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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: atomVector.C,v 1.13.30.1 2007/05/18 12:05:59 oliver Exp $
//
// Author:
// Oliver Kohlbacher
#include <BALL/MOLMEC/COMMON/atomVector.h>
#include <BALL/MOLMEC/COMMON/gradient.h>
#include <BALL/MATHS/vector3.h>
#include <BALL/CONCEPT/composite.h>
#include <BALL/KERNEL/atom.h>
#undef BALL_DEBUG
using namespace std;
namespace BALL
{
AtomVector::AtomVector()
{
}
AtomVector::AtomVector(const AtomVector& atoms, bool /* deep */)
: vector<Atom*>()
{
set(atoms);
}
AtomVector::AtomVector(const Composite& composite, bool selected_only)
{
set(composite, selected_only);
}
AtomVector::~AtomVector()
{
}
const AtomVector& AtomVector::operator = (const AtomVector& rhs)
{
set(rhs);
return *this;
}
const AtomVector& AtomVector::operator = (const Composite& rhs)
{
set(rhs, rhs.containsSelection());
return *this;
}
void AtomVector::set(const AtomVector& atoms)
{
// resize the vector and copy the contents of atoms
resize((Size)atoms.size());
copy(atoms.begin(), atoms.end(), begin());
// copy the saved positions
saved_position_.resize(atoms.saved_position_.size());
copy(atoms.saved_position_.begin(), atoms.saved_position_.end(), saved_position_.begin());
}
void AtomVector::set(const Composite& composite, bool selected_only)
{
// clear all saved positions and atom pointers
saved_position_.clear();
clear();
// iterate over all subcomposites and
// extract pointers to the atoms
Composite::CompositeConstIterator it = composite.beginComposite();
for (; +it; ++it)
{
Atom* atom = const_cast<Atom*>(dynamic_cast<const Atom*>(&*it));
if (atom != 0)
{
// store this atom only if it is selected or selected_only == false
if (!selected_only || atom->isSelected())
{
push_back(atom);
}
}
}
}
void AtomVector::savePositions()
{
// resize the saved positions
saved_position_.resize(size());
// copy all positions
ConstIterator it(begin());
vector<Vector3>::iterator pos_it(saved_position_.begin());
for (; it != end(); ++it, ++pos_it)
{
*pos_it = (*it)->getPosition();
}
}
void AtomVector::resetPositions()
{
// move only if a saved position exists for every atom
if (saved_position_.size() == size())
{
Iterator it(begin());
vector<Vector3>::const_iterator pos_it(saved_position_.begin());
for (; it != end(); ++it, ++pos_it)
{
(*it)->setPosition(*pos_it);
}
}
}
void AtomVector::moveTo(const Gradient& gradient, double step)
{
// move only if a saved position exists for every atom
if (gradient.size() == size())
{
// use the saves positions
if (saved_position_.size() == size())
{
Iterator it(begin());
vector<Vector3>::const_iterator pos_it(saved_position_.begin());
Gradient::ConstIterator grad_it(gradient.begin());
for (; it != end(); ++it, ++pos_it, ++grad_it)
{
(*it)->setPosition(*pos_it + *grad_it * step);
#ifdef BALL_DEBUG
Log << " - atom " << (*it)->getFullName() << " @ " << (*it)->getPosition() << std::endl;
#endif
}
}
// we don't have saved positions, use the current atom positions
else
{
Iterator it(begin());
Gradient::ConstIterator grad_it(gradient.begin());
for (; it != end(); ++it, ++grad_it)
{
(*it)->getPosition() += *grad_it * step;
#ifdef BALL_DEBUG
Log << " - atom " << (*it)->getFullName() << " @ " << (*it)->getPosition() << std::endl;
#endif
}
}
}
}
void AtomVector::moveTo(const Gradient& gradient, double step, Size number)
{
// move only if a saved position exists for every atom
if (gradient.size() == size())
{
// use the saves positions
if (saved_position_.size() == size())
{
Iterator it(begin());
vector<Vector3>::const_iterator pos_it(saved_position_.begin());
vector<Vector3>::const_iterator end(saved_position_.begin() + number);
Gradient::ConstIterator grad_it(gradient.begin());
for (; pos_it != end; ++it, ++pos_it, ++grad_it)
{
(*it)->setPosition(*pos_it + *grad_it * step);
#ifdef BALL_DEBUG
Log << " - atom " << (*it)->getFullName() << " @ " << (*it)->getPosition() << std::endl;
#endif
}
}
// we don't have saved positions, use the current atom positions
else
{
Iterator it(begin());
Gradient::ConstIterator grad_it(gradient.begin());
Gradient::ConstIterator end(gradient.begin() + number);
for (; grad_it != end; ++it, ++grad_it)
{
(*it)->getPosition() += *grad_it * step;
#ifdef BALL_DEBUG
Log << " - atom " << (*it)->getFullName() << " @ " << (*it)->getPosition() << std::endl;
#endif
}
}
}
}
void AtomVector::resize(Size new_size)
{
Size old_size = (Size)size();
::std::vector<Atom*>::resize(new_size);
for (Position p = old_size; p < new_size; p++)
{
(*this)[p] = 0;
}
}
} // namespace BALL
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