AtomImpl Class Reference

Atom implementation. More...

#include <atom_impl.hh>

Inherits ost::GenericPropContainerImpl.

Public Member Functions
	AtomImpl (const EntityImplPtr &ent, const ResidueImplPtr &res, const String &name, const geom::Vec3 &pos, const AtomProp &prop, unsigned long index)
	~AtomImpl ()
void	Apply (EntityVisitor &h)
const String &	GetName () const
void	SetName (const String &atom_name)
const geom::Vec3 &	GetPos () const
const geom::Vec3 &	GetOriginalPos () const
void	SetTransformedPos (const geom::Vec3 &pos)
void	SetOriginalPos (const geom::Vec3 &pos)
const AtomProp &	GetAtomProps () const
AtomProp &	GetAtomProps ()
ResidueImplPtr	GetResidue () const
void	SetPrimaryConnector (const ConnectorImplP &bp)
const ConnectorImplP &	GetPrimaryConnector () const
const ConnectorImplList &	GetSecondaryConnectors () const
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
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)

---

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

~AtomImpl

(

)

---

Member Function Documentation

void AddSecondaryConnector

(

const ConnectorImplP &

bp

)

void Apply

(

EntityVisitor &

h

)

void ClearDirectionality

(

)

void DeleteAllConnectors

(

)

void DeleteAllTorsions

(

)

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

AtomProp& GetAtomProps

(

)

[inline]

Definition at line 76 of file atom_impl.hh.

const AtomProp& GetAtomProps

(

)

const [inline]

Definition at line 74 of file atom_impl.hh.

int GetConnectorCount

(

)

const [inline]

Definition at line 104 of file atom_impl.hh.

EntityImplPtr GetEntity

(

)

const

Real GetFloatProperty

(

Prop::ID

prop_id

)

const

unsigned long GetIndex

(

)

const [inline]

Definition at line 142 of file atom_impl.hh.

int GetIntProperty

(

Prop::ID

prop_id

)

const

const String& GetName

(

)

const [inline]

Definition at line 59 of file atom_impl.hh.

const geom::Vec3& GetOriginalPos

(

)

const [inline]

Definition at line 68 of file atom_impl.hh.

const geom::Vec3& GetPos

(

)

const [inline]

Definition at line 66 of file atom_impl.hh.

const ConnectorImplP& GetPrimaryConnector

(

)

const [inline]

Definition at line 84 of file atom_impl.hh.

String GetQualifiedName

(

)

const

ResidueImplPtr GetResidue

(

)

const

const ConnectorImplList& GetSecondaryConnectors

(

)

const [inline]

Definition at line 88 of file atom_impl.hh.

unsigned int GetState

(

)

const [inline]

Definition at line 114 of file atom_impl.hh.

String GetStringProperty

(

Prop::ID

prop_id

)

const

bool HasPrevious

(

)

const [inline]

Definition at line 127 of file atom_impl.hh.

bool IsTraced

(

)

const [inline]

Definition at line 112 of file atom_impl.hh.

bool IsVisited

(

)

const [inline]

Definition at line 109 of file atom_impl.hh.

void SetIndex

(

unsigned long

index

)

[inline]

Definition at line 143 of file atom_impl.hh.

void SetName

(

const String &

atom_name

)

[inline]

Definition at line 61 of file atom_impl.hh.

void SetOriginalPos

(

const geom::Vec3 &

pos

)

[inline]

Definition at line 72 of file atom_impl.hh.

void SetPrimaryConnector

(

const ConnectorImplP &

bp

)

[inline]

Definition at line 80 of file atom_impl.hh.

void SetState

(

int

state

)

[inline]

Definition at line 118 of file atom_impl.hh.

void SetTraced

(

bool

f

)

[inline]

Definition at line 111 of file atom_impl.hh.

void SetTransformedPos

(

const geom::Vec3 &

pos

)

[inline]

Definition at line 70 of file atom_impl.hh.

void SetVisited

(

bool

f

)

[inline]

Definition at line 108 of file atom_impl.hh.

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

trace directionality

void UpdateFromICS

(

)

void UpdateFromXCS

(

)

---

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

• stage/include/ost/mol/impl/atom_impl.hh