OpenStructure
Public Member Functions
EntityImpl Class Reference

#include <entity_impl.hh>

Inherits GenericPropContainerImpl, and enable_shared_from_this< EntityImpl >.

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::Transform & GetTransform () 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)
 
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)
 
void RenumberChain (const String &name, 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 ( )

◆ ~EntityImpl()

~EntityImpl ( )

Member Function Documentation

◆ AddTorsion()

TorsionImplP AddTorsion ( const String &  name,
const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3,
const AtomImplPtr &  a4 
)

◆ Apply()

void Apply ( EntityVisitor &  v)

◆ ApplyTransform()

void ApplyTransform ( const geom::Transform &  t)

◆ AttachObserver()

void AttachObserver ( const EntityObserverPtr &  o)

◆ ClearTransform()

void ClearTransform ( )

◆ Connect()

ConnectorImplP Connect ( const AtomImplPtr &  first,
const AtomImplPtr &  second,
Real  len,
Real  theta,
Real  phi,
unsigned char  bond_order 
)

◆ Copy()

EntityImplPtr Copy ( )

copy entity

◆ CreateAtom()

AtomImplPtr CreateAtom ( const ResidueImplPtr &  rp,
const String &  name,
const geom::Vec3 &  pos,
const String &  ele 
)

◆ CreateFullView()

EntityView CreateFullView ( const EntityHandle &  h) const

◆ CreateResidue()

ResidueImplPtr CreateResidue ( const ChainImplPtr &  cp,
const ResNum &  n,
const ResidueKey &  k 
)

◆ DecICSEditorCount()

void DecICSEditorCount ( )

◆ DecXCSEditorCount()

void DecXCSEditorCount ( )

◆ DeleteAtom()

void DeleteAtom ( const AtomImplPtr &  atom)

◆ DeleteChain()

void DeleteChain ( const ChainImplPtr &  chain)

◆ DeleteFromConnMap()

void DeleteFromConnMap ( const ConnectorImplP &  conn)

◆ DetachObserver()

void DetachObserver ( const EntityObserverPtr &  o)

◆ EnableICS()

void EnableICS ( )

◆ FindAtom()

AtomImplPtr FindAtom ( const String &  chain_name,
const ResNum &  residue,
const String &  atom_name 
) const

◆ FindChain()

ChainImplPtr FindChain ( const String &  name) const

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

◆ FindResidue()

ResidueImplPtr FindResidue ( const String &  chain_name,
const ResNum &  residue 
) const

◆ FindTorsion()

TorsionImplP FindTorsion ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3,
const AtomImplPtr &  a4 
) const

Search for torsion.

◆ FindWithin()

AtomImplList FindWithin ( const geom::Vec3 &  pos,
Real  radius 
)

◆ FixTransform()

void FixTransform ( )

◆ GetAngle()

Real GetAngle ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3 
) const

◆ GetAngleICS()

Real GetAngleICS ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3 
) const

◆ GetAngleXCS()

Real GetAngleXCS ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3 
) const

◆ GetAtomCount()

int GetAtomCount ( ) const

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

◆ GetBondCount()

int GetBondCount ( ) const

Get total number of bonds belonging to this entity.

◆ GetBondList()

mol::BondHandleList GetBondList ( ) const

Get list of bonds.

◆ GetBounds()

geom::AlignedCuboid GetBounds ( ) const

returns the axis-aligned bounding box of the entity

◆ GetCenterOfAtoms()

geom::Vec3 GetCenterOfAtoms ( ) const

◆ GetCenterOfMass()

geom::Vec3 GetCenterOfMass ( ) const

◆ GetChain()

impl::ChainImplList::iterator GetChain ( const String &  name)

◆ GetChainCount()

int GetChainCount ( ) const

Get number of chains.

◆ GetChainIter()

pointer_it<ChainImplPtr> GetChainIter ( const String &  name)

◆ GetChainList() [1/2]

ChainImplList& GetChainList ( )
inline

Definition at line 209 of file entity_impl.hh.

◆ GetChainList() [2/2]

const ChainImplList& GetChainList ( ) const
inline

Definition at line 207 of file entity_impl.hh.

◆ GetDefaultQueryFlags()

QueryFlags GetDefaultQueryFlags ( ) const
inline

Definition at line 171 of file entity_impl.hh.

◆ GetMass()

Real GetMass ( ) const

◆ GetName()

const String& GetName ( ) const

◆ GetResidueCount()

int GetResidueCount ( ) const

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

◆ GetTorsionMap()

TorsionImplMap& GetTorsionMap ( )

◆ GetTransform()

const geom::Transform& GetTransform ( ) const
inline

Definition at line 151 of file entity_impl.hh.

◆ HasICS()

bool HasICS ( ) const

◆ HasTransform()

bool HasTransform ( ) const
inline

Definition at line 152 of file entity_impl.hh.

◆ IncICSEditorCount()

void IncICSEditorCount ( )

◆ IncXCSEditorCount()

void IncXCSEditorCount ( )

◆ InsertChain() [1/2]

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

◆ InsertChain() [2/2]

ChainImplPtr InsertChain ( const String &  cname)

◆ IsXCSDirty()

bool IsXCSDirty ( ) const

◆ MarkICSDirty()

void MarkICSDirty ( )

◆ MarkOrganizerDirty()

void MarkOrganizerDirty ( )

◆ MarkTraceDirty()

void MarkTraceDirty ( )

◆ MarkXCSDirty()

void MarkXCSDirty ( )

◆ NotifyObserver()

void NotifyObserver ( )

◆ RenameChain()

void RenameChain ( ChainImplPtr  chain,
const String &  new_name 
)

◆ RenumberAllResidues()

void RenumberAllResidues ( int  start,
bool  keep_spacing 
)

◆ RenumberChain()

void RenumberChain ( const String &  name,
int  start,
bool  keep_spacing 
)

◆ ReorderAllResidues()

void ReorderAllResidues ( )

◆ Select() [1/2]

EntityView Select ( const EntityHandle &  h,
const Query &  q 
) const

◆ Select() [2/2]

EntityView Select ( const EntityHandle &  h,
const Query &  q,
QueryFlags  flags 
) const

◆ SetAngle()

bool SetAngle ( const AtomImplPtr &  a1,
const AtomImplPtr &  a2,
const AtomImplPtr &  a3,
Real  angle 
)

◆ SetDefaultQueryFlags()

void SetDefaultQueryFlags ( QueryFlags  f)
inline

Definition at line 170 of file entity_impl.hh.

◆ SetName()

void SetName ( const String &  ent_name)

◆ SetTransform()

void SetTransform ( const geom::Transform &  t)

◆ Swap()

void Swap ( EntityImpl &  impl)

◆ TraceDirectionality()

void TraceDirectionality ( )

◆ UpdateFromICS()

void UpdateFromICS ( )

◆ UpdateFromXCS()

void UpdateFromXCS ( )

◆ UpdateICSIfNeeded()

void UpdateICSIfNeeded ( )

◆ UpdateOrganizer()

void UpdateOrganizer ( )

◆ UpdateOrganizerIfNeeded()

void UpdateOrganizerIfNeeded ( )

◆ UpdateTransformedPos()

void UpdateTransformedPos ( )

◆ UpdateXCSIfNeeded()

void UpdateXCSIfNeeded ( )
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