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Public Member Functions
AtomHandle Class Reference

#include <atom_handle.hh>

Inherits AtomBase.

Public Member Functions

 AtomHandle ()
 
 AtomHandle (const impl::AtomImplPtr &impl)
 
ResidueHandle GetResidue () const
 
EntityHandle GetEntity () const
 
AtomHandle GetHandle () const
 
long GetHashCode () const
 
bool operator== (const AtomHandle &ref) const
 
bool operator!= (const AtomHandle &ref) const
 
Bonds
int GetBondCount () const
 
BondHandleList GetBondList () const
 
BondHandle FindBondToAtom (const AtomHandle &handle) const
 
AtomHandleList GetBondPartners () const
 
Traversing the hierarchy
void Apply (EntityVisitor &)
 
- 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
 

Additional Inherited Members

- 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
 
- Protected Attributes inherited from AtomBase
impl::AtomImplPtr impl_
 

Detailed Description

Handle to atom datatype.

The bonds of an atom are accessible via GetBondList(). For a list of atoms that this atom is bonded to, use GetBondPartners().

New bonds are formed with one of the EditorBase::Connect() methods.

A valid atom handle is always part of a residue.

Definition at line 37 of file atom_handle.hh.

Constructor & Destructor Documentation

AtomHandle ( const impl::AtomImplPtr impl)

Member Function Documentation

void Apply ( EntityVisitor )

Apply visitor.

This method is used by the EntityVisitor interface to traverse the entity - chain - residue -atom hierarchy.

See Also
EntityVisitor
BondHandle FindBondToAtom ( const AtomHandle handle) const

Find bond to specific atom.

Returns
The bond or an invalid bond handle if no such bond exists.
int GetBondCount ( ) const

Get number of bonds this atom forms.

Count of all bonds where this atom is either the first or second atom.

See Also
BondHandle::GetFirst, BondHandle::GetSecond
BondHandleList GetBondList ( ) const

get bond list

Returns all bonds where this atom is either the first or second atom.

See Also
BondHandle::GetFirst, BondHandle::GetSecond
AtomHandleList GetBondPartners ( ) const

Get all atoms this atom is bonded to.

EntityHandle GetEntity ( ) const
AtomHandle GetHandle ( ) const

get this handle

Useful for duck-typing in Python and templated code.

long GetHashCode ( ) const

Get unique identifier for atom.

Get hash code that uniquely identifies every atom. The hash code is identical for all atom views pointing to a given atom.

ResidueHandle GetResidue ( ) const
bool operator!= ( const AtomHandle ref) const
bool operator== ( const AtomHandle ref) const

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