OpenStructure
Public Member Functions
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 ( )
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