AtomView Class Reference

#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)
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	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
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

Friends
class	EntityView

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

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Detailed Description

definition of AtomView

Definition at line 34 of file atom_view.hh.

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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()

Reimplemented from AtomBase.

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.

Reimplemented from AtomBase.

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.

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Friends And Related Function Documentation

friend class EntityView

friend

Definition at line 36 of file atom_view.hh.

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

• stage/include/ost/mol/atom_view.hh