#include <entity_view.hh>

Inherits EntityBase.

Public Member Functions
	EntityView ()

	EntityView (const EntityHandle &entity, ViewAddFlags flags=0)

View validity
	operator bool () const

bool	IsValid () const

Real	GetMass () const

geom::Vec3	GetCenterOfMass () const

geom::Vec3	GetCenterOfAtoms () const

geom::AlignedCuboid	GetBounds () const

Public Member Functions inherited from EntityBase
	EntityBase (const impl::EntityImplPtr &impl)

	EntityBase ()

const String &	GetName () const

void	SetName (const String &ent_name)

	operator bool () const

bool	IsValid () const

impl::EntityImplPtr &	Impl ()

const impl::EntityImplPtr &	Impl () const

Public Member Functions inherited from GenericPropContainer< EntityBase >
void	ClearProps ()

void	SetStringProp (const String &key, const String &value)

void	SetFloatProp (const String &key, Real value)

void	SetIntProp (const String &key, int value)

void	SetBoolProp (const String &key, bool value)

void	SetVec3Prop (const String &key, geom::Vec3 value)

void	RemoveProp (const String &key)

Public Member Functions inherited from ConstGenericPropContainer< H >
bool	HasProp (const String &key) const

String	GetPropAsString (const String &key) const

String	GetStringProp (const String &key) const

Real	GetFloatProp (const String &key) const

int	GetIntProp (const String &key) const

bool	GetBoolProp (const String &key) const

geom::Vec3	GetVec3Prop (const String &key) const

String	GetStringProp (const String &key, const String &def) const

Real	GetFloatProp (const String &key, Real def) const

int	GetIntProp (const String &key, int def) const

bool	GetBoolProp (const String &key, bool def) const

std::map< String, GenericPropValue >	GetPropMap () const

std::vector< String >	GetPropList () const

Friends
class	AtomView

class	ResidueView

Related Functions
(Note that these are not member functions.)
EntityView DLLEXPORT_OST_MOL	Union (const EntityView &ev1, const EntityView &ev2)

EntityView DLLEXPORT_OST_MOL	Difference (const EntityView &ev1, const EntityView &ev2)

EntityView DLLEXPORT_OST_MOL	Intersection (const EntityView &ev1, const EntityView &ev2)

EntityView DLLEXPORT_OST_MOL	CreateViewFromAtomList (const AtomHandleList &atoms)

EntityView DLLEXPORT_OST_MOL	CreateViewFromAtomList (const AtomViewList &atoms)

Internal
	EntityView (const EntityViewDataPtr &data, const impl::EntityImplPtr impl)

const EntityViewDataPtr &	ViewData () const

EntityViewDataPtr &	ViewData ()

EntityView	Copy () const

ChainView	AddChain (const ChainHandle &chain_handle, ViewAddFlags flags=0)

ChainView	AddChain (const ChainView &chain_view, ViewAddFlags flags=0)

ResidueView	AddResidue (const ResidueHandle &residue_handle, ViewAddFlags flags=0)

ResidueView	AddResidue (const ResidueView &residue_view, ViewAddFlags flags=0)

AtomView	AddAtom (const AtomHandle &atom_handle, ViewAddFlags flags=0)

AtomView	AddAtom (const AtomView &atom_view, ViewAddFlags flags=0)

EntityView	Select (const String &query_string, QueryFlags flags=0) const

EntityView	Select (const Query &query, QueryFlags flags=0) const

bool	AddBond (const BondHandle &bond_handle)

int	GetAtomCount () const

int	GetResidueCount () const

int	GetChainCount () const

ChainView	FindChain (const String &chain_name) const

ResidueView	FindResidue (const ResidueHandle &residue) const

ResidueView	FindResidue (const String &chain, const ResNum &num) const

ResidueView	ViewForHandle (const ResidueHandle &residue) const

AtomView	FindAtom (const AtomHandle &atom) const

AtomView	ViewForHandle (const AtomHandle &atom) const

AtomView	FindAtom (const String &chain_name, const ResNum &num, const String &atom_name) const

ChainView	FindChain (const ChainHandle &chain) const

ChainView	ViewForHandle (const ChainHandle &chain) const

bool	IsChainIncluded (const ChainHandle &chain) const

void	RemoveAtom (AtomView view)

void	RemoveResidue (ResidueView view)

void	RemoveChain (ChainView view)

void	AddAllInclusiveBonds ()

const BondHandleList &	GetBondList () const

AtomViewList	FindWithin (const geom::Vec3 &center, Real radius) const

int	GetBondCount () const

const ChainViewList &	GetChainList () const

ResidueViewList	GetResidueList () const

AtomViewList	GetAtomList () const

void	Apply (EntityVisitor &visitor)

void	Apply (EntityViewVisitor &visitor)

EntityHandle	GetHandle () const

std::pair< Real, Real >	GetMinMax (const String &prop, Prop::Level hint=Prop::UNSPECIFIED) const

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

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

EntityView	ExtendViewToResidues () const

EntityView	ExtendViewToSurrounding (Real gap) const

String	Dump () const

EntityView	CreateFullView () const

EntityView	CreateEmptyView () const

bool	HasAtoms () const

void	RemoveBond (const BondHandle &bond)

void	AddAtomInternal (const AtomView &av)

void	RemoveAtomInternal (const AtomView &av)

Additional Inherited Members
Protected Member Functions inherited from EntityBase
GenericPropContainerImpl *	GpImpl ()

const GenericPropContainerImpl *	GpImpl () const

void	CheckValidity () const

Protected Member Functions inherited from ConstGenericPropContainer< H >
template<typename T >
T	gp_get (const String &key) const

template<typename T >
T	gp_get (const String &key, const T &def) const

GenericPropContainerImpl *	GetImpl ()

const GenericPropContainerImpl *	GetImpl () const

Detailed Description

definition of EntityView

Views

Views are very widely used as an input to algorithms and the link between graphical objects and entities.

Views point to the same data as their corresponding handle classes. When modifying and entity, such as applying a coordinate transform to the atoms, these changes will also be reflected in the views.

The entity - chain -residue - atom hierarchy of the entity handles is replicated in the views, the most important difference being that not all atoms, residues and chains present in the entity must be present in the view. One can think of the views as a selection.

Creating Views

Views can be assembled in several different ways: To create a full view containing all the atoms, residues, chains and bonds of the entity, use EntityHandle::CreateFullView(), an empty view containing basically nothing is created with EntityHandle::CreateEmptyView().

Elements can be added with EntitView::AddAtom(), EntityView::AddResidue(), EntityView::AddChain(). The behaviour of these methods is influenced by a combination of ViewAddFlag. Note that none of the add methods insert bonds. Bonds can be added with EntityView::AddAllInclusiveBonds() or manually with EntityView::AddBond(). The elements can be removed with EntityView::RemoveChain(), EntityView::RemoveResidue() and EntityView::RemoveAtom().

A very convenient way to create views is with so-called Query query statements. The queries are executed via EntityHandle::Select() and EntityView::Select().

Boolean Operations on Views

Two views can be combined by applying boolean operators such as Union(), Intersection() and Difference().

Definition at line 86 of file entity_view.hh.

Constructor & Destructor Documentation

◆ EntityView() [1/3]

EntityView ( )

◆ EntityView() [2/3]

EntityView	(	const EntityHandle &	entity,
		ViewAddFlags	flags = `0`
	)

explicit

create new entity view from entity handle

Parameters

entity	The handle the view is created from.
flags	An ORed together list of ViewAddFlag

◆ EntityView() [3/3]

EntityView	(	const EntityViewDataPtr &	data,
		const impl::EntityImplPtr	impl
	)

construct entity view from data and entity impl

Member Function Documentation

◆ AddAllInclusiveBonds()

void AddAllInclusiveBonds ( )

clear bonds and add all inclusive ones (ie where both atoms are present)

◆ AddAtom() [1/2]

AtomView AddAtom	(	const AtomHandle &	atom_handle,
		ViewAddFlags	flags = `0`
	)

Add atom to view.

If the atom's chain or residue have not been added to the view, they will be added

Parameters

atom_handle	is the atom to add
flags	can be a ORed together combination of ViewAddFlag

Returns: The added atom view, or a reference to the existing atom view that points to the very same handle.

◆ AddAtom() [2/2]

AtomView AddAtom	(	const AtomView &	atom_view,
		ViewAddFlags	flags = `0`
	)

◆ AddAtomInternal()

void AddAtomInternal ( const AtomView & av )

protected

◆ AddBond()

bool AddBond ( const BondHandle & bond_handle )

Add a bond.

◆ AddChain() [1/2]

ChainView AddChain	(	const ChainHandle &	chain_handle,
		ViewAddFlags	flags = `0`
	)

Add chain to view.

If ViewAddFlag::CHECK_DUPLICATES is set, the method will ensure that the handle is not already included in the view.

Parameters

chain_handle	The chain handle to add
flags	Can be a ORed together combination of ViewAddFlag

Returns: The added chain view, or a reference to the existing chain view that points to the very same handle.

◆ AddChain() [2/2]

ChainView AddChain	(	const ChainView &	chain_view,
		ViewAddFlags	flags = `0`
	)

Add chain to view.

Same as AddChain(const ChainHandle&) but with the difference that only the residues or atoms included in the chain view are included when one of ViewAddFlag::INCLUDE_ATOMS or ViewAddFlag::INCLUDE_RESIDUES is set.

Parameters

chain_view	the handle that the view points to will be added to the view.
flags	can be a ORed together combination of ViewAddFlag

Returns: The added chain view, or a reference to the existing chain view that points to the very same handle.

◆ AddResidue() [1/2]

ResidueView AddResidue	(	const ResidueHandle &	residue_handle,
		ViewAddFlags	flags = `0`
	)

Add residue to view.

If the residues's chain has not been added to the chain already, it will be added.

Parameters

residue_handle	is the residue to add
flags	can be a ORed together combination of ViewAddFlag

Returns: The added residue view, or a reference to the existing residue view that points to the very same handle.

◆ AddResidue() [2/2]

ResidueView AddResidue	(	const ResidueView &	residue_view,
		ViewAddFlags	flags = `0`
	)

Add residue to view.

Same as AddReside(const ResidueHandle&, ViewAddFlags) but with the difference that only atoms included in the residue view are added when ViewAddFlag::INCLUDE_ATOMS is set.

See also: AddResidue(const ResidueHandle&, ViewAddFlags)

◆ Apply() [1/2]

void Apply ( EntityViewVisitor & visitor )

Apply entity view visitor to whole view.

◆ Apply() [2/2]

void Apply ( EntityVisitor & visitor )

Apply entity visitor to whole view.

◆ Copy()

EntityView Copy ( ) const

create copy of view

The copy has the semantics of a deep copy.

◆ CreateEmptyView()

EntityView CreateEmptyView ( ) const

create empty view

◆ CreateFullView()

EntityView CreateFullView ( ) const

create a new full view

This is an alias of EntityView::Copy()

◆ Dump()

String Dump ( ) const

returns a string containing a human-readable summary of the entity view

◆ ExtendViewToResidues()

EntityView ExtendViewToResidues ( ) const

Extend current view to include all atoms of each residue where at least one atom is selected currently.

◆ ExtendViewToSurrounding()

EntityView ExtendViewToSurrounding ( Real gap ) const

Extend current view to include all atoms that are within the sum of their vdw radii + gap.

Include all atoms within: at1.GetRadius() + at2.GetRadius() + gap

◆ FindAtom() [1/2]

AtomView FindAtom ( const AtomHandle & atom ) const

Find view for given atom handle.

deprecated. Use ViewForHandle instead

◆ FindAtom() [2/2]

AtomView FindAtom	(	const String &	chain_name,
		const ResNum &	num,
		const String &	atom_name
	)		const

locate atom view for given atom handle

returns an invalid AtomView if the residue could not be located in the structure

◆ FindChain() [1/2]

ChainView FindChain ( const ChainHandle & chain ) const

Find chain for given chain handle.

deprecated: Use ViewForHandle instead

◆ FindChain() [2/2]

ChainView FindChain ( const String & chain_name ) const

Find chain by name.

◆ FindResidue() [1/2]

ResidueView FindResidue ( const ResidueHandle & residue ) const

Find atom for given residue handle.

deprecated. Use ViewForHandle instead

◆ FindResidue() [2/2]

ResidueView FindResidue	(	const String &	chain,
		const ResNum &	num
	)		const

◆ FindWithin()

AtomViewList FindWithin	(	const geom::Vec3 &	center,
		Real	radius
	)		const

find atoms close to point

◆ GetAngle() [1/2]

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

Get angle in radians between bonds a1-a2 and a2-a3.

◆ GetAngle() [2/2]

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

Get angle in radians between bonds a1-a2 and a2-a3.

◆ GetAtomCount()

int GetAtomCount ( ) const

Get total number of atoms in this entity.

◆ GetAtomList()

AtomViewList GetAtomList ( ) const

Get list of all atoms included in the view.

◆ GetBondCount()

int GetBondCount ( ) const

Get number of bonds.

◆ GetBondList()

const BondHandleList& GetBondList ( ) const

◆ GetBounds()

geom::AlignedCuboid GetBounds ( ) const

◆ GetCenterOfAtoms()

geom::Vec3 GetCenterOfAtoms ( ) const

Get entity's center of atoms (not mass weighted)

Returns the center of all the atoms in an entity. This is similar to GetCenterOfMass(), but the atoms are not mass weighted

◆ GetCenterOfMass()

geom::Vec3 GetCenterOfMass ( ) const

Get entity's center of mass (mass weighted)

◆ GetChainCount()

int GetChainCount ( ) const

Get number of chains in this entity.

◆ GetChainList()

const ChainViewList& GetChainList ( ) const

◆ GetHandle()

EntityHandle GetHandle ( ) const

Get handle this view points to.

◆ GetMass()

Real GetMass ( ) const

Get entity's mass.

◆ GetMinMax()

std::pair<Real,Real> GetMinMax	(	const String &	prop,
		Prop::Level	hint = `Prop::UNSPECIFIED`
	)		const

Return the min/max pair for the given property.

◆ GetResidueCount()

int GetResidueCount ( ) const

Get total number of residues in this entity.

◆ GetResidueList()

ResidueViewList GetResidueList ( ) const

Get list of all residues included in the view.

◆ HasAtoms()

bool HasAtoms ( ) const

true if view contains at least one atom

◆ IsChainIncluded()

bool IsChainIncluded ( const ChainHandle & chain ) const

Check whether the view includes the given chain.

Returns: True, if the chain is included in the view, false if not.

◆ IsValid()

bool IsValid ( ) const

inline

check validity of handle

See also: operator bool()

Definition at line 109 of file entity_view.hh.

◆ operator bool()

operator bool ( ) const

inline

check validity of handle

check, whether the entity view points to a valid entity.

Note: It is an error to use any method other than IsValid, Impl and operator bool() when the handle is invalid. An InvalidHandle exception will be thrown.

Definition at line 106 of file entity_view.hh.

◆ RemoveAtom()

void RemoveAtom ( AtomView view )

remove atom from view

◆ RemoveAtomInternal()

void RemoveAtomInternal ( const AtomView & av )

protected

◆ RemoveBond()

void RemoveBond ( const BondHandle & bond )

◆ RemoveChain()

void RemoveChain ( ChainView view )

remove chain from view

◆ RemoveResidue()

void RemoveResidue ( ResidueView view )

remove residue from view

◆ Select() [1/2]

EntityView Select	(	const Query &	query,
		QueryFlags	flags = `0`
	)		const

Select a structural subset of the entity view.

See also: Query

◆ Select() [2/2]

EntityView Select	(	const String &	query_string,
		QueryFlags	flags = `0`
	)		const

Select a structural subset of the entity view.

See also: Query

◆ ViewData() [1/2]

EntityViewDataPtr& ViewData ( )

Get entity view-specific data.

◆ ViewData() [2/2]

const EntityViewDataPtr& ViewData ( ) const

Get entity view-specific data.

◆ ViewForHandle() [1/3]

AtomView ViewForHandle ( const AtomHandle & atom ) const

◆ ViewForHandle() [2/3]

ChainView ViewForHandle ( const ChainHandle & chain ) const

locate chain view for given chain handle

returns an invalid AtomView if the residue could not be located in the structure

◆ ViewForHandle() [3/3]

ResidueView ViewForHandle ( const ResidueHandle & residue ) const

locate residue view for given residue handle

returns an invalid ResidueView if the residue could not be located in the structure

Friends And Related Function Documentation

◆ AtomView

friend class AtomView

friend

Definition at line 87 of file entity_view.hh.

◆ CreateViewFromAtomList() [1/2]

EntityView DLLEXPORT_OST_MOL CreateViewFromAtomList ( const AtomHandleList & atoms )

Exceptions

IntegrityError if atoms belonging to different entities are encountered

◆ CreateViewFromAtomList() [2/2]

EntityView DLLEXPORT_OST_MOL CreateViewFromAtomList ( const AtomViewList & atoms )

Exceptions

IntegrityError if atoms belonging to different entities are encountered

◆ Difference()

EntityView DLLEXPORT_OST_MOL Difference	(	const EntityView &	ev1,
		const EntityView &	ev2
	)

a view containing elements in ev1 but not in ev2 is returned.

◆ Intersection()

EntityView DLLEXPORT_OST_MOL Intersection	(	const EntityView &	ev1,
		const EntityView &	ev2
	)

a view containing elements in ev1 and ev2 is returned

◆ ResidueView

friend class ResidueView

friend

Definition at line 88 of file entity_view.hh.

◆ Union()

EntityView DLLEXPORT_OST_MOL Union	(	const EntityView &	ev1,
		const EntityView &	ev2
	)

a view containing elements that are either in ev1 or ev2 are included. no duplicates are generated.

The documentation for this class was generated from the following files:

build-2.9.0-doc/stage/include/ost/mol/entity_view.hh
build-2.9.0-doc/stage/include/ost/mol/view_op.hh

Public Member Functions

Friends

Related Functions

Internal

Additional Inherited Members

Detailed Description

Views

Creating Views

Boolean Operations on Views

Constructor & Destructor Documentation

◆ EntityView() [1/3]

◆ EntityView() [2/3]

◆ EntityView() [3/3]

Member Function Documentation

◆ AddAllInclusiveBonds()

◆ AddAtom() [1/2]

◆ AddAtom() [2/2]

◆ AddAtomInternal()

◆ AddBond()

◆ AddChain() [1/2]

◆ AddChain() [2/2]

◆ AddResidue() [1/2]

◆ AddResidue() [2/2]

◆ Apply() [1/2]

◆ Apply() [2/2]

◆ Copy()

◆ CreateEmptyView()

◆ CreateFullView()

◆ Dump()

◆ ExtendViewToResidues()

◆ ExtendViewToSurrounding()

◆ FindAtom() [1/2]

◆ FindAtom() [2/2]

◆ FindChain() [1/2]

◆ FindChain() [2/2]

◆ FindResidue() [1/2]

◆ FindResidue() [2/2]

◆ FindWithin()

◆ GetAngle() [1/2]

◆ GetAngle() [2/2]

◆ GetAtomCount()

◆ GetAtomList()

◆ GetBondCount()

◆ GetBondList()

◆ GetBounds()

◆ GetCenterOfAtoms()

◆ GetCenterOfMass()

◆ GetChainCount()

◆ GetChainList()

◆ GetHandle()

◆ GetMass()

◆ GetMinMax()

◆ GetResidueCount()

◆ GetResidueList()

◆ HasAtoms()

◆ IsChainIncluded()

◆ IsValid()

◆ operator bool()

◆ RemoveAtom()

◆ RemoveAtomInternal()

◆ RemoveBond()

◆ RemoveChain()

◆ RemoveResidue()

◆ Select() [1/2]

◆ Select() [2/2]

◆ ViewData() [1/2]

◆ ViewData() [2/2]

◆ ViewForHandle() [1/3]

◆ ViewForHandle() [2/3]

◆ ViewForHandle() [3/3]

Friends And Related Function Documentation

◆ AtomView

◆ CreateViewFromAtomList() [1/2]

◆ CreateViewFromAtomList() [2/2]

◆ Difference()

◆ Intersection()

◆ ResidueView

◆ Union()