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Public Member Functions
EntityImpl Class Reference

#include <entity_impl.hh>

Inherits GenericPropContainerImpl.

Public Member Functions

 EntityImpl ()
 ~EntityImpl ()
EntityImplPtr Copy ()
Real GetMass () const
geom::Vec3 GetCenterOfMass () const
geom::Vec3 GetCenterOfAtoms () const
geom::AlignedCuboid GetBounds () const
AtomImplPtr CreateAtom (const ResidueImplPtr &rp, const String &name, const geom::Vec3 &pos, const String &ele)
ResidueImplPtr CreateResidue (const ChainImplPtr &cp, const ResNum &n, const ResidueKey &k)
ChainImplPtr InsertChain (const String &cname)
ChainImplPtr InsertChain (const ChainImplPtr &chain, bool deep)
ConnectorImplP Connect (const AtomImplPtr &first, const AtomImplPtr &second, Real len, Real theta, Real phi, unsigned char bond_order)
TorsionImplP AddTorsion (const String &name, const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, const AtomImplPtr &a4)
void TraceDirectionality ()
TorsionImplP FindTorsion (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, const AtomImplPtr &a4) const
void RenameChain (ChainImplPtr chain, const String &new_name)
bool SetAngle (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3, Real angle)
Real GetAngle (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const
Real GetAngleXCS (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const
Real GetAngleICS (const AtomImplPtr &a1, const AtomImplPtr &a2, const AtomImplPtr &a3) const
void UpdateFromICS ()
void UpdateFromXCS ()
void Apply (EntityVisitor &v)
void ApplyTransform (const geom::Transform &t)
void SetTransform (const geom::Transform &t)
const geom::Transform & GetTransform () const
bool HasTransform () const
void ClearTransform ()
void AttachObserver (const EntityObserverPtr &o)
void DetachObserver (const EntityObserverPtr &o)
void NotifyObserver ()
void UpdateOrganizer ()
AtomImplList FindWithin (const geom::Vec3 &pos, Real radius) const
EntityView Select (const EntityHandle &h, const Query &q) const
EntityView Select (const EntityHandle &h, const Query &q, QueryFlags flags) const
EntityView CreateFullView (const EntityHandle &h) const
void SetDefaultQueryFlags (QueryFlags f)
QueryFlags GetDefaultQueryFlags () const
ChainImplPtr FindChain (const String &name) const
ResidueImplPtr FindResidue (const String &chain_name, const ResNum &residue) const
AtomImplPtr FindAtom (const String &chain_name, const ResNum &residue, const String &atom_name) const
void Swap (EntityImpl &impl)
int GetAtomCount () const
int GetBondCount () const
mol::BondHandleList GetBondList () const
int GetResidueCount () const
int GetChainCount () const
const ChainImplList & GetChainList () const
ChainImplList & GetChainList ()
void DeleteFromConnMap (const ConnectorImplP &conn)
void DeleteChain (const ChainImplPtr &chain)
void DeleteAtom (const AtomImplPtr &atom)
void IncXCSEditorCount ()
void DecXCSEditorCount ()
void IncICSEditorCount ()
void DecICSEditorCount ()
TorsionImplMap & GetTorsionMap ()
void UpdateXCSIfNeeded ()
void UpdateICSIfNeeded ()
void UpdateOrganizerIfNeeded ()
void EnableICS ()
bool HasICS () const
bool IsXCSDirty () const
void MarkXCSDirty ()
void MarkICSDirty ()
void MarkTraceDirty ()
void MarkOrganizerDirty ()
void UpdateTransformedPos ()
const String & GetName () const
impl::ChainImplList::iterator GetChain (const String &name)
pointer_it< ChainImplPtr > GetChainIter (const String &name)
void SetName (const String &ent_name)
void ReorderAllResidues ()
void RenumberAllResidues (int start, bool keep_spacing)
- 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

Definition at line 82 of file entity_impl.hh.

Constructor & Destructor Documentation

EntityImpl ( )
~EntityImpl ( )

Member Function Documentation

TorsionImplP AddTorsion ( const String &  name,
const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3,
const AtomImplPtr &  a4 
)
void Apply ( EntityVisitor &  v)
void ApplyTransform ( const geom::Transform &  t)
void AttachObserver ( const EntityObserverPtr &  o)
void ClearTransform ( )
ConnectorImplP Connect ( const AtomImplPtr &  first,
const AtomImplPtr &  second,
Real  len,
Real  theta,
Real  phi,
unsigned char  bond_order 
)
EntityImplPtr Copy ( )

copy entity

AtomImplPtr CreateAtom ( const ResidueImplPtr &  rp,
const String &  name,
const geom::Vec3 &  pos,
const String &  ele 
)
EntityView CreateFullView ( const EntityHandle &  h) const
ResidueImplPtr CreateResidue ( const ChainImplPtr &  cp,
const ResNum &  n,
const ResidueKey &  k 
)
void DecICSEditorCount ( )
void DecXCSEditorCount ( )
void DeleteAtom ( const AtomImplPtr &  atom)
void DeleteChain ( const ChainImplPtr &  chain)
void DeleteFromConnMap ( const ConnectorImplP &  conn)
void DetachObserver ( const EntityObserverPtr &  o)
void EnableICS ( )
AtomImplPtr FindAtom ( const String &  chain_name,
const ResNum &  residue,
const String &  atom_name 
) const
ChainImplPtr FindChain ( const String &  name) const

Get chain by name. Returns an invalid ChainImplPtr if no chain with the given name exists.

ResidueImplPtr FindResidue ( const String &  chain_name,
const ResNum &  residue 
) const
TorsionImplP FindTorsion ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3,
const AtomImplPtr &  a4 
) const

Search for torsion.

AtomImplList FindWithin ( const geom::Vec3 &  pos,
Real  radius 
) const
Real GetAngle ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3 
) const
Real GetAngleICS ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3 
) const
Real GetAngleXCS ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3 
) const
int GetAtomCount ( ) const

Get total number of atoms of all chains belonging to this entity.

int GetBondCount ( ) const

Get total number of bonds belonging to this entity.

mol::BondHandleList GetBondList ( ) const

Get list of bonds.

geom::AlignedCuboid GetBounds ( ) const

returns the axis-aligned bounding box of the entity

geom::Vec3 GetCenterOfAtoms ( ) const
geom::Vec3 GetCenterOfMass ( ) const
impl::ChainImplList::iterator GetChain ( const String &  name)
int GetChainCount ( ) const

Get number of chains.

pointer_it<ChainImplPtr> GetChainIter ( const String &  name)
const ChainImplList& GetChainList ( ) const
inline

Definition at line 206 of file entity_impl.hh.

ChainImplList& GetChainList ( )
inline

Definition at line 208 of file entity_impl.hh.

QueryFlags GetDefaultQueryFlags ( ) const
inline

Definition at line 170 of file entity_impl.hh.

Real GetMass ( ) const
const String& GetName ( ) const
int GetResidueCount ( ) const

Get total number of residues of all chains belonging to this entity.

TorsionImplMap& GetTorsionMap ( )
const geom::Transform& GetTransform ( ) const
inline

Definition at line 151 of file entity_impl.hh.

bool HasICS ( ) const
bool HasTransform ( ) const
inline

Definition at line 152 of file entity_impl.hh.

void IncICSEditorCount ( )
void IncXCSEditorCount ( )
ChainImplPtr InsertChain ( const String &  cname)
ChainImplPtr InsertChain ( const ChainImplPtr &  chain,
bool  deep 
)

insert a new chain based on parameters of the given chain

The chain will have no residues and atoms

bool IsXCSDirty ( ) const
void MarkICSDirty ( )
void MarkOrganizerDirty ( )
void MarkTraceDirty ( )
void MarkXCSDirty ( )
void NotifyObserver ( )
void RenameChain ( ChainImplPtr  chain,
const String &  new_name 
)
void RenumberAllResidues ( int  start,
bool  keep_spacing 
)
void ReorderAllResidues ( )
EntityView Select ( const EntityHandle &  h,
const Query &  q 
) const
EntityView Select ( const EntityHandle &  h,
const Query &  q,
QueryFlags  flags 
) const
bool SetAngle ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3,
Real  angle 
)
void SetDefaultQueryFlags ( QueryFlags  f)
inline

Definition at line 169 of file entity_impl.hh.

void SetName ( const String &  ent_name)
void SetTransform ( const geom::Transform &  t)
void Swap ( EntityImpl &  impl)
void TraceDirectionality ( )
void UpdateFromICS ( )
void UpdateFromXCS ( )
void UpdateICSIfNeeded ( )
void UpdateOrganizer ( )
void UpdateOrganizerIfNeeded ( )
void UpdateTransformedPos ( )
void UpdateXCSIfNeeded ( )
The documentation for this class was generated from the following file:
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