#include <BALL/KERNEL/PDBAtom.h>

Inheritance diagram for BALL::PDBAtom:

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 Types inherited from BALL::Atom
enum	{ UNKNOWN_TYPE = -1 , ANY_TYPE = 0 , MAX_NUMBER_OF_BONDS = 12 }
enum	Property { NUMBER_OF_PROPERTIES = 0 }
enum	FullNameType { NO_VARIANT_EXTENSIONS , ADD_VARIANT_EXTENSIONS , ADD_RESIDUE_ID , ADD_VARIANT_EXTENSIONS_AND_ID , ADD_CHAIN_RESIDUE_ID , ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID }
typedef std::list< Atom * >	AtomPtrList
typedef std::list< Position >	AtomIndexList
typedef short	Type
typedef Index	BondIteratorPosition
typedef RandomAccessIterator< Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondIterator
typedef ConstRandomAccessIterator< Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondConstIterator
	Constant random access iterator for bonds.
typedef std::reverse_iterator< BondIterator >	BondReverseIterator
	Reverse random access iterator for bonds.
typedef std::reverse_iterator< BondConstIterator >	BondConstReverseIterator
	Constant reverse random access iterator for bonds.
Public Types inherited from BALL::Composite
enum	StampType { MODIFICATION = 1 , SELECTION = 2 , BOTH = 3 }
typedef UnaryPredicate< Composite >	KernelPredicateType
typedef ForwardIterator< Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorIterator
typedef ConstForwardIterator< Composite, Composite, Composite *, AncestorIteratorTraits >	AncestorConstIterator
typedef BidirectionalIterator< Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeIterator
typedef ConstBidirectionalIterator< Composite, Composite, Composite *, ChildCompositeIteratorTraits >	ChildCompositeConstIterator
typedef std::reverse_iterator< ChildCompositeIterator >	ChildCompositeReverseIterator
typedef std::reverse_iterator< ChildCompositeConstIterator >	ChildCompositeConstReverseIterator
typedef BidirectionalIterator< Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeIterator
typedef ConstBidirectionalIterator< Composite, Composite, Composite *, CompositeIteratorTraits >	CompositeConstIterator
typedef std::reverse_iterator< CompositeIterator >	CompositeReverseIterator
typedef std::reverse_iterator< CompositeConstIterator >	CompositeConstReverseIterator

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
PDBAtom &	operator= (const PDBAtom &pdb_atom)
void	swap (PDBAtom &pdb_atom)
virtual void	clear ()
Accessors
Protein *	getProtein ()
const Protein *	getProtein () const
Chain *	getChain ()
const Chain *	getChain () const
Residue *	getResidue ()
const Residue *	getResidue () 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
Public Member Functions inherited from BALL::Atom
	Atom ()
	Atom (const Atom &atom, bool deep=true)
	Atom (Element &element, const String &name, const String &type_name=BALL_ATOM_DEFAULT_TYPE_NAME, 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, Index formal_charge=BALL_ATOM_DEFAULT_FORMAL_CHARGE)
virtual	~Atom ()
void	set (const Atom &atom, bool deep=true)
void	get (Atom &atom, bool deep=true) const
Atom &	operator= (const Atom &atom)
void	swap (Atom &atom)
bool	operator== (const Atom &atom) const
bool	operator!= (const Atom &atom) const
void	setElement (const Element &element)
	Assign the atom's element.
const Element &	getElement () const
	Return the atom's element.
void	setCharge (float charge)
float	getCharge () const
void	setFormalCharge (Index formal_charge)
	Set the atom's formal charge.
Index	getFormalCharge () const
	Return the atom's formal charge.
const Molecule *	getMolecule () const
Molecule *	getMolecule ()
	Return the molecule the atom is contained in (mutable).
const Fragment *	getFragment () const
Fragment *	getFragment ()
	Return the fragment the atom is contained in (mutable).
const Residue *	getResidue () const
Residue *	getResidue ()
	Return the residue the atom is contained in (mutable).
const SecondaryStructure *	getSecondaryStructure () const
SecondaryStructure *	getSecondaryStructure ()
	Return the secondary structure the atom is contained in (mutable).
const Chain *	getChain () const
Chain *	getChain ()
	Return the chain the atom is contained in (mutable).
void	setName (const String &name)
	Set the atom name.
const String &	getName () const
	Return the atom name.
String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const
void	setPosition (const Vector3 &position)
Vector3 &	getPosition ()
	Return the atom coordinates (mutable).
const Vector3 &	getPosition () const
	Return the atom coordinates (const).
void	setRadius (float radius)
float	getRadius () const
	Return the atom radius.
void	setType (Type atom_type)
	Assign the numerical atom type.
Type	getType () const
	Return the (numerical) atom type.
String	getTypeName () const
	Return the atom type name.
void	setTypeName (const String &name)
	Assign the atom type name.
void	setVelocity (const Vector3 &velocity)
Vector3 &	getVelocity ()
const Vector3 &	getVelocity () const
void	setForce (const Vector3 &force)
const Vector3 &	getForce () const
	Return the atom's force vector (const).
Vector3 &	getForce ()
	Return the atom's force vector (mutable).
Size	countBonds () const
	Return the number of bonds.
Bond *	getBond (Position index)
const Bond *	getBond (Position index) const
Bond *	getBond (const Atom &atom)
const Bond *	getBond (const Atom &atom) const
bool	hasBond (const Bond &bond) const
bool	isBoundTo (const Atom &atom) const
bool	isBound () const
bool	isGeminal (const Atom &atom) const
bool	isVicinal (const Atom &atom) const
virtual bool	isAtom () const
virtual bool	isValid () const
bool	applyBonds (UnaryProcessor< Bond > &processor)
BondIterator	beginBond ()
	Return a bond iterator pointing to the first bond of the atom.
BondIterator	endBond ()
	Return a past-the-end bond iterator.
BondConstIterator	beginBond () const
	Return a constant bond iterator pointing to the first bond.
BondConstIterator	endBond () const
	Return a constant past-the-end bond iterator.
BondReverseIterator	rbeginBond ()
	Return a reverse bond iterator pointing to the last bond.
BondReverseIterator	rendBond ()
	Return a past-the-end bond iterator for reverse traversal.
BondConstReverseIterator	rbeginBond () const
	Return a constant reverse bond iterator pointing to the first atom.
BondConstReverseIterator	rendBond () const
	Return a constant past-the-end bond iterator for reverse traversal.
Bond *	createBond (Atom &atom)
Bond *	createBond (Bond &bond, Atom &atom)
Bond *	cloneBond (Bond &bond, Atom &atom)
bool	destroyBond (const Atom &atom)
void	destroyBonds ()
Atom *	getPartnerAtom (Position i)
const Atom *	getPartnerAtom (Position i) const
float	getDistance (const Atom &a) const
void	addInteraction (const Atom *atom, String interaction_type, double energy)
void	addInteraction (String interaction_type, double energy)
void	disableStoreInteractions ()
void	enableStoreInteractions ()
Public Member Functions inherited from BALL::Composite
template<typename T>
BALL_INLINE bool	apply (UnaryProcessor< T > &processor)
template<typename T>
BALL_INLINE bool	apply (ConstUnaryProcessor< T > &processor) const
template<typename T>
BALL_INLINE T *	getAncestor (const T &)
template<typename T>
BALL_INLINE const T *	getAncestor (const T &) const
template<typename T>
BALL_INLINE T *	getPrevious (const T &)
template<typename T>
BALL_INLINE const T *	getPrevious (const T &dummy) const
template<typename T>
BALL_INLINE T *	getNext (const T &)
template<typename T>
BALL_INLINE const T *	getNext (const T &dummy) const
template<typename T>
BALL_INLINE bool	hasAncestor (const T &dummy) const
	Composite ()
	Composite (const Composite &composite, bool deep=true)
virtual	~Composite ()
void	destroy (bool virtual_destroy)
void *	clone (Composite &root) const
bool	operator== (const Composite &composite) const
bool	operator!= (const Composite &composite) const
bool	isEmpty () const
bool	isRoot () const
bool	isRootOf (const Composite &composite) const
bool	isInterior () const
bool	hasChild () const
bool	isChildOf (const Composite &composite) const
bool	isFirstChild () const
bool	isFirstChildOf (const Composite &composite) const
bool	isLastChild () const
bool	isLastChildOf (const Composite &composite) const
bool	hasParent () const
bool	isParentOf (const Composite &composite) const
bool	hasSibling () const
bool	isSiblingOf (const Composite &composite) const
bool	hasPreviousSibling () const
bool	isPreviousSiblingOf (const Composite &composite) const
bool	hasNextSibling () const
bool	isNextSiblingOf (const Composite &composite) const
bool	isDescendantOf (const Composite &composite) const
template<typename T>
bool	hasAncestor (const T &dummy) const
bool	isAncestorOf (const Composite &composite) const
bool	isRelatedWith (const Composite &composite) const
bool	isHomomorph (const Composite &composite) const
bool	containsSelection () const
virtual bool	isMolecule () const
virtual bool	isProtein () const
virtual bool	isFragment () const
virtual bool	isResidue () const
virtual bool	isChain () const
void	host (Visitor< Composite > &visitor)
template<typename T>
bool	applyAncestor (UnaryProcessor< T > &processor)
template<typename T>
bool	applyAncestor (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyChild (UnaryProcessor< T > &processor)
template<typename T>
bool	applyChild (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)
template<typename T>
bool	applyDescendantPreorder (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)
template<typename T>
bool	applyDescendantPostorder (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyDescendant (UnaryProcessor< T > &processor)
template<typename T>
bool	applyDescendant (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyPreorder (UnaryProcessor< T > &processor)
template<typename T>
bool	applyPreorder (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyPostorder (UnaryProcessor< T > &processor)
template<typename T>
bool	applyPostorder (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	apply (UnaryProcessor< T > &processor)
template<typename T>
bool	apply (ConstUnaryProcessor< T > &processor) const
template<typename T>
bool	applyLevel (UnaryProcessor< T > &processor, long level)
template<typename T>
bool	applyLevel (ConstUnaryProcessor< T > &processor, long level) const
AncestorIterator	beginAncestor ()
AncestorIterator	endAncestor ()
AncestorConstIterator	beginAncestor () const
AncestorConstIterator	endAncestor () const
ChildCompositeIterator	beginChildComposite ()
ChildCompositeIterator	endChildComposite ()
ChildCompositeConstIterator	beginChildComposite () const
ChildCompositeConstIterator	endChildComposite () const
ChildCompositeReverseIterator	rbeginChildComposite ()
ChildCompositeReverseIterator	rendChildComposite ()
ChildCompositeConstReverseIterator	rbeginChildComposite () const
ChildCompositeConstReverseIterator	rendChildComposite () const
CompositeIterator	beginComposite ()
CompositeIterator	endComposite ()
CompositeConstIterator	beginComposite () const
CompositeConstIterator	endComposite () const
CompositeReverseIterator	rbeginComposite ()
CompositeReverseIterator	rendComposite ()
CompositeConstReverseIterator	rbeginComposite () const
CompositeConstReverseIterator	rendComposite () const
void	deleteChildrenList_ (std::list< Composite * > &composites)
void	set (const Composite &composite, bool deep=true)
Composite &	operator= (const Composite &composite)
void	get (Composite &composite, bool deep=true) const
Size	getDegree () const
Size	count (const KernelPredicateType &predicate) const
Size	countDescendants () const
Size	getPathLength (const Composite &composite) const
Size	getDepth () const
Size	getHeight () const
Composite &	getRoot ()
const Composite &	getRoot () const
Composite *	getLowestCommonAncestor (const Composite &composite)
const Composite *	getLowestCommonAncestor (const Composite &composite) const
template<typename T>
T *	getAncestor (const T &)
template<typename T>
const T *	getAncestor (const T &) const
template<typename T>
T *	getPrevious (const T &)
template<typename T>
const T *	getPrevious (const T &dummy) const
template<typename T>
T *	getNext (const T &)
template<typename T>
const T *	getNext (const T &dummy) const
Composite *	getParent ()
const Composite *	getParent () const
Composite *	getChild (Index index)
const Composite *	getChild (Index index) const
Composite *	getSibling (Index index)
const Composite *	getSibling (Index index) const
Composite *	getFirstChild ()
const Composite *	getFirstChild () const
Composite *	getLastChild ()
const Composite *	getLastChild () const
const PreciseTime &	getModificationTime () const
const PreciseTime &	getSelectionTime () const
void	stamp (StampType stamp=BOTH)
void	prependChild (Composite &composite)
void	appendChild (Composite &composite)
void	insertBefore (Composite &composite)
void	insertAfter (Composite &composite)
void	spliceBefore (Composite &composite)
void	spliceAfter (Composite &composite)
void	splice (Composite &composite)
bool	removeChild (Composite &child)
Size	removeSelected ()
Size	removeUnselected ()
void	replace (Composite &composite)
void	swap (Composite &composite)
virtual void	select ()
virtual void	deselect ()
Public Member Functions inherited from BALL::PersistentObject
	PersistentObject ()
virtual	~PersistentObject ()
PersistenceManager &	operator>> (PersistenceManager &pm) const
virtual void	finalize ()
Public Member Functions inherited from BALL::Object
	Object ()
	Default constructor.
	Object (const Object &object)
	Copy constructor.
virtual	~Object ()
	Destructor.
const Object &	operator= (const Object &)
bool	operator== (const Object &object) const
bool	operator!= (const Object &object) const
bool	operator< (const Object &object) const
bool	operator<= (const Object &object) const
bool	operator>= (const Object &object) const
bool	operator> (const Object &object) const
int	compare (const Object &object) const
virtual void	dump (::std::ostream &s=std::cout, Size depth=0) const
Handle	getHandle () const
Public Member Functions inherited from BALL::AutoDeletable
virtual	~AutoDeletable ()
void *	operator new (size_t size)
void	operator delete (void *ptr)
void *	operator new (size_t size, void *ptr)
void	operator delete (void ptr, void )
bool	isAutoDeletable () const
void	setAutoDeletable (bool enable)
Public Member Functions inherited from BALL::Selectable
	Selectable ()
	Selectable (const Selectable &selectable, bool deep=true)
virtual	~Selectable ()
void	set (const Selectable &selectable, bool deep=true)
const Selectable &	operator= (const Selectable &selectable)
void	get (Selectable &selectable, bool deep=true) const
void	swap (Selectable &selectable)
virtual void	setSelected (bool selected)
bool	isSelected () const
bool	operator== (const Selectable &selectable) const
bool	operator!= (const Selectable &selectable) const
void	write (PersistenceManager &pm) const
bool	read (PersistenceManager &pm)
virtual void	dump (::std::ostream &s=std::cout, Size depth=0) const
Public Member Functions inherited from BALL::PropertyManager
BALL_INLINE	PropertyManager ()
	Default constructor.
BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor.
virtual	~PropertyManager ()
	Destructor.
void	set (const PropertyManager &property_manager)
const PropertyManager &	operator= (const PropertyManager &property_manager)
void	get (PropertyManager &property_manager) const
void	swap (PropertyManager &property_manager)
BitVector &	getBitVector ()
const BitVector &	getBitVector () const
	operator BitVector & ()
void	setProperty (Property property)
void	clearProperty (Property property)
void	toggleProperty (Property property)
Size	countProperties () const
const NamedProperty &	getNamedProperty (Position index) const
NamedProperty &	getNamedProperty (Position index)
void	setProperty (const NamedProperty &property)
void	setProperty (const std::string &name)
void	setProperty (const std::string &name, bool value)
void	setProperty (const std::string &name, int value)
void	setProperty (const std::string &name, unsigned int value)
void	setProperty (const std::string &name, float value)
void	setProperty (const std::string &name, double value)
void	setProperty (const std::string &name, const std::string &value)
void	setProperty (const std::string &name, const PersistentObject &value)
const NamedProperty &	getProperty (const std::string &name) const
NamedPropertyIterator	beginNamedProperty ()
NamedPropertyIterator	endNamedProperty ()
void	clearProperty (const std::string &name)
Size	countNamedProperties () const
bool	hasProperty (Property property) const
	Query for an unnamed property.
bool	hasProperty (const std::string &name) const
	Query for a named property.
bool	operator== (const PropertyManager &pm) const
bool	operator!= (const PropertyManager &pm) const
	Inequality operator.
void	write (PersistenceManager &pm) const
	Persistent stream writing.
bool	read (PersistenceManager &pm)
	Persistent stream reading.
bool	isValid () const
void	dump (std::ostream &s=std::cout, Size depth=0) const

Friends
class	Bond

Debugging and Diagnostics
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const

Additional Inherited Members
static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)
static Handle	getNextHandle ()
static Handle	getNewHandle ()
static void	clearLastPtr ()
MolecularInteractions *	interactions
bool	store_interactions_disabled_
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR
static KernelPredicateType	DEFAULT_UNARY_PREDICATE
	AutoDeletable ()
	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)
String	name_
String	type_name_
const Element *	element_
float	radius_
Type	type_
unsigned char	number_of_bonds_
Bond *	bond_ [MAX_NUMBER_OF_BONDS]
Index	formal_charge_
Vector3	position_
float	charge_
Vector3	velocity_
Vector3	force_
bool	selected_
static AtomIndexList	free_list_

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

◆ Property

enum BALL::PDBAtom::Property

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.

Definition at line 76 of file PDBAtom.h.

◆ RemotenessIndicator

enum BALL::PDBAtom::RemotenessIndicator

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

◆ PDBAtom() [1/4]

BALL::PDBAtom::PDBAtom ( )

Default constructor.

◆ PDBAtom() [2/4]

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

Copy constructor.

◆ PDBAtom() [3/4]

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

Constructor.

◆ PDBAtom() [4/4]

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.

◆ ~PDBAtom()

virtual BALL::PDBAtom::~PDBAtom ( )

virtual

Destructor.

Member Function Documentation

◆ clear()

virtual void BALL::PDBAtom::clear ( )

virtual

Clear the contents of the atom.

Reimplemented from BALL::Atom.

◆ destroy()

virtual void BALL::PDBAtom::destroy ( )

virtual

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

Reimplemented from BALL::Atom.

◆ dump()

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

s	output stream where to output the internal state of the instance
depth	the dumping depth

Reimplemented from BALL::Atom.

◆ get()

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_atom the PDBAtom to be assigned to

◆ getAlternateLocationIndicator()

char BALL::PDBAtom::getAlternateLocationIndicator ( ) const

Get the alternate location indicator.

Returns: char the alternate location indicator

◆ getBranchDesignator()

char BALL::PDBAtom::getBranchDesignator ( ) const

Get the branch designator.

Returns: char the branch designator

◆ getChain() [1/2]

Chain * BALL::PDBAtom::getChain ( )

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

◆ getChain() [2/2]

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

◆ getOccupancy()

float BALL::PDBAtom::getOccupancy ( ) const

Get the occupancy.

Returns: float occupancy the occupancy

◆ getProtein() [1/2]

Protein * BALL::PDBAtom::getProtein ( )

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

◆ getProtein() [2/2]

const Protein * BALL::PDBAtom::getProtein ( ) const

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

◆ getRemotenessIndicator()

char BALL::PDBAtom::getRemotenessIndicator ( ) const

Get the remoteness indicator.

Returns: char the remoteness indicator

◆ getResidue() [1/2]

Residue * BALL::PDBAtom::getResidue ( )

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

◆ getResidue() [2/2]

const Residue * BALL::PDBAtom::getResidue ( ) const

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

◆ getTemperatureFactor()

float BALL::PDBAtom::getTemperatureFactor ( ) const

Get the temperature factor.

Returns: float the temperature factor

◆ operator!=()

bool BALL::PDBAtom::operator!= ( const PDBAtom & pdb_atom ) const

Inequality operator

See also: operator ==

◆ operator=()

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

Assignment operator. The assignment is deep.

Parameters

pdb_atom the PDBAtom to be copied (cloned)

Returns: pdb_atom& - the instance

◆ operator==()

bool BALL::PDBAtom::operator== ( const PDBAtom & pdb_atom ) const

Equality operator.

See also: Object::operator ==

◆ persistentRead()

void BALL::PDBAtom::persistentRead ( PersistenceManager & pm )

virtual

Reads a PDBAtom object from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Atom.

◆ persistentWrite()

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

virtual

Writes a PDBAtom object to a persistent stream.

Parameters

pm	the persistence manager
name	the instance name

Reimplemented from BALL::Atom.

◆ set()

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_atom	the PDBAtom to be copied (cloned)
deep	make a deep (=true) or shallow (=false) copy

◆ setAlternateLocationIndicator()

void BALL::PDBAtom::setAlternateLocationIndicator ( char alternate_location_indicator )

Set the alternate location indicator.

Parameters

alternate_location_indicator the alternate location indicator

◆ setBranchDesignator()

void BALL::PDBAtom::setBranchDesignator ( char branch_designator )

Set the branch designator.

Parameters

branch_designator the branch designator

◆ setOccupancy()

void BALL::PDBAtom::setOccupancy ( float occupancy )

Set the occupancy.

Parameters

occupancy the occupancy

◆ setRemotenessIndicator()

void BALL::PDBAtom::setRemotenessIndicator ( char remoteness_indicator )

Set the remoteness indicator.

Parameters

remoteness_indicator the remoteness indicator

◆ setTemperatureFactor()

void BALL::PDBAtom::setTemperatureFactor ( float temperature_factor )

Set the temperature factor.

Parameters

temperature_factor the temperature factor

◆ swap()

void BALL::PDBAtom::swap ( PDBAtom & pdb_atom )

Swapping of PDBAtoms.

Parameters

pdb_atom the PDBAtom {*this} is being swapped with

◆ Bond

friend class Bond

friend

Definition at line 43 of file PDBAtom.h.

Public Types

Public Member Functions

Friends

Debugging and Diagnostics

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ Property

◆ RemotenessIndicator

Constructor & Destructor Documentation

◆ PDBAtom() [1/4]

◆ PDBAtom() [2/4]

◆ PDBAtom() [3/4]

◆ PDBAtom() [4/4]

◆ ~PDBAtom()

Member Function Documentation

◆ clear()

◆ destroy()

◆ dump()

◆ get()

◆ getAlternateLocationIndicator()

◆ getBranchDesignator()

◆ getChain() [1/2]

◆ getChain() [2/2]

◆ getOccupancy()

◆ getProtein() [1/2]

◆ getProtein() [2/2]

◆ getRemotenessIndicator()

◆ getResidue() [1/2]

◆ getResidue() [2/2]

◆ getTemperatureFactor()

◆ operator!=()

◆ operator=()

◆ operator==()

◆ persistentRead()

◆ persistentWrite()

◆ set()

◆ setAlternateLocationIndicator()

◆ setBranchDesignator()

◆ setOccupancy()

◆ setRemotenessIndicator()

◆ setTemperatureFactor()

◆ swap()

Friends And Related Symbol Documentation

◆ Bond