#include <BALL/KERNEL/atom.h>

Inheritance diagram for BALL::Atom:

Classes
class	BondIteratorTraits

Public Types
Enumerations
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 }

Efficient handling of atom attributes
typedef std::list< Atom * >	AtomPtrList

typedef std::list< Position >	AtomIndexList

Public Types inherited from BALL::Composite
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

enum	StampType { MODIFICATION = 1, SELECTION = 2, BOTH = 3 }

typedef UnaryPredicate< Composite >	KernelPredicateType

Public Member Functions
Constructors
	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)

Destructors
virtual	~Atom ()

virtual void	clear ()

virtual void	destroy ()

Persistence
virtual void	persistentWrite (PersistenceManager &pm, const char *name=0) const

virtual void	persistentRead (PersistenceManager &pm)

Assignment methods
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

Accessors
void	setElement (const Element &element)
	Assign the atom's element. More...

const Element &	getElement () const
	Return the atom's element. More...

void	setCharge (float charge)

float	getCharge () const

void	setFormalCharge (Index formal_charge)
	Set the atom's formal charge. More...

Index	getFormalCharge () const
	Return the atom's formal charge. More...

const Molecule *	getMolecule () const

Molecule *	getMolecule ()
	Return the molecule the atom is contained in (mutable) More...

const Fragment *	getFragment () const

Fragment *	getFragment ()
	Return the fragment the atom is contained in (mutable) More...

const Residue *	getResidue () const

Residue *	getResidue ()
	Return the residue the atom is contained in (mutable) More...

const SecondaryStructure *	getSecondaryStructure () const

SecondaryStructure *	getSecondaryStructure ()
	Return the secondary structure the atom is contained in (mutable) More...

const Chain *	getChain () const

Chain *	getChain ()
	Return the chain the atom is contained in (mutable) More...

void	setName (const String &name)
	Set the atom name. More...

const String &	getName () const
	Return the atom name. More...

String	getFullName (FullNameType type=ADD_VARIANT_EXTENSIONS) const

void	setPosition (const Vector3 &position)

Vector3 &	getPosition ()
	Return the atom coordinates (mutable) More...

const Vector3 &	getPosition () const
	Return the atom coordinates (const) More...

void	setRadius (float radius)

float	getRadius () const
	Return the atom radius. More...

void	setType (Type atom_type)
	Assign the numerical atom type. More...

Type	getType () const
	Return the (numerical) atom type. More...

String	getTypeName () const
	Return the atom type name. More...

void	setTypeName (const String &name)
	Assign the atom type name. More...

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) More...

Vector3 &	getForce ()
	Return the atom's force vector (mutable) More...

Size	countBonds () const
	Return the number of bonds. More...

Bond *	getBond (Position index)

const Bond *	getBond (Position index) const

Bond *	getBond (const Atom &atom)

const Bond *	getBond (const Atom &atom) const

Miscellaneous
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

Predicates
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

Debuggers and diagnostics
virtual bool	isValid () const

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

Internal iteration
bool	applyBonds (UnaryProcessor< Bond > &processor)

Public Member Functions inherited from BALL::Composite
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)

template<typename T >
BALL_INLINE bool	apply (UnaryProcessor< T > &processor)

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

void	host (Visitor< Composite > &visitor)

template<typename T >
bool	applyAncestor (UnaryProcessor< T > &processor)

template<typename T >
bool	applyChild (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendantPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyDescendant (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPreorder (UnaryProcessor< T > &processor)

template<typename T >
bool	applyPostorder (UnaryProcessor< T > &processor)

template<typename T >
bool	apply (UnaryProcessor< T > &processor)

template<typename T >
bool	applyLevel (UnaryProcessor< T > &processor, long level)

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. More...

	Object (const Object &object)
	Copy constructor. More...

virtual	~Object ()
	Destructor. More...

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. More...

BALL_INLINE	PropertyManager (const PropertyManager &property_manager)
	Copy constructor. More...

virtual	~PropertyManager ()
	Destructor. More...

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 string &name)

void	setProperty (const string &name, bool value)

void	setProperty (const string &name, int value)

void	setProperty (const string &name, unsigned int value)

void	setProperty (const string &name, float value)

void	setProperty (const string &name, double value)

void	setProperty (const string &name, const string &value)

void	setProperty (const string &name, const PersistentObject &value)

const NamedProperty &	getProperty (const string &name) const

NamedPropertyIterator	beginNamedProperty ()

NamedPropertyIterator	endNamedProperty ()

void	clearProperty (const string &name)

Size	countNamedProperties () const

bool	hasProperty (Property property) const
	Query for an unnamed property. More...

bool	hasProperty (const string &name) const
	Query for a named property. More...

bool	operator== (const PropertyManager &pm) const

bool	operator!= (const PropertyManager &pm) const
	Inequality operator. More...

void	write (PersistenceManager &pm) const
	Persistent stream writing. More...

bool	read (PersistenceManager &pm)
	Persistent stream reading. More...

bool	isValid () const

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

Private Member Functions
void	clear_ ()

void	swapLastBond_ (const Atom *atom)

Class friends
- class Bond
typedef short	Type

class	Bond

External iteration
typedef Index	BondIteratorPosition

typedef RandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondIterator

typedef ConstRandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondConstIterator
	Constant random access iterator for bonds. More...

typedef std::reverse_iterator < BondIterator >	BondReverseIterator
	Reverse random access iterator for bonds. More...

typedef std::reverse_iterator < BondConstIterator >	BondConstReverseIterator
	Constant reverse random access iterator for bonds. More...

class	BondIteratorTraits

BondIterator	beginBond ()
	Return a bond iterator pointing to the first bond of the atom. More...

BondIterator	endBond ()
	Return a past-the-end bond iterator. More...

BondConstIterator	beginBond () const
	Return a constant bond iterator pointing to the first bond. More...

BondConstIterator	endBond () const
	Return a constant past-the-end bond iterator. More...

BondReverseIterator	rbeginBond ()
	Return a reverse bond iterator pointing to the last bond. More...

BondReverseIterator	rendBond ()
	Return a past-the-end bond iterator for reverse traversal. More...

BondConstReverseIterator	rbeginBond () const
	Return a constant reverse bond iterator pointing to the first atom. More...

BondConstReverseIterator	rendBond () const
	Return a constant past-the-end bond iterator for reverse traversal. More...

Attributes
static AtomIndexList	free_list_

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_

Additional Inherited Members
Static Public Member Functions inherited from BALL::Composite
static bool	insertParent (Composite &parent, Composite &first, Composite &last, bool destroy_parent=true)

Static Public Member Functions inherited from BALL::Object
static Handle	getNextHandle ()

static Handle	getNewHandle ()

Static Public Member Functions inherited from BALL::AutoDeletable
static void	clearLastPtr ()

Static Public Attributes inherited from BALL::Composite
static UnaryProcessor< Composite >	DEFAULT_PROCESSOR

static KernelPredicateType	DEFAULT_UNARY_PREDICATE

Protected Member Functions inherited from BALL::AutoDeletable
	AutoDeletable ()

	AutoDeletable (const AutoDeletable &auto_deletable, bool deep=false)

Protected Attributes inherited from BALL::Selectable
bool	selected_

Detailed Description

Atom class. A class representing atoms. During each runtime instance of a program an atom is unique and identified by a Object::Handle . Atom equality is defined as atom identity, so there cannot be any two identical atoms. A linear ordering of atoms is defined as the linear order of the Object::Handle s.

: Two atoms can be connected via a Bond . There can be only one bond between any two atoms (double bonds etc. are expressed via the bond order attribute of the bond) and the total number of bonds of an atom is limited to eight (can be changed at compile time, see MAX_NUMBER_OF_BONDS ).

: Since Atom is derived from ProperyManager , it may contain arbitrary, user-defined properties. An atom may be inserted in a Fragment instance ("parent fragment"). The "state" of an atom is defined by its attributes:

"element" - an instance of Element
"formal charge" - the formal charge of the atom
"charge" - the charge in multiples of the the proton charge
"name" - a string identifier
"type name" - a string identifier, meaningful in the the context of a forcefield only
"position" - the absolute position in cartesian coordinates (Angstrom)
"radius" - the radius (Angstrom)
"type" - an integer type, meaningful only in the context of a forcefield
"velocity" - velocity the velocity of the atom (Angstrom/ps)
"force" - the force experienced by the atom (for forcefield calculations, in units of Newton)
"bonds" - up to MAX_NUMBER_OF_BONDS bonds to other atoms

See Also
Bond

Molecule

AtomContainer

Definition at line 86 of file atom.h.

Member Typedef Documentation

typedef std::list<Position> BALL::Atom::AtomIndexList

Definition at line 938 of file atom.h.

typedef std::list<Atom*> BALL::Atom::AtomPtrList

Definition at line 935 of file atom.h.

typedef ConstRandomAccessIterator<Atom, Bond, BondIteratorPosition, BondIteratorTraits> BALL::Atom::BondConstIterator

Constant random access iterator for bonds.

Definition at line 885 of file atom.h.

typedef std::reverse_iterator<BondConstIterator> BALL::Atom::BondConstReverseIterator

Constant reverse random access iterator for bonds.

Definition at line 915 of file atom.h.

typedef RandomAccessIterator<Atom, Bond, BondIteratorPosition, BondIteratorTraits> BALL::Atom::BondIterator

Random access iterator for bonds.

Definition at line 868 of file atom.h.

typedef Index BALL::Atom::BondIteratorPosition

Definition at line 707 of file atom.h.

typedef std::reverse_iterator<BondIterator> BALL::Atom::BondReverseIterator

Reverse random access iterator for bonds.

Definition at line 900 of file atom.h.

typedef short BALL::Atom::Type

Atom type.

Definition at line 102 of file atom.h.

Member Enumeration Documentation

anonymous enum

Unnamed enumeration of all non-categorized constants.

Enumerator
UNKNOWN_TYPE	Unknown atom type. The type assigned for default-constructed atoms.
ANY_TYPE	Any atom type. Used as a wild card in the context of forcefields mainly
MAX_NUMBER_OF_BONDS	Maximum number of bonds of an atom.

Definition at line 110 of file atom.h.

enum BALL::Atom::FullNameType

The type of name used for getFullName.

See Also: getFullName

Enumerator
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

Definition at line 137 of file atom.h.

enum BALL::Atom::Property

Predefined properties. Enumeration of all properties that are used by the BALL kernel.

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 129 of file atom.h.

Constructor & Destructor Documentation

BALL::Atom::Atom ( )

Default constructor. The state of this instance is:

element type is unknown (Element::UNKNOWN)
formal charge is 0
charge is 0
name is empty string
type name is "?"
position is Vector3 (0,0,0)
radius is 0
type INVALID_TYPE
velocity is Vector3 (0,0,0)
force is Vector3 (0,0,0)
bond table is empty (atom has no bonds)
Returns
Atom - new atom

See Also
Composite::Composite

PropertyManager::PropertyManager

BALL::Atom::Atom	(	const Atom &	atom,
		bool	deep = `true`
	)

Copy constructor. The copy is either deep (default) or shallow.

: Note: Deep copying of atoms does not include bond cloning.

Parameters

atom	the atom to be copied (cloned)
deep	make a deep (=`true`) or shallow (=`false`) copy of atom

Returns: Atom - new constructed atom cloned from atom

See Also: Composite::Composite; PropertyManager::PropertyManager

BALL::Atom::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`
	)

Detailed state initializing constructor. The item bond table is empty (atom has no bonds).

Parameters

element	element type of the constructed atom
name	name of the constructed atom
type_name	type name name of the constructed atom
atom_type	type of the constructed atom
position	position of the constructed atom
velocity	velocity of the constructed atom
force	force acting upon the constructed atom
charge	charge of the constructed atom
formal_charge	formal charge of the constructed atom
radius	radius of the constructed atom

Returns: Atom - new constructed atom

See Also: Composite::Composite; PropertyManager::PropertyManager

virtual BALL::Atom::~Atom ( )

virtual

Destructor. If the atom has bonds in common with an other atom that atom is disconnected and the associated Bond instance is destroyed. Calls Atom::destroy .

See Also: Atom::destroy

Member Function Documentation

bool BALL::Atom::applyBonds ( UnaryProcessor< Bond > & processor )

Application of an unary processor on every contained bond.

Parameters

processor a typed unary processor for Bond instances

Returns: bool - true if application has been terminated successfully, false otherwise

BondIterator BALL::Atom::beginBond ( )

inline

Return a bond iterator pointing to the first bond of the atom.

Definition at line 871 of file atom.h.

BondConstIterator BALL::Atom::beginBond ( ) const

inline

Return a constant bond iterator pointing to the first bond.

Definition at line 888 of file atom.h.

virtual void BALL::Atom::clear ( )

virtual

Explicit default initialization. Calls Composite::clear and resets the attributes to the default values. In contrast to destroy , the atom is not removed from any composite structure, i.e. its parent fragment pointer remains unchanged.

See Also: Composite::clear; destroy

Reimplemented from BALL::Composite.

Reimplemented in BALL::PDBAtom.

void BALL::Atom::clear_ ( )

private

Bond* BALL::Atom::cloneBond	(	Bond &	bond,
		Atom &	atom
	)

Create a copy of a bond. This is mostly for internal use and should not be required by most users.

Size BALL::Atom::countBonds ( ) const

Return the number of bonds.

Bond* BALL::Atom::createBond ( Atom & atom )

Create a new bond to an atom. Create a new instance of Bond connecting this instance to atom . Calls Bond::createBond . The state of the bond is initialized to the default values.

Returns: Bond* - default initialized Bond instance that connects this instance to atom

Exceptions

Exception::TooManyBonds if one of the atom already possesses Atom::MAX_NUMBER_OF_BONDS bonds.

See Also: Bond::createBond

Bond* BALL::Atom::createBond	(	Bond &	bond,
		Atom &	atom
	)

Create a new bond from an already existing instance of Bond. Initialize the bond bond to connect this instance to atom . Calls Bond::createBond . The state of the bond is initialzed to the default values.

: Note: This method is recommended for use if a subclass of the Bond is to be used as the new bond. This permits extensibility of bonds to the framework client.

Returns: Bond* - default initialized bond bond that connects this instance to atom

Exceptions

Exception::TooManyBonds if one of the atom already possesses Atom::MAX_NUMBER_OF_BONDS bonds.

See Also: Bond::createBond

virtual void BALL::Atom::destroy ( )

virtual

Explicit destructor. Destroy this instance explicitly and reset its attributes to the default values.

See Also: Composite::clear

Reimplemented from BALL::Composite.

Reimplemented in BALL::PDBAtom.

bool BALL::Atom::destroyBond ( const Atom & atom )

Explicit bond destruction. Destroy the bond connecting {*this atom} and atom explicitly. If the bond is auto-deletable the default destructor is called otherwise Bond::destroy .

: Note: This method is recommended to destroy a bond of an atom explicitly instead of using the keyword delete. This is due to erroneous explicit destruction of statically allocated bonds.

Parameters

atom	the atom that should be disconnected from this instance

See Also: AutoDeletable; Bond::destroy

void BALL::Atom::destroyBonds ( )

Explicit bond table destruction. Destroy all the bonds connecting {*this atom} with another atom explicitly. If the bonds are auto-deletable the default destructors are called otherwise Bond::destroy .

: Note: This method is recommended to destroy all bonds of an atom explicitly instead of using the keyword delete. This is due to erroneous explicit destruction of statically allocated bonds.

Parameters

atom	the atom that should be disconnected from this instance

See Also: AutoDeletable; Bond::destroy

virtual void BALL::Atom::dump	(	std::ostream &	s = `std::cout`,
		Size	depth = `0`
	)		const

virtual

Internal state dump. Dump the current internal state of this instance to the output ostream s with dumping depth depth . For debugging purposes only.

Parameters

s	- output stream where to output the internal state
depth	- the dumping depth

Reimplemented from BALL::Composite.

Reimplemented in BALL::PDBAtom.

BondIterator BALL::Atom::endBond ( )

inline

Return a past-the-end bond iterator.

Definition at line 877 of file atom.h.

BondConstIterator BALL::Atom::endBond ( ) const

inline

Return a constant past-the-end bond iterator.

Definition at line 894 of file atom.h.

void BALL::Atom::get	(	Atom &	atom,
		bool	deep = `true`
	)		const

Deep/shallow assignment. The inverse operation to set , behaves identically.

Parameters

atom	the atom to be assigned to

See Also: Atom::set

Bond* BALL::Atom::getBond ( Position index )

Return a bond by its index (mutable). The reference is 0 if this instance does not have a bond with index index .

: Note: No corresponding mutator Atom::setBond exists to consider design of contract - an atom may not insert a bond in its bond table at a given index. The atom's bond table is an implementation detail that is not relevant to and should not be relied on by the client programmer. A bond must always be created via Bond::Bond or Atom::createBond .

Parameters

index the index of the bond to be accessed to

Returns: Bond* - mutable pointer to the bond that is indexed in this instance's bond table, 0 if this instance does not have a bond with index index

Exceptions

IndexOverflow if index >= MAX_NUMBER_OF_BONDS

const Bond* BALL::Atom::getBond ( Position index ) const

Return a bond by its index (const).

Exceptions

IndexOverflow if index >= MAX_NUMBER_OF_BONDS

Bond* BALL::Atom::getBond ( const Atom & atom )

Return a bond by its partner atom (const). The reference is 0 if this instance does not have a bond with atom .

Parameters

atom	the atom that is considered to have a bond with this instance

Returns: Bond* - mutable pointer to the bond that connects atom with this instance, 0 if this instance does not have a bond with atom

See Also: Atom::createBond

const Bond* BALL::Atom::getBond ( const Atom & atom ) const

Return a bond by its partner atom (mutable) The reference is 0 if this instance does not have a bond with atom .

Parameters

atom	the atom that is considered to have a bond with this instance

Returns: Bond* - constant pointer to the bond that connects atom with this instance, 0 if this instance does not have a bond with atom

See Also: Atom::createBond

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

Return the chain the atom is contained in (const). A NULL pointer is returned if this atom is not part of a chain.

Returns: Chain* - constant pointer to the chain

Chain* BALL::Atom::getChain ( )

Return the chain the atom is contained in (mutable)

float BALL::Atom::getCharge ( ) const

Return the atom's (partial) charge. Charges should be assigned in multiples of the proton charge (elementary charge).

float BALL::Atom::getDistance ( const Atom & a ) const

A convenience function for computing the distance between two atoms. This is equivalent to calling this->getPosition().getDistance(a.getPosition())

Parameters

a	the atom to which to compute the distance

const Element& BALL::Atom::getElement ( ) const

Return the atom's element.

const Vector3& BALL::Atom::getForce ( ) const

Return the atom's force vector (const)

Vector3& BALL::Atom::getForce ( )

Return the atom's force vector (mutable)

Index BALL::Atom::getFormalCharge ( ) const

Return the atom's formal charge.

const Fragment* BALL::Atom::getFragment ( ) const

Return the fragment the atom is contained in (const). A NULL pointer is returned if this atom is not part of a fragment.

: Use Fragment::insert to insert an atom into a fragment and Fragment::remove to remove it.

Returns: Fragment* - constant pointer to the fragment

Fragment* BALL::Atom::getFragment ( )

Return the fragment the atom is contained in (mutable)

String BALL::Atom::getFullName ( FullNameType type = ADD_VARIANT_EXTENSIONS ) const

Assemble a fully specified atom name. This method returns at fully specified atom name as used for charge and type assignments. The name consists of the name of the residue the atom is contained in, a colon, and the atom name. Blanks are removed from both names. For example, for the alpha carbon atom of isoleucine getFullName will return the name ILE:CA. For N terminal residues, -N is appended to the residue name, for C terminal residues -C. If the residue is a CYS involved in a disulphide bridge, an additional -S or S (for terminal residue) is appended. For single amino acids (C and N terminal) -M is added.

: If the atom is not contained in a residue, the name of the parent fragment is taken instead of the residue name. If there is no parent fragment, the name of the parent molecule is taken. If the atom is not contained in any superstructure, getFullname returns getName.

: Overview of the returned strings:

<residue>:<atom> – if contained in a residue
<residue>-C:<atom> – for C terminal residues
<residue>-N:<atom> – for N terminal residues
CYS-S:<atom> – for CYS residues involved in a SS bond
CYS-NS:<atom> – for N terminal CYS residues involved in a SS bond
CYS-CS:<atom> – for C terminal CYS residues involved in a SS bond
<fragment>:atom – for atoms contained in a fragment, but not in a residue
<molecule>:atom – for atoms contained in a molecule, but not in a fragment

Parameters

type	if type is set to `Atom::NO_VARIANT_EXTENSIONS`, the variant extension (`-XX`) is omitted

Returns: String the full name

const Molecule* BALL::Atom::getMolecule ( ) const

Return the molecule the atom is contained in (const). A NULL pointer is returned if this atom is not part of a molecule.

: Use Molecule::insert to insert an atom into a molecule and Molecule::remove to remove it.

Returns: Molecule* - constant pointer to the parent molecule

Molecule* BALL::Atom::getMolecule ( )

Return the molecule the atom is contained in (mutable)

const String& BALL::Atom::getName ( ) const

Return the atom name.

Atom* BALL::Atom::getPartnerAtom ( Position i )

Returns the Atom bound at the i-th bond. This is a convenience function for: getBond(i)->getBoundAtom(*this)

Parameters

i	The index of the partner atom

Exceptions

Exception::IndexOverflow is thrown if i >= countBonds(). This exception originates from getBond(i)

const Atom* BALL::Atom::getPartnerAtom ( Position i ) const

Returns the Atom bound at the i-th bond. This is a convenience function for: getBond(i)->getBoundAtom(*this)

Parameters

i	The index of the partner atom

Exceptions

Exception::IndexOverflow is thrown if i >= countBonds(). This exception originates from getBond(i)

Vector3& BALL::Atom::getPosition ( )

Return the atom coordinates (mutable)

const Vector3& BALL::Atom::getPosition ( ) const

Return the atom coordinates (const)

float BALL::Atom::getRadius ( ) const

Return the atom radius.

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

Return the residue the atom is contained in (const). A NULL pointer is returned if this atom is not part of a residue.

: Use Residue::insert to insert an atom into a residue and Residue::remove to remove it.

Returns: Residue* - constant pointer to the residue

Residue* BALL::Atom::getResidue ( )

Return the residue the atom is contained in (mutable)

const SecondaryStructure* BALL::Atom::getSecondaryStructure ( ) const

Return the secondary structure the atom is contained in (const). A NULL pointer is returned if this atom is not part of a secondary structure.

Returns: SecondaryStructure* - constant pointer to the secondary structure

SecondaryStructure* BALL::Atom::getSecondaryStructure ( )

Return the secondary structure the atom is contained in (mutable)

Type BALL::Atom::getType ( ) const

Return the (numerical) atom type.

String BALL::Atom::getTypeName ( ) const

Return the atom type name.

Vector3& BALL::Atom::getVelocity ( )

Return the atom velocity. BALL uses units of ${\AA}/ps$ for the velocity.

const Vector3& BALL::Atom::getVelocity ( ) const

Return the atom velocity. BALL uses units of ${\AA}/ps$ for the velocity.

bool BALL::Atom::hasBond ( const Bond & bond ) const

Determine whether the atom takes part in a certain bond.

Parameters

bond	the bond in question

Returns: bool true if the bond bond connects this instance with another atom, false otherwise

See Also: Atom::hasBond

bool BALL::Atom::isBound ( ) const

Determine whether the atom has any bond.

Returns: bool - true if an atom is bound to this instance, false otherwise

See Also: Atom::hasBond

bool BALL::Atom::isBoundTo ( const Atom & atom ) const

Determine whether there exists a bond to another atom. Calls Atom::getBond . Hydrogen bonds (type = Bond::TYPE__HYDROGEN) are ignored.

Parameters

atom	the atom in question

Returns: bool - true if bond connects atom with {*this atom}, false otherwise

See Also: Atom::getBond

bool BALL::Atom::isGeminal ( const Atom & atom ) const

True if the two atoms are geminal. Two atoms are geminal if they do not share a common bond but both have a bond to a third atom. For example the two hydrogen atoms in water are geminal. Hydrogen bonds (type = Bond::TYPE__HYDROGEN) are ignored.

Parameters

atom	the second atom

Returns: bool - true if atom is geminal to this instance

virtual bool BALL::Atom::isValid ( ) const

virtual

Internal state and consistency self-validation.

Returns: bool - true if the internal state of this instance is correct (self-validated) and consistent, false otherwise

Reimplemented from BALL::Composite.

bool BALL::Atom::isVicinal ( const Atom & atom ) const

True if the two atoms are vicinal. Two atoms are vicinal if they are separated by three bonds (1-4 position). Hydrogen bonds (type = Bond::TYPE__HYDROGEN) are ignored.

Parameters

atom	the second atom

Returns: bool - true if atom is vicinal to this instance

bool BALL::Atom::operator!= ( const Atom & atom ) const

Inequality operator

See Also: operator ==

Atom& BALL::Atom::operator= ( const Atom & atom )

Assignment operator. The assignment is always deep. Calls Atom::set .

: Note: Bonds are not copied

Parameters

atom	the atom to be copied

Returns: Atom& - this instance

See Also: Atom::set

bool BALL::Atom::operator== ( const Atom & atom ) const

PredicatesEquality operator. Two atoms are equal if they have the same handle.

See Also: Object::operator ==

virtual void BALL::Atom::persistentRead ( PersistenceManager & pm )

virtual

Read an Atom from a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::PDBAtom.

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

virtual

Write an Atom to a persistent stream.

Parameters

pm	the persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::PDBAtom.

BondReverseIterator BALL::Atom::rbeginBond ( )

inline

Return a reverse bond iterator pointing to the last bond.

Definition at line 903 of file atom.h.

BondConstReverseIterator BALL::Atom::rbeginBond ( ) const

inline

Return a constant reverse bond iterator pointing to the first atom.

Definition at line 918 of file atom.h.

BondReverseIterator BALL::Atom::rendBond ( )

inline

Return a past-the-end bond iterator for reverse traversal.

Definition at line 909 of file atom.h.

BondConstReverseIterator BALL::Atom::rendBond ( ) const

inline

Return a constant past-the-end bond iterator for reverse traversal.

Definition at line 924 of file atom.h.

void BALL::Atom::set	(	const Atom &	atom,
		bool	deep = `true`
	)

Deep/shallow assignment. The assignment is either deep or shallow (default is deep). In the case of a deep assignment, all composites contained in atom are copied as well.

: Caveat: Bonds are not copied!

Parameters

atom	the atom to be copied
deep	make a deep (=true) or shallow (=false) copy of `atom`

void BALL::Atom::setCharge ( float charge )

Set the atom's (partial) charge. Charges should be assigned in multiples of the proton charge (elementary charge).

void BALL::Atom::setElement ( const Element & element )

Assign the atom's element.

void BALL::Atom::setForce ( const Vector3 & force )

Assign the atom's force vevtor. BALL uses units of Newton (1 N = 1 J/m) as the unit of force.

void BALL::Atom::setFormalCharge ( Index formal_charge )

Set the atom's formal charge.

void BALL::Atom::setName ( const String & name )

Set the atom name.

void BALL::Atom::setPosition ( const Vector3 & position )

Assign the atom coordinates. BALL uses units of Angstrom for atom coordinates.

void BALL::Atom::setRadius ( float radius )

Set the atom radius. BALL uses units of Angstrom for the atom radii.

void BALL::Atom::setType ( Type atom_type )

Assign the numerical atom type.

void BALL::Atom::setTypeName ( const String & name )

Assign the atom type name.

void BALL::Atom::setVelocity ( const Vector3 & velocity )

Set the atom velocity BALL uses units of ${\AA}/ps$ for the velocity.

void BALL::Atom::swap ( Atom & atom )

Swap the contents of two atoms. The static attributes are swapped by exchanging the indices of the two atoms!

Parameters

atom	the atom being swapped with this instance

void BALL::Atom::swapLastBond_ ( const Atom * atom )

private

Friends And Related Function Documentation

friend class Bond

friend

Definition at line 96 of file atom.h.

friend class BondIteratorTraits

friend

Definition at line 862 of file atom.h.

Member Data Documentation

Bond* BALL::Atom::bond_[MAX_NUMBER_OF_BONDS]

protected

Definition at line 963 of file atom.h.

float BALL::Atom::charge_

protected

Definition at line 969 of file atom.h.

const Element* BALL::Atom::element_

protected

Definition at line 955 of file atom.h.

Vector3 BALL::Atom::force_

protected

Definition at line 973 of file atom.h.

Index BALL::Atom::formal_charge_

protected

Definition at line 965 of file atom.h.

AtomIndexList BALL::Atom::free_list_

staticprotected

Definition at line 948 of file atom.h.

String BALL::Atom::name_

protected

Definition at line 951 of file atom.h.

unsigned char BALL::Atom::number_of_bonds_

protected

Definition at line 961 of file atom.h.

Vector3 BALL::Atom::position_

protected

Definition at line 967 of file atom.h.

float BALL::Atom::radius_

protected

Definition at line 957 of file atom.h.

Type BALL::Atom::type_

protected

Definition at line 959 of file atom.h.

String BALL::Atom::type_name_

protected

Definition at line 953 of file atom.h.

Vector3 BALL::Atom::velocity_

protected

Definition at line 971 of file atom.h.

Classes

Public Types

Public Member Functions

Private Member Functions

Class friends

External iteration

Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation