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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/KERNEL/PDBAtom.h>
#include <BALL/KERNEL/chain.h>
#include <BALL/KERNEL/protein.h>
#include <BALL/KERNEL/residue.h>
using namespace::std;
namespace BALL
{
PDBAtom::PDBAtom()
: Atom(),
branch_designator_(BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR),
remoteness_indicator_(BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR),
alternate_location_indicator_(BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR),
occupancy_(BALL_PDBATOM_DEFAULT_OCCUPANCY),
temperature_factor_(BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR)
{
}
PDBAtom::PDBAtom(const PDBAtom& pdb_atom, bool deep)
: Atom(pdb_atom, deep),
branch_designator_(pdb_atom.branch_designator_),
remoteness_indicator_(pdb_atom.remoteness_indicator_),
alternate_location_indicator_(pdb_atom.alternate_location_indicator_),
occupancy_(pdb_atom.occupancy_),
temperature_factor_(pdb_atom.temperature_factor_)
{
}
PDBAtom::PDBAtom
(Element& element,
const String& name,
const String& type_name,
Atom::Type atom_type,
const Vector3& position,
const Vector3& velocity,
const Vector3& force,
float charge,
float radius,
char branch_designator,
char remoteness_indicator,
char alternate_location_indicator,
float occupancy,
float temperature_factor)
: Atom(element, name, type_name, atom_type, position, velocity, force, charge, radius),
branch_designator_(branch_designator),
remoteness_indicator_(remoteness_indicator),
alternate_location_indicator_(alternate_location_indicator),
occupancy_(occupancy),
temperature_factor_(temperature_factor)
{
}
PDBAtom::PDBAtom(const String& name)
: Atom(),
branch_designator_(BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR),
remoteness_indicator_(BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR),
alternate_location_indicator_(BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR),
occupancy_(BALL_PDBATOM_DEFAULT_OCCUPANCY),
temperature_factor_(BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR)
{
Atom::setName(name);
}
PDBAtom::~PDBAtom()
{
destroy();
}
void PDBAtom::clear()
{
Atom::clear();
clear_();
}
void PDBAtom::destroy()
{
Atom::destroy();
clear_();
}
void PDBAtom::persistentWrite(PersistenceManager& pm, const char* name) const
{
pm.writeObjectHeader(this, name);
Atom::persistentWrite(pm);
pm.writePrimitive(branch_designator_, "branch_designator_");
pm.writePrimitive(remoteness_indicator_, "remoteness_indicator_");
pm.writePrimitive(alternate_location_indicator_, "alternate_location_indicator_");
pm.writePrimitive(occupancy_, "occupancy_");
pm.writePrimitive(temperature_factor_, "temperature_factor_");
pm.writeObjectTrailer(name);
}
void PDBAtom::persistentRead(PersistenceManager& pm)
{
pm.checkObjectHeader(RTTI::getStreamName<Atom>());
Atom::persistentRead(pm);
pm.checkObjectTrailer(0);
pm.readPrimitive(branch_designator_, "branch_designator_");
pm.readPrimitive(remoteness_indicator_, "remoteness_indicator_");
pm.readPrimitive(alternate_location_indicator_, "alternate_location_indicator_");
pm.readPrimitive(occupancy_, "occupancy_");
pm.readPrimitive(temperature_factor_, "temperature_factor_");
}
void PDBAtom::set(const PDBAtom& pdb_atom, bool deep)
{
Atom::set(pdb_atom, deep);
branch_designator_ = pdb_atom.branch_designator_;
remoteness_indicator_ = pdb_atom.remoteness_indicator_;
alternate_location_indicator_ = pdb_atom.alternate_location_indicator_;
occupancy_ = pdb_atom.occupancy_;
temperature_factor_ = pdb_atom.temperature_factor_;
}
void PDBAtom::get(PDBAtom& pdb_atom, bool deep) const
{
pdb_atom.set(*this, deep);
}
PDBAtom& PDBAtom::operator = (const PDBAtom& pdb_atom)
{
Atom::operator =(pdb_atom);
branch_designator_ = pdb_atom.branch_designator_;
remoteness_indicator_ = pdb_atom.remoteness_indicator_;
alternate_location_indicator_ = pdb_atom.alternate_location_indicator_;
occupancy_ = pdb_atom.occupancy_;
temperature_factor_ = pdb_atom.temperature_factor_;
return *this;
}
void PDBAtom::swap(PDBAtom& pdb_atom)
{
Atom::swap(pdb_atom);
char temp = branch_designator_;
branch_designator_ = pdb_atom.branch_designator_;
pdb_atom.branch_designator_ = temp;
temp = remoteness_indicator_;
remoteness_indicator_ = pdb_atom.remoteness_indicator_;
pdb_atom.remoteness_indicator_ = temp;
temp = alternate_location_indicator_;
alternate_location_indicator_ = pdb_atom.alternate_location_indicator_;
pdb_atom.alternate_location_indicator_ = temp;
float temp_float = occupancy_;
occupancy_ = pdb_atom.occupancy_;
pdb_atom.occupancy_ = temp_float;
temp_float = temperature_factor_;
temperature_factor_ = pdb_atom.temperature_factor_;
pdb_atom.temperature_factor_ = temp_float;
}
Protein* PDBAtom::getProtein()
{
for (Composite::AncestorIterator ancestor_it = beginAncestor();
!ancestor_it.isEnd(); ++ancestor_it)
{
if (RTTI::isKindOf<Protein>(&*ancestor_it))
{
return (Protein *)&*ancestor_it;
}
}
return 0;
}
const Protein* PDBAtom::getProtein() const
{
return ((PDBAtom *)this)->getProtein();
}
Chain* PDBAtom::getChain()
{
for (Composite::AncestorIterator ancestor_it = beginAncestor();
!ancestor_it.isEnd(); ++ancestor_it)
{
if (RTTI::isKindOf<Chain>(&*ancestor_it))
{
return (Chain *)&*ancestor_it;
}
}
return 0;
}
const Chain* PDBAtom::getChain() const
{
return ((PDBAtom *)this)->getChain();
}
Residue* PDBAtom::getResidue()
{
for (Composite::AncestorIterator ancestor_it = beginAncestor();
!ancestor_it.isEnd(); ++ancestor_it)
{
if (RTTI::isKindOf<Residue>(&*ancestor_it))
{
return (Residue *)&*ancestor_it;
}
}
return 0;
}
const Residue* PDBAtom::getResidue() const
{
return ((PDBAtom *)this)->getResidue();
}
void PDBAtom::setBranchDesignator(char branch_designator)
{
branch_designator_ = branch_designator;
}
char PDBAtom::getBranchDesignator() const
{
return branch_designator_;
}
void PDBAtom::setRemotenessIndicator(char remoteness_indicator)
{
remoteness_indicator_ = remoteness_indicator;
}
char PDBAtom::getRemotenessIndicator() const
{
return remoteness_indicator_;
}
void PDBAtom::setAlternateLocationIndicator(char alternate_location_indicator)
{
alternate_location_indicator_ = alternate_location_indicator;
}
char PDBAtom::getAlternateLocationIndicator() const
{
return alternate_location_indicator_;
}
void PDBAtom::setOccupancy(float occupancy)
{
occupancy_ = occupancy;
}
float PDBAtom::getOccupancy() const
{
return occupancy_;
}
void PDBAtom::setTemperatureFactor(float temperature_factor)
{
temperature_factor_ = temperature_factor;
}
float PDBAtom::getTemperatureFactor() const
{
return temperature_factor_;
}
void PDBAtom::dump(ostream& s, Size depth) const
{
BALL_DUMP_STREAM_PREFIX(s)
Atom::dump(s, depth);
// just to avoid these damned compiler warnings
// (dump_indent_depth_ was declared but never referenced)
if (dump_indent_depth_ == 0) {};
BALL_DUMP_STREAM_SUFFIX(s)
}
void PDBAtom::clear_()
{
branch_designator_ = BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR;
remoteness_indicator_ = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR;
alternate_location_indicator_ = BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR;
occupancy_ = BALL_PDBATOM_DEFAULT_OCCUPANCY;
temperature_factor_ = BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR;
}
bool PDBAtom::operator == (const PDBAtom& pdb_atom) const
{
return(Object::operator == (pdb_atom));
}
bool PDBAtom::operator != (const PDBAtom& pdb_atom) const
{
return ! (*this == pdb_atom);
}
} // namespace BALL
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