AtomBase Class Reference

base class for AtomHandle and AtomView More...

#include <atom_base.hh>

Inherits GenericPropContainer< AtomBase >.

Public Member Functions
	AtomBase ()
	AtomBase (const impl::AtomImplPtr &impl)
const String &	GetName () const
void	SetName (const String &atom_name)
const geom::Vec3 &	GetPos () const
const geom::Vec3 &	GetOriginalPos () const
geom::Vec3	GetAltPos (const String &alt_group) const
Real	GetAltBFactor (const String &alt_group) const
Real	GetAltOcc (const String &alt_group) const
std::vector< String >	GetAltGroupNames () const
String	GetQualifiedName () const
String	GetStringProperty (Prop::ID prop_id) const
Real	GetFloatProperty (Prop::ID prop_id) const
int	GetIntProperty (Prop::ID prop_id) const
unsigned long	GetIndex () const
Real	GetRadius () const
const String &	GetElement () const
bool	IsHetAtom () const
Real	GetBFactor () const
void	SetBFactor (Real factor)
void	SetOccupancy (Real occ)
void	SetCharge (Real charge)
void	SetMass (Real mass)
void	SetHetAtom (bool het)
void	SetRadius (Real radius)
void	SetIndex (const unsigned long index)
const geom::Mat3 &	GetAnisou () const
void	SetAnisou (const geom::Mat3 &anisou)
Real	GetMass () const
Real	GetCharge () const
Real	GetOccupancy () const
const impl::AtomImplPtr &	Impl () const
impl::AtomImplPtr &	Impl ()
void	SetElement (const String &element)
Handle validity

	operator bool () const
bool	IsValid () const
Protected Member Functions
GenericPropContainerImpl *	GpImpl ()
const GenericPropContainerImpl *	GpImpl () const
void	CheckValidity () const
Protected Attributes
impl::AtomImplPtr	impl_
Friends
class	ConstGenericPropContainer< AtomBase >

Detailed Description

base class for AtomHandle and AtomView

Groups common functionality for AtomView and AtomHandle.

Like ResidueBase residues, chains and entities atoms are generic property containers and may as such store custom properties.

The position of the atoms can be accessed via GetPos(). Note, however that the position of an atom is undefined when there are pending changes of an ICSEditor in buffered edit mode. Before calling GetPos(), ICSEditor::UpdateXCS() should be called explicitly.

Definition at line 44 of file atom_base.hh.

Constructor & Destructor Documentation

AtomBase ( )

AtomBase ( const impl::AtomImplPtr & impl )

Member Function Documentation

void CheckValidity ( ) const [protected]

Real GetAltBFactor ( const String & alt_group ) const

std::vector<String> GetAltGroupNames ( ) const

Real GetAltOcc ( const String & alt_group ) const

geom::Vec3 GetAltPos ( const String & alt_group ) const

get alternative atom position

const geom::Mat3& GetAnisou ( ) const

Real GetBFactor ( ) const

Get isotropic temperature factor of atom.

The returned value may be zero for some structures

Real GetCharge ( ) const

get charge

const String& GetElement ( ) const

returns the element name of the atom

Real GetFloatProperty ( Prop::ID prop_id ) const

Get float property by id.

unsigned long GetIndex ( ) const

Get the internal index.

int GetIntProperty ( Prop::ID prop_id ) const

Get int property by id.

Real GetMass ( ) const

get mass of atom

The returned value may be zero

const String& GetName ( ) const

Get atom name.

In Python the atom name may also be accesssed over the property Name

Real GetOccupancy ( ) const

get atom occupancy

const geom::Vec3& GetOriginalPos ( ) const

Get original global position in cartesian coordinates (no entity transformation is applied).

const geom::Vec3& GetPos ( ) const

Get global position in cartesian coordinates with entity transformations applied.

String GetQualifiedName ( ) const

Get qualified name for atom.

The qualified name consists of the atom name as well as a unique residue identifier and chain name. For CA of a glycine with residue number 2 of chain A, the qualified name is "A.GLY2.CA".

Real GetRadius ( ) const

returns the van-der-Waals radius of the atom

String GetStringProperty ( Prop::ID prop_id ) const

Get String property by id.

const GenericPropContainerImpl* GpImpl ( ) const [protected]

GenericPropContainerImpl* GpImpl ( ) [protected]

impl::AtomImplPtr& Impl ( )

get atom implementation

const impl::AtomImplPtr& Impl ( ) const

get atom implementation.

Intended for internal use.

bool IsHetAtom ( ) const

whether the atom is a hetatm

bool IsValid ( ) const [inline]

check validity of handle

See also:: operator bool()

Reimplemented in AtomView.

Definition at line 60 of file atom_base.hh.

operator bool ( ) const [inline]

check validity of handle

check, whether the bond handle points to a valid atom.

Note:: It is an error to use any method other than IsValid, Impl and operator bool() when the handle is invalid. An InvalidHandle exception will be thrown.

Reimplemented in AtomView.

Definition at line 57 of file atom_base.hh.

void SetAnisou ( const geom::Mat3 & anisou )

void SetBFactor ( Real factor )

void SetCharge ( Real charge )

void SetElement ( const String & element )

void SetHetAtom ( bool het )

void SetIndex ( const unsigned long index )

void SetMass ( Real mass )

void SetName ( const String & atom_name )

Set atom name.

You are free to set the atom name to whatever you want. You must be aware that certain algorithms and routines rely on proper naming of the atoms. It is thus advised to use IUPAC naming rules.

Parameters:

atom_name

is the new atom name.