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 String &ele, unsigned long index)
 ~AtomImpl ()
void Apply (EntityVisitor &h)
const StringName () const
StringName ()
const StringGetName () const
const geom::Vec3TransformedPos () const
geom::Vec3TransformedPos ()
const geom::Vec3OriginalPos () const
geom::Vec3OriginalPos ()
ResidueImplPtr GetResidue () const
void SetPrimaryConnector (const ConnectorImplP &bp)
const ConnectorImplPGetPrimaryConnector () const
const ConnectorImplListGetSecondaryConnectors () 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 StringGetElement () const
void SetElement (const String &ele)
bool HasDefaultProps () const
void SetAnisou (const geom::Mat3 &anisou)
const geom::Mat3GetAnisou () 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:
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