OpenStructure
Public Member Functions
AtomBase Class Reference

#include <atom_base.hh>

Inherits GenericPropContainer< AtomBase >.

Inherited by AtomHandle, and AtomView.

Public Member Functions

 AtomBase ()
 
 AtomBase (const impl::AtomImplPtr &impl)
 
- 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
 

Handle validity

class ConstGenericPropContainer< AtomBase >
 
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)
 
GenericPropContainerImplGpImpl ()
 
const GenericPropContainerImplGpImpl () const
 
void CheckValidity () const
 

Additional Inherited Members

- 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
 

Detailed Description

base class for AtomHandle and AtomView

Groups common functionality for AtomView and AtomHandle.

Like ResidueBase residues, chains and entities atoms are generic property containers and may as such store custom properties.

The position of the atoms can be accessed via GetPos(). Note, however that the position of an atom is undefined when there are pending changes of an ICSEditor in buffered edit mode. Before calling GetPos(), ICSEditor::UpdateXCS() should be called explicitly.

Definition at line 44 of file atom_base.hh.

Constructor & Destructor Documentation

◆ AtomBase() [1/2]

AtomBase ( )

◆ AtomBase() [2/2]

AtomBase ( const impl::AtomImplPtr impl)

Member Function Documentation

◆ CheckValidity()

void CheckValidity ( ) const
protected

◆ GetAltBFactor()

Real GetAltBFactor ( const String alt_group) const

◆ GetAltGroupNames()

std::vector<String> GetAltGroupNames ( ) const

◆ GetAltOcc()

Real GetAltOcc ( const String alt_group) const

◆ GetAltPos()

geom::Vec3 GetAltPos ( const String alt_group) const

get alternative atom position

◆ GetAnisou()

const geom::Mat3& GetAnisou ( ) const

◆ GetBFactor()

Real GetBFactor ( ) const

Get isotropic temperature factor of atom.

The returned value may be zero for some structures

◆ GetCharge()

Real GetCharge ( ) const

get charge

◆ GetElement()

const String& GetElement ( ) const

returns the element name of the atom

◆ GetFloatProperty()

Real GetFloatProperty ( Prop::ID  prop_id) const

Get float property by id

◆ GetIndex()

unsigned long GetIndex ( ) const

Get the internal index.

◆ GetIntProperty()

int GetIntProperty ( Prop::ID  prop_id) const

Get int property by id.

◆ GetMass()

Real GetMass ( ) const

get mass of atom

The returned value may be zero

◆ GetName()

const String& GetName ( ) const

Get atom name.

In Python the atom name may also be accesssed over the property Name

◆ GetOccupancy()

Real GetOccupancy ( ) const

get atom occupancy

◆ GetOriginalPos()

const geom::Vec3& GetOriginalPos ( ) const

Get original global position in cartesian coordinates (no entity transformation is applied)

◆ GetPos()

const geom::Vec3& GetPos ( ) const

Get global position in cartesian coordinates with entity transformations applied.

◆ GetQualifiedName()

String GetQualifiedName ( ) const

Get qualified name for atom.

The qualified name consists of the atom name as well as a unique residue identifier and chain name. For CA of a glycine with residue number 2 of chain A, the qualified name is "A.GLY2.CA".

◆ GetRadius()

Real GetRadius ( ) const

returns the van-der-Waals radius of the atom

◆ GetStringProperty()

String GetStringProperty ( Prop::ID  prop_id) const

Get String property by id

◆ GpImpl() [1/2]

GenericPropContainerImpl* GpImpl ( )
protected

◆ GpImpl() [2/2]

const GenericPropContainerImpl* GpImpl ( ) const
protected

◆ Impl() [1/2]

impl::AtomImplPtr& Impl ( )

get atom implementation

◆ Impl() [2/2]

const impl::AtomImplPtr& Impl ( ) const

get atom implementation.

Intended for internal use.

◆ IsHetAtom()

bool IsHetAtom ( ) const

whether the atom is a hetatm

◆ IsValid()

bool IsValid ( ) const

check validity of handle

See also
operator bool()

◆ operator bool()

operator bool ( ) const
inline

check validity of handle

check, whether the bond handle 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 57 of file atom_base.hh.

◆ SetAnisou()

void SetAnisou ( const geom::Mat3 anisou)

◆ SetBFactor()

void SetBFactor ( Real  factor)

◆ SetCharge()

void SetCharge ( Real  charge)

◆ SetElement()

void SetElement ( const String element)

◆ SetHetAtom()

void SetHetAtom ( bool  het)

◆ SetIndex()

void SetIndex ( const unsigned long  index)

◆ SetMass()

void SetMass ( Real  mass)

◆ SetName()

void SetName ( const String atom_name)

Set atom name.

You are free to set the atom name to whatever you want. You must be aware that certain algorithms and routines rely on proper naming of the atoms. It is thus advised to use IUPAC naming rules.

Parameters
atom_nameis the new atom name.
See also
AtomBase::GetName

◆ SetOccupancy()

void SetOccupancy ( Real  occ)

◆ SetRadius()

void SetRadius ( Real  radius)

Friends And Related Function Documentation

◆ ConstGenericPropContainer< AtomBase >

friend class ConstGenericPropContainer< AtomBase >
friend

Definition at line 60 of file atom_base.hh.

Field Documentation

◆ impl_

impl::AtomImplPtr impl_
protected

Definition at line 173 of file atom_base.hh.


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