AtomImpl Class Reference

Atom implementation. More...

#include <atom_impl.hh>

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
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)

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 String &	ele,
		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`
	)

const geom::Mat3& GetAnisou ( ) const [inline]

Definition at line 134 of file atom_impl.hh.

Real GetBFactor ( ) const [inline]

Definition at line 111 of file atom_impl.hh.

Real GetCharge ( ) const [inline]

Definition at line 156 of file atom_impl.hh.

int GetConnectorCount ( ) const [inline]

Definition at line 100 of file atom_impl.hh.

const String& GetElement ( ) const [inline]

Definition at line 113 of file atom_impl.hh.

EntityImplPtr GetEntity ( ) const

Real GetFloatProperty ( Prop::ID prop_id ) const

unsigned long GetIndex ( ) const [inline]

Definition at line 220 of file atom_impl.hh.

int GetIntProperty ( Prop::ID prop_id ) const

Real GetMass ( ) const [inline]

Definition at line 155 of file atom_impl.hh.

const String& GetName ( ) const [inline]

Definition at line 66 of file atom_impl.hh.

Real GetOccupancy ( ) const [inline]

Definition at line 148 of file atom_impl.hh.

const ConnectorImplP& GetPrimaryConnector ( ) const [inline]

Definition at line 80 of file atom_impl.hh.

String GetQualifiedName ( ) const

Real GetRadius ( ) const [inline]

Definition at line 153 of file atom_impl.hh.

ResidueImplPtr GetResidue ( ) const

const ConnectorImplList& GetSecondaryConnectors ( ) const [inline]

Definition at line 84 of file atom_impl.hh.

unsigned int GetState ( ) const [inline]

Definition at line 190 of file atom_impl.hh.

String GetStringProperty ( Prop::ID prop_id ) const

bool HasDefaultProps ( ) const [inline]

Definition at line 122 of file atom_impl.hh.

bool HasPrevious ( ) const [inline]

Definition at line 205 of file atom_impl.hh.

bool IsHetAtom ( ) [inline]

Definition at line 158 of file atom_impl.hh.

bool IsTraced ( ) const [inline]

Definition at line 108 of file atom_impl.hh.

bool IsVisited ( ) const [inline]

Definition at line 105 of file atom_impl.hh.

String& Name ( ) [inline]

Definition at line 63 of file atom_impl.hh.

const String& Name ( ) const [inline]

Definition at line 62 of file atom_impl.hh.

geom::Vec3& OriginalPos ( ) [inline]

Definition at line 72 of file atom_impl.hh.

const geom::Vec3& OriginalPos ( ) const [inline]

Definition at line 71 of file atom_impl.hh.

void SetAnisou ( const geom::Mat3 & anisou ) [inline]

Definition at line 123 of file atom_impl.hh.

void SetBFactor ( Real factor ) [inline]

Definition at line 138 of file atom_impl.hh.

void SetCharge ( Real charge ) [inline]

Definition at line 180 of file atom_impl.hh.

void SetElement ( const String & ele ) [inline]

Definition at line 115 of file atom_impl.hh.

void SetHetAtom ( bool het ) [inline]

Definition at line 160 of file atom_impl.hh.

void SetIndex ( unsigned long index ) [inline]

Definition at line 221 of file atom_impl.hh.

void SetMass ( Real mass ) [inline]

Definition at line 162 of file atom_impl.hh.

void SetOccupancy ( Real occ ) [inline]

Definition at line 143 of file atom_impl.hh.

void SetPrimaryConnector ( const ConnectorImplP & bp ) [inline]

Definition at line 76 of file atom_impl.hh.

void SetRadius ( Real radius ) [inline]

Definition at line 171 of file atom_impl.hh.

void SetState ( int state ) [inline]

Definition at line 195 of file atom_impl.hh.

void SetTraced ( bool f ) [inline]

Definition at line 107 of file atom_impl.hh.

void SetVisited ( bool f ) [inline]

Definition at line 104 of file atom_impl.hh.

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

trace directionality

geom::Vec3& TransformedPos ( ) [inline]

Definition at line 69 of file atom_impl.hh.

const geom::Vec3& TransformedPos ( ) const [inline]

Definition at line 68 of file atom_impl.hh.

void UpdateFromICS ( )

void UpdateFromXCS ( )

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

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

AtomImpl Class Reference

Public Member Functions

Detailed Description

Connectors

Constructor & Destructor Documentation

Member Function Documentation