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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/MOLMEC/AMBER/amberStretch.h>
#include <BALL/MOLMEC/AMBER/amber.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/forEach.h>
using namespace std;
namespace BALL
{
// default constructor
AmberStretch::AmberStretch()
{
// set component name
setName( "Amber Stretch" );
}
// constructor
AmberStretch::AmberStretch(ForceField& force_field)
: StretchComponent(force_field)
{
// set component name
setName( "Amber Stretch" );
}
// destructor
AmberStretch::~AmberStretch()
{
}
// setup the internal datastructures for the component
bool AmberStretch::setup()
{
if (getForceField() == 0)
{
Log.error() << "AmberStretch::setup(): component not bound to force field" << endl;
return false;
}
// throw away the old contents
stretch_.clear();
Options& options = getForceField()->options;
if (options.has(AMBER_STRETCH_ENABLED))
{
if (!options.getBool(AMBER_STRETCH_ENABLED))
{
setEnabled(false);
return true;
}
else
{
setEnabled(true);
}
}
AmberFF* amber_force_field = dynamic_cast<AmberFF*>(force_field_);
if ((amber_force_field == 0) || !amber_force_field->hasInitializedParameters())
{
bool result = stretch_parameters_.extractSection(getForceField()->getParameters(), "QuadraticBondStretch");
if (!result)
{
Log.error() << "cannot find section QuadraticBondStretch" << endl;
return false;
}
}
QuadraticBondStretch::Values values;
bool use_selection = getForceField()->getUseSelection();
// retrieve all stretch parameters
Atom::BondIterator bond_iterator;
AtomVector::ConstIterator atom_it = getForceField()->getAtoms().begin();
for ( ; atom_it != getForceField()->getAtoms().end(); ++atom_it)
{
for (Atom::BondIterator it = (*atom_it)->beginBond(); +it ; ++it)
{
if (*atom_it == it->getFirstAtom())
{
Bond& bond = const_cast<Bond&>(*it);
if (bond.getType() == Bond::TYPE__HYDROGEN)
{
// Ignore hydrogen bonds!
continue;
}
if (!use_selection ||
(use_selection && bond.getFirstAtom()->isSelected() &&
bond.getSecondAtom()->isSelected()))
{
Atom::Type atom_type_A = bond.getFirstAtom()->getType();
Atom::Type atom_type_B = bond.getSecondAtom()->getType();
stretch_.push_back(QuadraticBondStretch::Data());
stretch_.back().atom1 = bond.getFirstAtom();
stretch_.back().atom2 = bond.getSecondAtom();
// Pay attention to the symmetric database input
if (stretch_parameters_.hasParameters(atom_type_A, atom_type_B))
{
stretch_parameters_.assignParameters(values, atom_type_A, atom_type_B);
}
else if (stretch_parameters_.hasParameters(atom_type_A, Atom::ANY_TYPE))
{
stretch_parameters_.assignParameters(values, atom_type_A, Atom::ANY_TYPE);
}
else if (stretch_parameters_.hasParameters(Atom::ANY_TYPE, atom_type_B))
{
stretch_parameters_.assignParameters(values, Atom::ANY_TYPE, atom_type_B);
}
else if (stretch_parameters_.hasParameters(Atom::ANY_TYPE, Atom::ANY_TYPE))
{
stretch_parameters_.assignParameters(values,Atom::ANY_TYPE, Atom::ANY_TYPE);
}
else
{
getForceField()->error() << "cannot find stretch parameters for atom types "
<< force_field_->getParameters().getAtomTypes().getTypeName(atom_type_A) << "-"
<< force_field_->getParameters().getAtomTypes().getTypeName(atom_type_B)
<< " (atoms are: "
<< stretch_.back().atom1->getFullName(Atom::ADD_VARIANT_EXTENSIONS_AND_ID)
<< "/" << stretch_.back().atom2->getFullName(
Atom::ADD_VARIANT_EXTENSIONS_AND_ID) << ")" << endl;
// we don't want to get any force or energy component
// from this stretch
values.k = 0.0;
values.r0 = 1.0;
getForceField()->getUnassignedAtoms().insert(bond.getFirstAtom());
getForceField()->getUnassignedAtoms().insert(bond.getSecondAtom());
}
stretch_.back().values = values;
}
}
}
}
// Everything went well.
return true;
}
} // namespace BALL
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