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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: atomBondModelBaseProcessor.C,v 1.15.18.1 2007/03/25 22:02:28 oliver Exp $
//
#include <BALL/VIEW/MODELS/atomBondModelBaseProcessor.h>
#include <BALL/KERNEL/forEach.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/residue.h>
#include <BALL/QSAR/ringPerceptionProcessor.h>
using namespace std;
namespace BALL
{
namespace VIEW
{
AtomBondModelBaseProcessor::AtomBondModelBaseProcessor()
: ModelProcessor(),
used_atoms_(),
atom_set_()
{
}
AtomBondModelBaseProcessor::AtomBondModelBaseProcessor(const AtomBondModelBaseProcessor& processor)
: ModelProcessor(processor),
used_atoms_(),
atom_set_()
{
}
AtomBondModelBaseProcessor::~AtomBondModelBaseProcessor()
{
#ifdef BALL_VIEW_DEBUG
Log.info() << "Destructing object " << this << " of class AtomBondModelBaseProcessor" << std::endl;
#endif
}
void AtomBondModelBaseProcessor::clear()
{
ModelProcessor::clear();
atom_set_.clear();
used_atoms_.clear();
rings_.clear();
ring_atoms_.clear();
}
void AtomBondModelBaseProcessor::set(const AtomBondModelBaseProcessor& processor)
{
clear();
ModelProcessor::set(processor);
}
const AtomBondModelBaseProcessor& AtomBondModelBaseProcessor::operator = (const AtomBondModelBaseProcessor& processor)
{
set(processor);
return *this;
}
void AtomBondModelBaseProcessor::clearComposites()
{
atom_set_.clear();
used_atoms_.clear();
}
void AtomBondModelBaseProcessor::dump(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_DEPTH(s, depth);
s << "used atoms: " << used_atoms_.size() << endl;
BALL_DUMP_STREAM_SUFFIX(s);
}
void AtomBondModelBaseProcessor::buildBondModels_()
{
// generate bond primitive
const Atom* second_atom_ptr = 0;
AtomBondConstIterator bond_it;
list<const Atom*>::const_iterator atom_it;
// for all used atoms
for (atom_it = getAtomList_().begin();
atom_it != getAtomList_().end(); ++atom_it)
{
// for all bonds connected from first- to second atom
BALL_FOREACH_ATOM_BOND(**atom_it, bond_it)
{
if (*atom_it != bond_it->getSecondAtom())
{
second_atom_ptr = bond_it->getSecondAtom();
}
else
{
second_atom_ptr = bond_it->getFirstAtom();
}
// use only atoms with greater handles than first atom
// or
// second atom not a used atom, but smaller as the first atom
// process bond between them
if (**atom_it < *second_atom_ptr && getAtomSet_().has(second_atom_ptr))
{
visualiseBond_(*bond_it);
}
}
}
}
void AtomBondModelBaseProcessor::visualiseBond_(const Bond& /*bond*/)
{
}
bool AtomBondModelBaseProcessor::createGeometricObjects()
{
ring_atoms_.clear();
vector<vector<Atom*> >::iterator it = rings_.begin();
for(; it != rings_.end(); it++)
{
vector<Atom*>& ring = *it;
if (ring.size() != 5 && ring.size() != 6) continue;
vector<Atom*>::iterator ait = ring.begin();
for (; ait != ring.end(); ait++)
{
ring_atoms_.insert(*ait);
}
}
buildBondModels_();
visualiseRings_();
rings_.clear();
return true;
}
Processor::Result AtomBondModelBaseProcessor::operator () (Composite& composite)
{
Fragment* residue = dynamic_cast<Fragment*>(&composite);
if (residue == 0)
{
return Processor::CONTINUE;
}
RingPerceptionProcessor rpp;
try
{
rpp.calculateSSSR(rings_, *residue);
}
catch (Exception::GeneralException e)
{
Log.warn() << "Exception of type " << e.getName() << " occurred in line "
<< e.getLine() << " of " << e.getFile() << endl;
Log.warn() << "Error message: " << e.getMessage() << endl;
}
return Processor::CONTINUE;
}
# ifdef BALL_NO_INLINE_FUNCTIONS
# include <BALL/VIEW/MODELS/atomBondModelBaseProcessor.iC>
# endif
} // namespace VIEW
} // namespace BALL
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