM_SUFFIX(s);
}
void AddSurfaceModel::clearComposites()
{
atoms_.clear();
}
bool AddSurfaceModel::createGeometricObjects()
{
ModelProcessor::createGeometricObjects();
Mesh* mesh = new Mesh;
if (mesh == 0) return false;
SurfaceProcessor sp;
sp.setType(getType());
sp.setProbeRadius(probe_radius_);
sp.start();
if (getSurfaceDrawingPrecision() != -1)
{
sp.setDensity(getSurfaceDrawingPrecision());
}
else
{
if (getDrawingPrecision() >= DRAWING_PRECISION_LOW &&
getDrawingPrecision() <= DRAWING_PRECISION_ULTRA)
{
sp.setDensity(SurfaceDrawingPrecisions[getDrawingPrecision()]);
}
else
{
Log.error() << "Invalid Drawing Precision " << getDrawingPrecision()
<< " in " << __FILE__ << " " << __LINE__ << std::endl;
sp.setDensity(1.5);
}
}
bool ok = true;
try
{
// Since we have container of *pointers* only, we have to
// do the iteration on our own.
HashSet<Atom*>::Iterator it(atoms_.begin());
for (; +it; ++it)
{
if (sp.operator () (**it) != Processor::CONTINUE)
{
ok = false;
break;
}
}
}
catch (Exception::GeneralException& e)
{
Log.error() << "SurfaceModel: caught exception while calculating molecular surface "<<endl;// << e << endl;
}
catch (std::exception& e)
{
Log.error() << "SurfaceModel: caught exception while calculating molecular surface: " << e.what() << endl;
}
catch (...)
{
Log.error() << "SurfaceModel: caught unknown exception while calculating molecular surface" << endl;
}
// Compute the surface
ok &= sp.finish();
if (!ok)
{
Log.error() << "Unknown error occurred while calculating molecular surface" << std::endl;
}
*static_cast<Surface*>(mesh) = sp.getSurface();
// normalize normal length:
vector<Vector3>& normals = mesh->normal;
for (Position p = 0; p < normals.size(); p++)
{
float square_length = normals[p].getSquareLength();
if (square_length == 0) continue;
normals[p] /= sqrt(square_length);
}
geometric_objects_.push_back(mesh);
return true;
}
} // namespace VIEW
} // namespace BALL
|
