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
int GetBondCount () const
BondHandleList GetBondList () const
BondHandle FindBondToAtom (const AtomHandle &handle) const
AtomHandleList GetBondPartners () const
Traversing the hierarchy
void Apply (EntityVisitor &)
AtomHandle GetHandle () const
unsigned long GetHashCode () const
bool operator== (const AtomHandle &ref) const
bool operator!= (const AtomHandle &ref) const
- Public Member Functions inherited from AtomBase
 AtomBase ()
 AtomBase (const impl::AtomImplPtr &impl)
 operator bool () const
bool IsValid () const
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)
- 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< H >
bool HasProp (const String &key) const
String GetPropAsString (const String &key) const
String GetStringProp (const String &key) const
Real GetFloatProp (const String &key) const
int GetIntProp (const String &key) const
bool GetBoolProp (const String &key) const
geom::Vec3 GetVec3Prop (const String &key) const
String GetStringProp (const String &key, const String &def) const
Real GetFloatProp (const String &key, Real def) const
int GetIntProp (const String &key, int def) const
bool GetBoolProp (const String &key, bool def) const
std::map< String, GenericPropValueGetPropMap () 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< H >
template<typename T >
gp_get (const String &key) const
template<typename T >
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() [1/2]

◆ AtomHandle() [2/2]

AtomHandle ( const impl::AtomImplPtr impl)

Member Function Documentation

◆ Apply()

void Apply ( EntityVisitor )

Apply visitor.

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

See also

◆ FindBondToAtom()

BondHandle FindBondToAtom ( const AtomHandle handle) const

Find bond to specific atom.

The bond or an invalid bond handle if no such bond exists.

◆ GetBondCount()

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

◆ GetBondList()

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

◆ GetBondPartners()

AtomHandleList GetBondPartners ( ) const

Get all atoms this atom is bonded to.

◆ GetEntity()

EntityHandle GetEntity ( ) const

◆ GetHandle()

AtomHandle GetHandle ( ) const

get this handle

Useful for duck-typing in Python and templated code.

◆ GetHashCode()

unsigned 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.

◆ GetResidue()

ResidueHandle GetResidue ( ) const

◆ operator!=()

bool operator!= ( const AtomHandle ref) const

◆ operator==()

bool operator== ( const AtomHandle ref) const

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