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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 StringGetName () const
 
void SetName (const String &atom_name)
 
const geom::Vec3GetPos () const
 
const geom::Vec3GetOriginalPos () 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< StringGetAltGroupNames () 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 StringGetElement () 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::Mat3GetAnisou () const
 
void SetAnisou (const geom::Mat3 &anisou)
 
Real GetMass () const
 
Real GetCharge () const
 
Real GetOccupancy () const
 
const impl::AtomImplPtrImpl () const
 
impl::AtomImplPtrImpl ()
 
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< StringGetPropList () const
 

Protected Member Functions

bool AddBond (const BondHandle &bond)
 
void RemoveBondInternal (const BondHandle &bond)
 
- Protected Member Functions inherited from AtomBase
GenericPropContainerImplGpImpl ()
 
const GenericPropContainerImplGpImpl () const
 
void CheckValidity () const
 
- Protected Member Functions inherited from ConstGenericPropContainer< AtomBase >
gp_get (const String &key) const
 
gp_get (const String &key, const T &def) const
 
GenericPropContainerImplGetImpl ()
 
const GenericPropContainerImplGetImpl () 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
bondThe 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: