#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
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	IsPolypeptide () const
bool	IsPolynucleotide () const
impl::ChainImplPtr &	Impl ()
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	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
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

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.

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

inline

check validity of handle

See also:: operator bool()

Reimplemented from ChainBase.

Definition at line 59 of file chain_view.hh.

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.

Reimplemented from ChainBase.

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:

stage/include/ost/mol/chain_view.hh

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation