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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/KERNEL/bond.h>
using namespace::std;
namespace BALL
{
using namespace BALL::Exception;
Bond::NotBound::NotBound(const char* file, int line)
: Exception::GeneralException(file, line, "Bond::NotBound", "The bond is not connected to any atom.")
{
}
Bond::Bond()
: Composite(),
PropertyManager(),
first_(BALL_BOND_DEFAULT_FIRST_ATOM),
second_(BALL_BOND_DEFAULT_SECOND_ATOM),
name_(BALL_BOND_DEFAULT_NAME),
bond_order_(BALL_BOND_DEFAULT_ORDER),
bond_type_(BALL_BOND_DEFAULT_TYPE)
{
}
Bond::Bond(const Bond& bond, bool deep)
: Composite(bond, deep),
PropertyManager(bond),
first_(bond.first_),
second_(bond.second_),
name_(bond.name_),
bond_order_(bond.bond_order_),
bond_type_(bond.bond_type_)
{
}
Bond::Bond(const String& name, Atom& first, Atom& second, Bond::Order order, Type type)
: Composite(),
PropertyManager(),
first_(BALL_BOND_DEFAULT_FIRST_ATOM),
second_(BALL_BOND_DEFAULT_SECOND_ATOM),
name_(name),
bond_order_(order),
bond_type_(type)
{
try
{
createBond(*this, first, second);
}
catch (TooManyBonds& e)
{
first_ = 0;
second_ = 0;
throw(e);
}
}
Bond* Bond::createBond(Bond& bond, Atom& first, Atom& second)
{
// first check the cases where no new bond will be created.
if (&first == &second)
{
return 0;
}
Bond* bond_ptr = first.getBond(second);
if (bond_ptr != 0)
{
return bond_ptr;
}
// throw an exception if there is no possibility to create another bond
// for any of the two atoms
if (((Size)first.number_of_bonds_ >= (Size)Atom::MAX_NUMBER_OF_BONDS)
|| ((Size)second.number_of_bonds_ >= (Size)Atom::MAX_NUMBER_OF_BONDS))
{
delete bond_ptr;
bond_ptr = 0;
throw TooManyBonds(__FILE__, __LINE__,
first.getFullName() + String(" and ") + second.getFullName() + ".");
}
// if the bond is already bound, delete it and create
// it anew
if (bond.isBound())
{
bond.clear();
}
first.bond_[first.number_of_bonds_]
= second.bond_[second.number_of_bonds_]
= &bond;
++(first.number_of_bonds_);
++(second.number_of_bonds_);
// keep the order
if (first < second)
{
bond.first_ = &first;
bond.second_ = &second;
}
else
{
bond.first_ = &second;
bond.second_ = &first;
}
return &bond;
}
Bond::~Bond()
{
arrangeBonds_();
}
void Bond::persistentWrite(PersistenceManager& pm, const char* name) const
{
pm.writeObjectHeader(this, name);
Composite::persistentWrite(pm);
pm.writeStorableObject(dynamic_cast<const PropertyManager&>(*this), "PropertyManager");
pm.writeObjectPointer(first_, "first_");
pm.writeObjectPointer(second_, "second_");
pm.writePrimitive(name_, "name_");
pm.writePrimitive((Index)bond_order_, "bond_order_");
pm.writePrimitive((Index)bond_type_, "bond_type_");
pm.writeObjectTrailer(name);
}
void Bond::persistentRead(PersistenceManager& pm)
{
pm.checkObjectHeader(RTTI::getStreamName<Composite>());
Composite::persistentRead(pm);
pm.checkObjectTrailer(0);
pm.readStorableObject(dynamic_cast<PropertyManager&>(*this), "PropertyManager");
pm.readObjectPointer(first_, "first_");
pm.readObjectPointer(second_, "second_");
pm.readPrimitive(name_, "name_");
Index tmp;
pm.readPrimitive(tmp, "bond_order_");
bond_order_ = (BondType)tmp;
pm.readPrimitive(tmp, "bond_type_");
bond_type_ = (Bond::Order)tmp;
}
Bond& Bond::operator = (const Bond& bond)
{
PropertyManager::operator = (bond);
first_ = bond.first_;
second_ = bond.second_;
name_ = bond.name_;
bond_order_ = bond.bond_order_;
bond_type_ = bond.bond_type_;
return *this;
}
void Bond::swap(Bond &bond)
{
PropertyManager::swap(bond);
Atom* temp_atom = first_;
first_ = bond.first_;
bond.first_ = temp_atom;
temp_atom = second_;
second_ = bond.second_;
bond.second_ = temp_atom;
name_.swap(bond.name_);
Order temp_order = bond_order_;
bond_order_ = bond.bond_order_;
bond.bond_order_ = temp_order;
Type temp_type = bond_type_;
bond_type_ = bond.bond_type_;
bond.bond_type_ = temp_type;
}
void Bond::dump(ostream& s, Size depth) const
{
BALL_DUMP_STREAM_PREFIX(s);
Composite::dump(s, depth);
BALL_DUMP_DEPTH(s, depth);
s << " name: " << name_ << endl;
BALL_DUMP_DEPTH(s, depth);
s << " order: " << bond_order_ << endl;
BALL_DUMP_DEPTH(s, depth);
s << " type: " << bond_type_ << endl;
BALL_DUMP_DEPTH(s, depth);
s << " first atom: " << first_ << endl;
BALL_DUMP_DEPTH(s, depth);
s << " second atom: " << second_ << endl;
BALL_DUMP_STREAM_SUFFIX(s);
}
void Bond::arrangeBonds_()
{
if (first_ != 0 && second_ != 0)
{
if (first_->number_of_bonds_ > 0)
{
first_->swapLastBond_(second_);
}
if (second_->number_of_bonds_ > 0)
{
second_->swapLastBond_(first_);
}
}
}
# ifdef BALL_NO_INLINE_FUNCTIONS
# include <BALL/KERNEL/bond.iC>
# endif
} // namespace BALL
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