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::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) 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)
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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The documentation for this class was generated from the following file:

• stage/include/ost/mol/impl/entity_impl.hh