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AtomBase Class Reference

#include <atom_base.hh>

Inherits GenericPropContainer< AtomBase >.

Inherited by AtomHandle, and AtomView.

Public Member Functions

 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)
Handle validity
 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 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< StringGetPropList () const

Protected Member Functions

GenericPropContainerImplGpImpl ()
const GenericPropContainerImplGpImpl () const
void CheckValidity () const

Protected Attributes

impl::AtomImplPtr impl_

Friends

class ConstGenericPropContainer< AtomBase >

Detailed Description

base class for AtomHandle and AtomView

Groups common functionality for AtomView and AtomHandle.

Most of the atom properties such as temperature factor, element, radius and charge can be accessed with #GetAtomProps() that returns an object of type AtomProp.

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 48 of file atom_base.hh.


Constructor & Destructor Documentation

AtomBase ( )
AtomBase ( const impl::AtomImplPtr impl)

Member Function Documentation

void CheckValidity ( ) const
protected
Real GetAltBFactor ( const String alt_group) const
std::vector<String> GetAltGroupNames ( ) const
Real GetAltOcc ( const String alt_group) const
geom::Vec3 GetAltPos ( const String alt_group) const

get alternative atom position

const geom::Mat3& GetAnisou ( ) const
Real GetBFactor ( ) const

Get isotropic temperature factor of atom.

The returned value may be zero for some structures

Real GetCharge ( ) const

get charge

const String& GetElement ( ) const

returns the element name of the atom

Real GetFloatProperty ( Prop::ID  prop_id) const

Get float property by id.

unsigned long GetIndex ( ) const

Get the internal index.

int GetIntProperty ( Prop::ID  prop_id) const

Get int property by id.

Real GetMass ( ) const

get mass of atom

The returned value may be zero

const String& GetName ( ) const

Get atom name.

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

Real GetOccupancy ( ) const

get atom occupancy

const geom::Vec3& GetOriginalPos ( ) const

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

const geom::Vec3& GetPos ( ) const

Get global position in cartesian coordinates with entity transformations applied.

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".

Real GetRadius ( ) const

returns the van-der-Waals radius of the atom

String GetStringProperty ( Prop::ID  prop_id) const

Get String property by id.

GenericPropContainerImpl* GpImpl ( )
protected
const GenericPropContainerImpl* GpImpl ( ) const
protected
const impl::AtomImplPtr& Impl ( ) const

get atom implementation.

Intended for internal use.

impl::AtomImplPtr& Impl ( )

get atom implementation

bool IsHetAtom ( ) const

whether the atom is a hetatm

bool IsValid ( ) const
inline

check validity of handle

See also:
operator bool()

Reimplemented in AtomView.

Definition at line 64 of file atom_base.hh.

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.

Reimplemented in AtomView.

Definition at line 61 of file atom_base.hh.

void SetAnisou ( const geom::Mat3 anisou)
void SetBFactor ( Real  factor)
void SetCharge ( Real  charge)
void SetElement ( const String element)
void SetHetAtom ( bool  het)
void SetIndex ( const unsigned long  index)
void SetMass ( Real  mass)
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
void SetOccupancy ( Real  occ)
void SetRadius ( Real  radius)

Friends And Related Function Documentation

friend class ConstGenericPropContainer< AtomBase >
friend

Definition at line 66 of file atom_base.hh.


Field Documentation

impl::AtomImplPtr impl_
protected

Definition at line 177 of file atom_base.hh.


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