BALL  1.4.1
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Private Member Functions | Private Attributes | Friends
BALL::PDBAtom Class Reference

#include <BALL/KERNEL/PDBAtom.h>

Inheritance diagram for BALL::PDBAtom:
BALL::Atom BALL::Composite BALL::PropertyManager BALL::PersistentObject BALL::Selectable BALL::Object BALL::AutoDeletable

List of all members.

Public Types

Enums
enum  RemotenessIndicator {
  REMOTENESS_INDICATOR__UNKNOWN = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, REMOTENESS_INDICATOR__ALPHA = 'A', REMOTENESS_INDICATOR__alpha = 'a', REMOTENESS_INDICATOR__BETA = 'B',
  REMOTENESS_INDICATOR__beta = 'b', REMOTENESS_INDICATOR__GAMMA = 'G', REMOTENESS_INDICATOR__gamma = 'g', REMOTENESS_INDICATOR__DELTA = 'D',
  REMOTENESS_INDICATOR__delta = 'd', REMOTENESS_INDICATOR__EPSILON = 'E', REMOTENESS_INDICATOR__epsilon = 'e', REMOTENESS_INDICATOR__ZETA = 'Z',
  REMOTENESS_INDICATOR__zeta = 'z', REMOTENESS_INDICATOR__ETA = 'H', REMOTENESS_INDICATOR__eta = 'h', NUMBER_OF_REMOTENESS_INDICATORS
}
enum  Property { PROPERTY__HETATM = Atom::NUMBER_OF_PROPERTIES + 1, NUMBER_OF_PROPERTIES }

Public Member Functions

Constructors and Destructors
 PDBAtom ()
 Default constructor.
 PDBAtom (const PDBAtom &pdb_atom, bool deep=true)
 Copy constructor.
 PDBAtom (const String &name)
 Constructor.
 PDBAtom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, Atom::Type atom_type=BALL_ATOM_DEFAULT_TYPE, const Vector3 &position=Vector3(BALL_ATOM_DEFAULT_POSITION), const Vector3 &velocity=Vector3(BALL_ATOM_DEFAULT_VELOCITY), const Vector3 &force=Vector3(BALL_ATOM_DEFAULT_FORCE), float charge=BALL_ATOM_DEFAULT_CHARGE, float radius=BALL_ATOM_DEFAULT_RADIUS, char branch_designator=BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR, char remoteness_indicator=BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, char alternate_location_indicator=BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR, float occupancy=BALL_PDBATOM_DEFAULT_OCCUPANCY, float temperature_factor=BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR)
 Detailed constructor.
virtual ~PDBAtom ()
 Destructor.
virtual void destroy ()
Predicates
bool operator== (const PDBAtom &pdb_atom) const
bool operator!= (const PDBAtom &pdb_atom) const
Persistence
void persistentWrite (PersistenceManager &pm, const char *name=0) const
void persistentRead (PersistenceManager &pm)
Assignment
void set (const PDBAtom &pdb_atom, bool deep=true)
void get (PDBAtom &pdb_atom, bool deep=true) const
PDBAtomoperator= (const PDBAtom &pdb_atom)
void swap (PDBAtom &pdb_atom)
virtual void clear ()
Accessors
ProteingetProtein ()
const ProteingetProtein () const
ChaingetChain ()
const ChaingetChain () const
ResiduegetResidue ()
const ResiduegetResidue () const
void setBranchDesignator (char branch_designator)
char getBranchDesignator () const
void setRemotenessIndicator (char remoteness_indicator)
char getRemotenessIndicator () const
void setAlternateLocationIndicator (char alternate_location_indicator)
char getAlternateLocationIndicator () const
void setOccupancy (float occupancy)
float getOccupancy () const
void setTemperatureFactor (float temperature_factor)
float getTemperatureFactor () const
Debugging and Diagnostics
virtual void dump (std::ostream &s=std::cout, Size depth=0) const

Private Member Functions

void clear_ ()

Private Attributes

char branch_designator_
char remoteness_indicator_
char alternate_location_indicator_
float occupancy_
float temperature_factor_

Friends

class Bond

Detailed Description

Atom class with additional attributes. This class represents atoms read from PDB files. It contains additional attributes to hold the crystallographic properties of atoms from a PDB file (e.g., temperature factor, occupancy). For details on the PDB format and the detailed meaning of those fields, please refer to the PDB documentation at http://www.rcsb.org

See also:
PDBFile

Definition at line 38 of file PDBAtom.h.


Member Enumeration Documentation

Properties of the PDBAtom.

Enumerator:
PROPERTY__HETATM 

Property which indicates whether the current atom is a HETATM.

NUMBER_OF_PROPERTIES 

The number of properties in PDBAtom.

Reimplemented from BALL::Atom.

Definition at line 76 of file PDBAtom.h.

Possible values for the PDB remoteness indicator

Enumerator:
REMOTENESS_INDICATOR__UNKNOWN 
REMOTENESS_INDICATOR__ALPHA 
REMOTENESS_INDICATOR__alpha 
REMOTENESS_INDICATOR__BETA 
REMOTENESS_INDICATOR__beta 
REMOTENESS_INDICATOR__GAMMA 
REMOTENESS_INDICATOR__gamma 
REMOTENESS_INDICATOR__DELTA 
REMOTENESS_INDICATOR__delta 
REMOTENESS_INDICATOR__EPSILON 
REMOTENESS_INDICATOR__epsilon 
REMOTENESS_INDICATOR__ZETA 
REMOTENESS_INDICATOR__zeta 
REMOTENESS_INDICATOR__ETA 
REMOTENESS_INDICATOR__eta 
NUMBER_OF_REMOTENESS_INDICATORS 

Definition at line 53 of file PDBAtom.h.


Constructor & Destructor Documentation

Default constructor.

BALL::PDBAtom::PDBAtom ( const PDBAtom pdb_atom,
bool  deep = true 
)

Copy constructor.

BALL::PDBAtom::PDBAtom ( const String name)

Constructor.

BALL::PDBAtom::PDBAtom ( Element element,
const String name,
const String type_name = BALL_ATOM_DEFAULT_TYPE_NAME,
Atom::Type  atom_type = BALL_ATOM_DEFAULT_TYPE,
const Vector3 position = Vector3(BALL_ATOM_DEFAULT_POSITION),
const Vector3 velocity = Vector3(BALL_ATOM_DEFAULT_VELOCITY),
const Vector3 force = Vector3(BALL_ATOM_DEFAULT_FORCE),
float  charge = BALL_ATOM_DEFAULT_CHARGE,
float  radius = BALL_ATOM_DEFAULT_RADIUS,
char  branch_designator = BALL_PDBATOM_DEFAULT_BRANCH_DESIGNATOR,
char  remoteness_indicator = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR,
char  alternate_location_indicator = BALL_PDBATOM_DEFAULT_ALTERNATE_LOCATION_INDICATOR,
float  occupancy = BALL_PDBATOM_DEFAULT_OCCUPANCY,
float  temperature_factor = BALL_PDBATOM_DEFAULT_TEMPERATURE_FACTOR 
)

Detailed constructor.

virtual BALL::PDBAtom::~PDBAtom ( ) [virtual]

Destructor.


Member Function Documentation

virtual void BALL::PDBAtom::clear ( ) [virtual]

Clear the contents of the atom.

Reimplemented from BALL::Atom.

void BALL::PDBAtom::clear_ ( ) [private]

Reimplemented from BALL::Atom.

virtual void BALL::PDBAtom::destroy ( ) [virtual]

Clears the contents of the atom and removes it from all composite structures.

Reimplemented from BALL::Atom.

virtual void BALL::PDBAtom::dump ( std::ostream &  s = std::cout,
Size  depth = 0 
) const [virtual]

Internal state dump. Dump the current internal state of {*this} to the output ostream s with dumping depth depth .

Parameters:
soutput stream where to output the internal state of the instance
depththe dumping depth

Reimplemented from BALL::Atom.

void BALL::PDBAtom::get ( PDBAtom pdb_atom,
bool  deep = true 
) const

Copy this instance to {pdb_atom}. The assignment is either deep or shallow (default).

Parameters:
pdb_atomthe PDBAtom to be assigned to

Get the alternate location indicator.

Returns:
char the alternate location indicator

Get the branch designator.

Returns:
char the branch designator

Get a pointer to the parent chain. The pointer is 0 if the instance does not have a parent chain.

Returns:
Chain* - mutable pointer to the parent chain

Reimplemented from BALL::Atom.

const Chain* BALL::PDBAtom::getChain ( ) const

Get a pointer to the parent chain. The pointer is 0 if the instance does not have a parent chain.

Returns:
Chain* - constant pointer to the parent chain

Reimplemented from BALL::Atom.

Get the occupancy.

Returns:
float occupancy the occupancy

Get a pointer to the parent protein. The pointer is 0 if the instance does not have a parent protein.

Returns:
Protein* - mutable pointer to the parent protein

Get a pointer to the parent protein. The pointer is 0 if the instance does not have a parent protein.

Returns:
Protein* - constant pointer to the parent protein

Get the remoteness indicator.

Returns:
char the remoteness indicator

Get a pointer to the parent residue. The pointer is 0 if the instance does not have a parent residue.

Returns:
Residue* - mutable pointer to the parent residue

Reimplemented from BALL::Atom.

Get a pointer to the parent residue. The pointer is 0 if the instance does not have a parent residue.

Returns:
Residue* - constant pointer to the parent residue

Reimplemented from BALL::Atom.

Get the temperature factor.

Returns:
float the temperature factor
bool BALL::PDBAtom::operator!= ( const PDBAtom pdb_atom) const

Inequality operator

See also:
operator ==
PDBAtom& BALL::PDBAtom::operator= ( const PDBAtom pdb_atom)

Assignment operator. The assignment is deep.

Parameters:
pdb_atomthe PDBAtom to be copied (cloned)
Returns:
pdb_atom& - the instance
bool BALL::PDBAtom::operator== ( const PDBAtom pdb_atom) const

Equality operator.

See also:
Object::operator ==

Reads a PDBAtom object from a persistent stream.

Parameters:
pmthe persistence manager

Reimplemented from BALL::Atom.

void BALL::PDBAtom::persistentWrite ( PersistenceManager pm,
const char *  name = 0 
) const [virtual]

Writes a PDBAtom object to a persistent stream.

Parameters:
pmthe persistence manager
namethe instance name

Reimplemented from BALL::Atom.

void BALL::PDBAtom::set ( const PDBAtom pdb_atom,
bool  deep = true 
)

Assignment with cloning facility. The assignment is either deep or shallow (default).

Parameters:
pdb_atomthe PDBAtom to be copied (cloned)
deepmake a deep (=true) or shallow (=false) copy
void BALL::PDBAtom::setAlternateLocationIndicator ( char  alternate_location_indicator)

Set the alternate location indicator.

Parameters:
alternate_location_indicatorthe alternate location indicator
void BALL::PDBAtom::setBranchDesignator ( char  branch_designator)

Set the branch designator.

Parameters:
branch_designatorthe branch designator
void BALL::PDBAtom::setOccupancy ( float  occupancy)

Set the occupancy.

Parameters:
occupancythe occupancy
void BALL::PDBAtom::setRemotenessIndicator ( char  remoteness_indicator)

Set the remoteness indicator.

Parameters:
remoteness_indicatorthe remoteness indicator
void BALL::PDBAtom::setTemperatureFactor ( float  temperature_factor)

Set the temperature factor.

Parameters:
temperature_factorthe temperature factor
void BALL::PDBAtom::swap ( PDBAtom pdb_atom)

Swapping of PDBAtoms.

Parameters:
pdb_atomthe PDBAtom {*this} is being swapped with

Friends And Related Function Documentation

friend class Bond [friend]

Reimplemented from BALL::Atom.

Definition at line 43 of file PDBAtom.h.


Member Data Documentation

Definition at line 308 of file PDBAtom.h.

Definition at line 300 of file PDBAtom.h.

Definition at line 312 of file PDBAtom.h.

Definition at line 304 of file PDBAtom.h.

Definition at line 316 of file PDBAtom.h.

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