#include <chain_view.hh>

Inherits ChainBase.

Public Member Functions
	ChainView ()

	ChainView (ChainViewDataPtr data, impl::ChainImplPtr impl)

	ChainView (const EntityView &entity, const ChainHandle &chain)

EntityView	GetEntity () const

void	Apply (EntityVisitor &visitor)

void	Apply (EntityViewVisitor &visitor)

int	GetResidueCount () const

int	GetAtomCount () const

int	GetBondCount () const

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)

ResidueView	FindResidue (const ResNum &number) const

AtomView	FindAtom (const AtomHandle &atom) const

AtomView	ViewForHandle (const AtomHandle &atom) const

AtomView	FindAtom (const ResNum &num, const String &name) const

ResidueView	ViewForHandle (const ResidueHandle &handle) const

ResidueView	FindResidue (const ResidueHandle &handle) const

bool	IsResidueIncluded (const ResidueHandle &handle) const

ChainHandle	GetHandle () const

const ResidueViewList &	GetResidueList () const

void	RemoveResidue (ResidueView view)

int	GetResidueIndex (const ResNum &number) const

ResidueView	GetResidueByIndex (int index) const

Real	GetMass () const

geom::Vec3	GetCenterOfMass () const

geom::Vec3	GetCenterOfAtoms () const

geom::AlignedCuboid	GetBounds () const

void	RemoveResidues ()

Handle validity
	operator bool () const

bool	IsValid () const

Internal
ChainViewDataPtr &	ViewData ()

const ChainViewDataPtr &	ViewData () const

bool	InSequence () const

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

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

unsigned long	GetHashCode () const

bool	operator== (const ChainView &rhs) const

bool	operator!= (const ChainView &rhs) const

bool	HasAtoms () const

Public Member Functions inherited from ChainBase
	ChainBase ()

	ChainBase (const impl::ChainImplPtr &impl)

String	GetName () const

ChainType	GetType () const

String	GetDescription () const

const impl::ChainImplPtr &	Impl () const

bool	IsPolymer () const

bool	IsPolysaccharide () const

bool	IsOligosaccharide () const

bool	IsPolypeptide () const

bool	IsPolynucleotide () const

impl::ChainImplPtr &	Impl ()

	operator bool () const

bool	IsValid () const

Public Member Functions inherited from GenericPropContainer< ChainBase >
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< ChainBase >
bool	HasProp (const String &key) const

String	GetPropAsString (const String &key) const

String	GetStringProp (const String &key) const

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

Real	GetFloatProp (const String &key) const

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

int	GetIntProp (const String &key) const

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

bool	GetBoolProp (const String &key) const

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

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

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

std::vector< String >	GetPropList () const

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

const GenericPropContainerImpl *	GpImpl () const

void	CheckValidity () const

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

T	gp_get (const String &key, const T &def) const

GenericPropContainerImpl *	GetImpl ()

const GenericPropContainerImpl *	GetImpl () const

Detailed Description

definition of ChainView

Definition at line 37 of file chain_view.hh.

Constructor & Destructor Documentation

ChainView ( )

ChainView	(	ChainViewDataPtr	data,
		impl::ChainImplPtr	impl
	)

ChainView	(	const EntityView &	entity,
		const ChainHandle &	chain
	)

Member Function Documentation

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

Add atom to view.

If the atoms's residue has not been added to the view it will be added.

Parameters

atom_handle	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.

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

Add residue to view.

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

Parameters

residue_handle	The residue handle to add
flags	Can be a ORed together combination of ViewAddFlag. Flags that do not affect the operation are silently ignored.

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

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

Add residue to view.

This method is identical to AddResidue(const ResidueHandle&) except that in case ViewAddFlag::INCLUDE_ATOMS is set only the atoms included in the residue view are considered.

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

Parameters

residue_view	The residue view to add
flags	Can be a ORed together combination of ViewAddFlag. Flags that do not affect the operation are silently ignored.

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

void Apply ( EntityVisitor & visitor )

void Apply ( EntityViewVisitor & visitor )

AtomView FindAtom ( const AtomHandle & atom ) const

Find view for given atom handle Deprecated: Use ViewForHandle instead.

AtomView FindAtom	(	const ResNum &	num,
		const String &	name
	)		const

ResidueView FindResidue ( const ResNum & number ) const

Find residue by number.

ResidueView FindResidue ( const ResidueHandle & handle ) const

int GetAtomCount ( ) const

Get number of atoms in this chain view.

int GetBondCount ( ) const

Get number of all inclusive bonds of this chain.

Warning: For a bond between two different chains, it is not clearly defined to which chain it belongs. Therefore, this method will only return the number of bonds where both bonded atoms are within the same chain (all inclusive bonds).

geom::AlignedCuboid GetBounds ( ) const

Get entity's axis aligned bounding box.

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

geom::Vec3 GetCenterOfMass ( ) const

Get entity's center of mass (mass weighted)

EntityView GetEntity ( ) const

Get parent entity view.

ChainHandle GetHandle ( ) const

Get handle this view points to.

unsigned long GetHashCode ( ) const

get unique id

The unique id is the same for all ChainViews pointing to the same chain view data.

Real GetMass ( ) const

Get entity's mass.

ResidueView GetResidueByIndex ( int index ) const

get residue by index

returns an invalid residue handle if the index is out of bounds

int GetResidueCount ( ) const

Get number of residues in this chain view.

int GetResidueIndex ( const ResNum & number ) const

const ResidueViewList& GetResidueList ( ) const

Get residues of this chain view.

Todo:: Residue list may be unordered. Is it the responsibility of the method building the view to have them ordered or is it our job?

bool HasAtoms ( ) const

bool InSequence ( ) const

whether the residues form an ordered sequence with respect to their residue numbers.

bool IsResidueIncluded ( const ResidueHandle & handle ) const

Check whether the view includes the given residue.

bool IsValid ( ) const

check validity of handle

See Also: operator bool()

operator bool ( ) const

inline

check validity of handle

check, whether the chain handle points to a valid handle.

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 56 of file chain_view.hh.

bool operator!= ( const ChainView & rhs ) const

bool operator== ( const ChainView & rhs ) const

void RemoveResidue ( ResidueView view )

remove given residue from the view

void RemoveResidues ( )

///

remove all residues from the view

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

return view based on a query object

See Also: Query

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

return view based on query String.

See Also: Query

ChainViewDataPtr& ViewData ( )

inline

Get view data.

Definition at line 180 of file chain_view.hh.

const ChainViewDataPtr& ViewData ( ) const

inline

Get view data.

Definition at line 185 of file chain_view.hh.

AtomView ViewForHandle ( const AtomHandle & atom ) const

ResidueView ViewForHandle ( const ResidueHandle & handle ) const

Find residue by residue handle.

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

build-2.7-doc/stage/include/ost/mol/chain_view.hh

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation