AtomImpl Class Reference

#include <atom_impl.hh>

Inherits GenericPropContainerImpl, and enable_shared_from_this< AtomImpl >.

Public Member Functions
	AtomImpl (const EntityImplPtr &ent, const ResidueImplPtr &res, const String &name, const geom::Vec3 &pos, const String &ele, unsigned long index)
	~AtomImpl ()
void	Apply (EntityVisitor &h)
const String &	Name () const
String &	Name ()
const String &	GetName () const
const geom::Vec3 &	TransformedPos () const
geom::Vec3 &	TransformedPos ()
const geom::Vec3 &	OriginalPos () const
geom::Vec3 &	OriginalPos ()
ResidueImplPtr	GetResidue () const
void	SetPrimaryConnector (const ConnectorImplP &bp)
const ConnectorImplP &	GetPrimaryConnector () const
const ConnectorImplList &	GetSecondaryConnectors () const
ConnectorImplList &	GetSecondaryConnectors ()
void	AddSecondaryConnector (const ConnectorImplP &bp)
void	UpdateFromICS ()
void	UpdateFromXCS ()
String	GetQualifiedName () const
EntityImplPtr	GetEntity () const
int	GetConnectorCount () const
void	SetVisited (bool f)
bool	IsVisited () const
void	SetTraced (bool f)
bool	IsTraced () const
Real	GetBFactor () const
const String &	GetElement () const
void	SetElement (const String &ele)
bool	HasDefaultProps () const
void	SetAnisou (const geom::Mat3 &anisou)
const geom::Mat3 &	GetAnisou () const
void	SetBFactor (Real factor)
void	SetOccupancy (Real occ)
Real	GetOccupancy () const
Real	GetRadius () const
Real	GetMass () const
Real	GetCharge () const
bool	IsHetAtom ()
void	SetHetAtom (bool het)
void	SetMass (Real mass)
void	SetRadius (Real radius)
void	SetCharge (Real charge)
unsigned int	GetState () const
void	SetState (int state)
void	ClearDirectionality ()
void	TraceDirectionality (FragmentImplP frag, ConnectorImplP conn, int n, unsigned int &c)
bool	HasPrevious () const
void	DeleteAllConnectors ()
void	DeleteConnector (const ConnectorImplP &conn, bool delete_other=true)
void	DeleteAllTorsions ()
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
void	SetIndex (unsigned long index)
void	SetFragment (FragmentImplP fragment)
Public Member Functions inherited from GenericPropContainerImpl
	GenericPropContainerImpl ()
	~GenericPropContainerImpl ()
	GenericPropContainerImpl (const GenericPropContainerImpl &rhs)
GenericPropContainerImpl &	operator= (const GenericPropContainerImpl &r)
GenericPropValue &	GenericProp (const String &key)
const GenericPropValue &	GenericProp (const String &key) const
bool	HasProp (const String &key) const
void	ClearProps ()
void	RemoveProp (const String &key)
void	Assign (const GenericPropContainerImpl &impl)
PropertyMap	GetPropMap () const
std::vector< String >	GetPropList () const

Detailed Description

Atom implementation.

Connectors

each atom distinguishes between two types of connectors: primary and secondary. each atoms has at most one primary connector: this connects the atom with the atom that serves as the frame of reference for the internal coordinates. the secondary connectors connect this atom with the atoms that themselves depend on the coordinate system of this atom.

Definition at line 49 of file atom_impl.hh.

Constructor & Destructor Documentation

AtomImpl()

AtomImpl	(	const EntityImplPtr &	ent,
		const ResidueImplPtr &	res,
		const String &	name,
		const geom::Vec3 &	pos,
		const String &	ele,
		unsigned long	index
	)

~AtomImpl()

~AtomImpl

(

)

Member Function Documentation

AddSecondaryConnector()

void AddSecondaryConnector

(

const ConnectorImplP &

bp

)

Apply()

void Apply

(

EntityVisitor &

h

)

ClearDirectionality()

void ClearDirectionality

(

)

DeleteAllConnectors()

void DeleteAllConnectors

(

)

DeleteAllTorsions()

void DeleteAllTorsions

(

)

DeleteConnector()

void DeleteConnector	(	const ConnectorImplP &	conn,
		bool	delete_other = true
	)

GetAnisou()

const geom::Mat3& GetAnisou ( ) const

inline

Definition at line 144 of file atom_impl.hh.

GetBFactor()

Real GetBFactor ( ) const

inline

Definition at line 115 of file atom_impl.hh.

GetCharge()

Real GetCharge ( ) const

inline

Definition at line 166 of file atom_impl.hh.

GetConnectorCount()

int GetConnectorCount ( ) const

inline

Definition at line 104 of file atom_impl.hh.

GetElement()

const String& GetElement ( ) const

inline

Definition at line 117 of file atom_impl.hh.

GetEntity()

EntityImplPtr GetEntity

(

)

const

GetFloatProperty()

Real GetFloatProperty

(

Prop::ID

prop_id

)

const

GetIndex()

unsigned long GetIndex ( ) const

inline

Definition at line 230 of file atom_impl.hh.

GetIntProperty()

int GetIntProperty

(

Prop::ID

prop_id

)

const

GetMass()

Real GetMass ( ) const

inline

Definition at line 165 of file atom_impl.hh.

GetName()

const String& GetName ( ) const

inline

Definition at line 66 of file atom_impl.hh.

GetOccupancy()

Real GetOccupancy ( ) const

inline

Definition at line 158 of file atom_impl.hh.

GetPrimaryConnector()

const ConnectorImplP& GetPrimaryConnector ( ) const

inline

Definition at line 80 of file atom_impl.hh.

GetQualifiedName()

String GetQualifiedName

(

)

const

GetRadius()

Real GetRadius ( ) const

inline

Definition at line 163 of file atom_impl.hh.

GetResidue()

ResidueImplPtr GetResidue

(

)

const

GetSecondaryConnectors() [1/2]

ConnectorImplList& GetSecondaryConnectors ( )

inline

Definition at line 88 of file atom_impl.hh.

GetSecondaryConnectors() [2/2]

const ConnectorImplList& GetSecondaryConnectors ( ) const

inline

Definition at line 84 of file atom_impl.hh.

GetState()

unsigned int GetState ( ) const

inline

Definition at line 200 of file atom_impl.hh.

GetStringProperty()

String GetStringProperty

(

Prop::ID

prop_id

)

const

HasDefaultProps()

bool HasDefaultProps ( ) const

inline

Definition at line 132 of file atom_impl.hh.

HasPrevious()

bool HasPrevious ( ) const

inline

Definition at line 215 of file atom_impl.hh.

IsHetAtom()

bool IsHetAtom ( )

inline

Definition at line 168 of file atom_impl.hh.

IsTraced()

bool IsTraced ( ) const

inline

Definition at line 112 of file atom_impl.hh.

IsVisited()

bool IsVisited ( ) const

inline

Definition at line 109 of file atom_impl.hh.

Name() [1/2]

String& Name ( )

inline

Definition at line 63 of file atom_impl.hh.

Name() [2/2]

const String& Name ( ) const

inline

Definition at line 62 of file atom_impl.hh.

OriginalPos() [1/2]

geom::Vec3& OriginalPos ( )

inline

Definition at line 72 of file atom_impl.hh.

OriginalPos() [2/2]

const geom::Vec3& OriginalPos ( ) const

inline

Definition at line 71 of file atom_impl.hh.

SetAnisou()

void SetAnisou ( const geom::Mat3 &  anisou )

inline

Definition at line 133 of file atom_impl.hh.

SetBFactor()

void SetBFactor ( Real  factor )

inline

Definition at line 148 of file atom_impl.hh.

SetCharge()

void SetCharge ( Real  charge )

inline

Definition at line 190 of file atom_impl.hh.

SetElement()

void SetElement ( const String &  ele )

inline

Definition at line 119 of file atom_impl.hh.

SetFragment()

void SetFragment ( FragmentImplP  fragment )

inline

Definition at line 233 of file atom_impl.hh.

SetHetAtom()

void SetHetAtom ( bool  het )

inline

Definition at line 170 of file atom_impl.hh.

SetIndex()

void SetIndex ( unsigned long  index )

inline

Definition at line 231 of file atom_impl.hh.

SetMass()

void SetMass ( Real  mass )

inline

Definition at line 172 of file atom_impl.hh.

SetOccupancy()

void SetOccupancy ( Real  occ )

inline

Definition at line 153 of file atom_impl.hh.

SetPrimaryConnector()

void SetPrimaryConnector ( const ConnectorImplP &  bp )

inline

Definition at line 76 of file atom_impl.hh.

SetRadius()

void SetRadius ( Real  radius )

inline

Definition at line 181 of file atom_impl.hh.

SetState()

void SetState ( int  state )

inline

Definition at line 205 of file atom_impl.hh.

SetTraced()

void SetTraced ( bool  f )

inline

Definition at line 111 of file atom_impl.hh.

SetVisited()

void SetVisited ( bool  f )

inline

Definition at line 108 of file atom_impl.hh.

TraceDirectionality()

void TraceDirectionality	(	FragmentImplP	frag,
		ConnectorImplP	conn,
		int	n,
		unsigned int &	c
	)

trace directionality

TransformedPos() [1/2]

geom::Vec3& TransformedPos ( )

inline

Definition at line 69 of file atom_impl.hh.

TransformedPos() [2/2]

const geom::Vec3& TransformedPos ( ) const

inline

Definition at line 68 of file atom_impl.hh.

UpdateFromICS()

void UpdateFromICS

(

)

UpdateFromXCS()

void UpdateFromXCS

(

)

---

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

• build-2.9.0-doc/stage/include/ost/mol/impl/atom_impl.hh