EntityImpl Class Reference

#include <entity_impl.hh>

Inherits ost::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 String &chain_name, 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::TransformGetTransform () const
bool HasTransform () const
void ClearTransform ()
void FixTransform ()
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 ChainImplListGetChainList () const
ChainImplListGetChainList ()
void DeleteFromConnMap (const ConnectorImplP &conn)
void DeleteChain (const ChainImplPtr &chain)
void DeleteAtom (const AtomImplPtr &atom)
void IncXCSEditorCount ()
void DecXCSEditorCount ()
void IncICSEditorCount ()
void DecICSEditorCount ()
TorsionImplMapGetTorsionMap ()
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 StringGetName () const
impl::ChainImplList::iterator GetChain (const String &name)
pointer_it< ChainImplPtrGetChainIter (const String &name)
void SetName (const String &ent_name)
void ReorderAllResidues ()
void RenumberAllResidues (int start, bool keep_spacing)
void RenumberChain (const String &name, int start, bool keep_spacing)

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
void FixTransform (  ) 
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  ) 
ChainImplList& GetChainList (  )  [inline]

Definition at line 209 of file entity_impl.hh.

const ChainImplList& GetChainList (  )  const [inline]

Definition at line 207 of file entity_impl.hh.

QueryFlags GetDefaultQueryFlags (  )  const [inline]

Definition at line 171 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 chain_name,
const ChainImplPtr chain,
bool  deep 
)

insert a new chain based on parameters of the given chain

The chain will have no residues and atoms

ChainImplPtr InsertChain ( const String cname  ) 
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 RenumberChain ( const String name,
int  start,
bool  keep_spacing 
)
void ReorderAllResidues (  ) 
EntityView Select ( const EntityHandle h,
const Query q,
QueryFlags  flags 
) const
EntityView Select ( const EntityHandle h,
const Query q 
) const
bool SetAngle ( const AtomImplPtr a1,
const AtomImplPtr a2,
const AtomImplPtr a3,
Real  angle 
)
void SetDefaultQueryFlags ( QueryFlags  f  )  [inline]

Definition at line 170 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 (  ) 

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