#include <atom_view.hh>

Inherits AtomBase.

Public Member Functions
	AtomView ()

	AtomView (const ResidueView &residue_view, const AtomHandle &atom)

ResidueView	GetResidue () const

EntityView	GetEntity () const

AtomHandle	GetHandle () const

BondHandleList	GetBondList () const

int	GetBondCount () const

AtomViewList	GetBondPartners () const

void	RemoveBonds ()

void	Apply (EntityVisitor &visitor)

void	Apply (EntityViewVisitor &visitor)

long	GetHashCode () const

bool	operator== (const AtomView &rhs) const

bool	operator!= (const AtomView &rhs) const

View validity
	operator bool () const

bool	IsValid () const

Public Member Functions inherited from AtomBase
	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)

	operator bool () const

bool	IsValid () const

Public Member Functions inherited from GenericPropContainer< AtomBase >
void	ClearProps ()

void	SetStringProp (const String &key, const String &value)

void	SetFloatProp (const String &key, Real value)

void	SetIntProp (const String &key, int value)

void	SetBoolProp (const String &key, bool value)

void	SetVec3Prop (const String &key, geom::Vec3 value)

void	RemoveProp (const String &key)

Public Member Functions inherited from ConstGenericPropContainer< AtomBase >
bool	HasProp (const String &key) const

String	GetPropAsString (const String &key) const

String	GetStringProp (const String &key) const

String	GetStringProp (const String &key, const String &def) const

Real	GetFloatProp (const String &key) const

Real	GetFloatProp (const String &key, Real def) const

int	GetIntProp (const String &key) const

int	GetIntProp (const String &key, int def) const

bool	GetBoolProp (const String &key) const

bool	GetBoolProp (const String &key, bool def) const

geom::Vec3	GetVec3Prop (const String &key) const

std::map< String, GenericPropValue >	GetPropMap () const

std::vector< String >	GetPropList () const

Protected Member Functions
bool	AddBond (const BondHandle &bond)

void	RemoveBondInternal (const BondHandle &bond)

Protected Member Functions inherited from AtomBase
GenericPropContainerImpl *	GpImpl ()

const GenericPropContainerImpl *	GpImpl () const

void	CheckValidity () const

Protected Member Functions inherited from ConstGenericPropContainer< AtomBase >
T	gp_get (const String &key) const

T	gp_get (const String &key, const T &def) const

GenericPropContainerImpl *	GetImpl ()

const GenericPropContainerImpl *	GetImpl () const

Friends
class	EntityView

Additional Inherited Members
Protected Attributes inherited from AtomBase
impl::AtomImplPtr	impl_

Detailed Description

definition of AtomView

Definition at line 34 of file atom_view.hh.

Constructor & Destructor Documentation

AtomView ( )

AtomView	(	const ResidueView &	residue_view,
		const AtomHandle &	atom
	)

Member Function Documentation

bool AddBond ( const BondHandle & bond )

protected

Add bond to atom. If the bond is already present, it will not be added again.

Parameters

bond	The bond to add

Returns: true if the bond has been added, false if the bond was already present in the list

void Apply ( EntityVisitor & visitor )

Apply entity visitor to this atom.

void Apply ( EntityViewVisitor & visitor )

int GetBondCount ( ) const

Get bond count Only bonds included in the view will be counted. To count all bonds of the the atom, use atom.GetHandle().GetBondCount().

BondHandleList GetBondList ( ) const

Get bond list Only bonds included in the view will be returned. To get all bonds of the the atom, use atom.GetHandle().GetBondList().

AtomViewList GetBondPartners ( ) const

Get all atoms this atom is bonded to.

EntityView GetEntity ( ) const

Shortcut to entity.

AtomHandle GetHandle ( ) const

Get handle this view points to.

long GetHashCode ( ) const

get unique id

The unique id is the same for all AtomViews pointing to the same atom view data.

ResidueView GetResidue ( ) const

Get parent residue view.

bool IsValid ( ) const

inline

check validity of handle

See Also: operator bool()

Definition at line 50 of file atom_view.hh.

operator bool ( ) const

inline

check validity of view

check, whether the atom view 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.

Definition at line 47 of file atom_view.hh.

bool operator!= ( const AtomView & rhs ) const

bool operator== ( const AtomView & rhs ) const

void RemoveBondInternal ( const BondHandle & bond )

protected

void RemoveBonds ( )

Remove all bonds this atom is involved in.

Friends And Related Function Documentation

friend class EntityView

friend

Definition at line 36 of file atom_view.hh.

The documentation for this class was generated from the following file:

stage/include/ost/mol/atom_view.hh

Public Member Functions

Protected Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation