BALL::Atom Class Reference
[Molecular Datastructures]

Atom class. More...

#include <atom.h>

Inheritance diagram for BALL::Atom:

[legend]


Public Types
Enumerations
enum	{ UNKNOWN_TYPE = -1, ANY_TYPE = 0, MAX_NUMBER_OF_BONDS = 12 }
	Unnamed enumeration of all non-categorized constants. More...
enum	Property { NUMBER_OF_PROPERTIES = 0 }
	Predefined properties. More...
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 }
	The type of name used for getFullName. More...
Public Member Functions
Constructors
	Atom ()
	Default constructor.
	Atom (const Atom &atom, bool deep=true)
	Copy constructor.
	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.
Destructors
virtual	~Atom ()
	Destructor.
virtual void	clear ()
	Explicit default initialization.
virtual void	destroy ()
	Explicit destructor.
Persistence
virtual void	persistentWrite (PersistenceManager &pm, const char *name=0) const throw (Exception::GeneralException)
	Write an Atom to a persistent stream.
virtual void	persistentRead (PersistenceManager &pm) throw (Exception::GeneralException)
	Read an Atom from a persistent stream.
Assignment methods
void	set (const Atom &atom, bool deep=true)
	Deep/shallow assignment.
void	get (Atom &atom, bool deep=true) const
	Deep/shallow assignment.
Atom &	operator= (const Atom &atom)
	Assignment operator.
void	swap (Atom &atom)
	Swap the contents of two atoms.

bool	operator== (const Atom &atom) const
	Predicates.
bool	operator!= (const Atom &atom) const
	Inequality operator.
Accessors
void	setElement (const Element &element)
	Assign the atom's element.
const Element &	getElement () const
	Return the atom's element.
void	setCharge (float charge)
	Set the atom's (partial) charge.
float	getCharge () const
	Return the atom's (partial) charge.
void	setFormalCharge (Index formal_charge)
	Set the atom's formal charge.
Index	getFormalCharge () const
	Return the atom's formal charge.
const Molecule *	getMolecule () const
	Return the molecule the atom is contained in (const).
Molecule *	getMolecule ()
	Return the molecule the atom is contained in (mutable).
const Fragment *	getFragment () const
	Return the fragment the atom is contained in (const).
Fragment *	getFragment ()
	Return the fragment the atom is contained in (mutable).
const Residue *	getResidue () const
	Return the residue the atom is contained in (const).
Residue *	getResidue ()
	Return the residue the atom is contained in (mutable).
const SecondaryStructure *	getSecondaryStructure () const
	Return the secondary structure the atom is contained in (const).
SecondaryStructure *	getSecondaryStructure ()
	Return the secondary structure the atom is contained in (mutable).
const Chain *	getChain () const
	Return the chain the atom is contained in (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
	Assemble a fully specified atom name.
void	setPosition (const Vector3 &position)
	Assign the atom coordinates.
Vector3 &	getPosition ()
	Return the atom coordinates (mutable).
const Vector3 &	getPosition () const
	Return the atom coordinates (const).
void	setRadius (float radius)
	Set the atom 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)
	Set the atom velocity BALL uses units of ${\AA}/ps$ for the velocity.
const Vector3 &	getVelocity () const
	Return the atom velocity.
void	setForce (const Vector3 &force)
	Assign the atom's force vevtor.
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) throw (Exception::IndexOverflow)
	Return a bond by its index (mutable).
const Bond *	getBond (Position index) const throw (Exception::IndexOverflow)
	Return a bond by its index (const).
Bond *	getBond (const Atom &atom)
	Return a bond by its partner atom (const).
const Bond *	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 .
Miscellaneous
Bond *	createBond (Atom &atom) throw (Exception::TooManyBonds)
	Create a new bond to an atom.
Bond *	createBond (Bond &bond, Atom &atom) throw (Exception::TooManyBonds)
	Create a new bond from an already existing instance of Bond.
Bond *	cloneBond (Bond &bond, Atom &atom)
	Create a copy of a bond.
bool	destroyBond (const Atom &atom)
	Explicit bond destruction.
void	destroyBonds ()
	Explicit bond table destruction.
Atom *	getPartnerAtom (Position i) throw (Exception::IndexOverflow)
	Returns the Atom bound at the i-th bond.
const Atom *	getPartnerAtom (Position i) const throw (Exception::IndexOverflow)
	Returns the Atom bound at the i-th bond.
float	getDistance (const Atom &a) const
	A convenience function for computing the distance between two atoms.
Predicates
bool	hasBond (const Bond &bond) const
	Determine whether the atom takes part in a certain bond.
bool	isBoundTo (const Atom &atom) const
	Determine whether there exists a bond to another atom.
bool	isBound () const
	Determine whether the atom has any bond.
bool	isGeminal (const Atom &atom) const
	True if the two atoms are geminal.
bool	isVicinal (const Atom &atom) const
	True if the two atoms are vicinal.
Debuggers and diagnostics
virtual bool	isValid () const
	Internal state and consistency self-validation.
virtual void	dump (std::ostream &s=std::cout, Size depth=0) const
	Internal state dump.
Internal iteration
bool	applyBonds (UnaryProcessor< Bond > &processor)
	Application of an unary processor on every contained bond.
Class friends
class Bond
typedef short	Type
	Atom type.
class	Bond
External iteration
typedef Index	BondIteratorPosition
typedef RandomAccessIterator < Atom, Bond, BondIteratorPosition, BondIteratorTraits >	BondIterator
	Random access iterator for bonds.
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.
class	BondIteratorTraits
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.
Efficient handling of atom attributes
typedef std::list< Atom * >	AtomPtrList
typedef std::list< Position >	AtomIndexList
Position	getIndex () const
	Return the index in the static attribute array.
StaticAtomAttributes *	getAttributePtr ()
const StaticAtomAttributes *	getAttributePtr () const
static Position	compact (const AtomIndexList &indices) throw (Exception::OutOfRange)
	Compact memory for a list of atoms.
static AttributeVector &	getAttributes ()
	Access to the static attribute array.
static const PreciseTime &	getAttributesModificationTime ()
	Get the time, when the attributes vector was last modified.
Attributes
static AttributeVector	static_attributes_
static AtomIndexList	free_list_
static PreciseTime	attributes_changed_time_
	time of the last resize of the attributes vector
Position	index_
const Element *	element_
String	name_
String	type_name_
float	radius_
unsigned char	number_of_bonds_
Bond *	bond_ [MAX_NUMBER_OF_BONDS]

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

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.

enum BALL::Atom::FullNameType

The type of name used for getFullName.

See also:: getFullName

enum BALL::Atom::Property

Predefined properties.

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

Reimplemented in BALL::PDBAtom.

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

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.

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.

static Position BALL::Atom::compact ( const AtomIndexList & indices ) throw (Exception::OutOfRange) [static]

Compact memory for a list of atoms.

This method packs the static attributes of the atom in the given range into a contiguous memory segment in order to increase locality.

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

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

See also:: Bond::createBond

Bond* BALL::Atom::createBond ( Atom & atom ) throw (Exception::TooManyBonds)

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

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.

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

static const PreciseTime& BALL::Atom::getAttributesModificationTime ( ) [static]

Get the time, when the attributes vector was last modified.

This needed for the GeometricObject 's in VIEW, because they store pointer to the position of atoms. These have to be updated, after a resize of the vector.

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

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 ( Position index ) const throw (Exception::IndexOverflow)

Return a bond by its index (const).

Exceptions:

IndexOverflow if index >= MAX_NUMBER_OF_BONDS

Bond* BALL::Atom::getBond ( Position index ) throw (Exception::IndexOverflow)

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 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

Reimplemented in BALL::PDBAtom.

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 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

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

const Atom* BALL::Atom::getPartnerAtom ( Position i ) const throw (Exception::IndexOverflow)

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

Atom* BALL::Atom::getPartnerAtom ( Position i ) throw (Exception::IndexOverflow)

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 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

Reimplemented in BALL::PDBAtom.

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

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

Predicates.

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

See also:: Object::operator ==

virtual void BALL::Atom::persistentRead ( PersistenceManager & pm ) throw (Exception::GeneralException) [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 throw (Exception::GeneralException) `[virtual]`

Write an Atom to a persistent stream.

Parameters:

pm

the persistence manager

Reimplemented from BALL::Composite.

Reimplemented in BALL::PDBAtom.

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::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::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::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

BALL::Atom Class Reference [Molecular Datastructures]

Public Types

Public Member Functions

Class friends

External iteration

Efficient handling of atom attributes

Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

BALL::Atom Class Reference
[Molecular Datastructures]