#include <residue_view.hh>

Inherits ResidueBase.

Public Member Functions
	ResidueView ()

	ResidueView (const ChainView &chain, const ResidueHandle &residue)

AtomView	FindAtom (const String &atom_name) const

AtomView	ViewForHandle (const AtomHandle &handle) const

AtomView	FindAtom (const AtomHandle &handle) const

bool	IsAtomIncluded (const AtomHandle &handle) const

void	RemoveAtom (AtomView view)

void	RemoveAtoms ()

void	Apply (EntityVisitor &visitor)

void	Apply (EntityViewVisitor &visitor)

int	GetAtomCount () const

const AtomViewList &	GetAtomList () const

ResidueHandle	GetHandle () const

EntityView	GetEntity () const

int	GetIndex () const

ChainView	GetChain () const

double	GetMass () const

geom::Vec3	GetCenterOfMass () const

geom::Vec3	GetCenterOfAtoms () const

geom::AlignedCuboid	GetBounds () const

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

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

bool	operator== (const ResidueView &rhs) const

bool	operator!= (const ResidueView &rhs) const

bool	HasAtoms () const

Handle validity
	operator bool () const

bool	IsValid () const

internal
	ResidueView (const ResidueViewDataPtr &data, const impl::ResidueImplPtr &impl)

const ResidueViewDataPtr &	ViewData () const

ResidueViewDataPtr &	ViewData ()

Adding and removing atoms
AtomView	AddAtom (const AtomView &atom_view, ViewAddFlags flags=0)

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

Public Member Functions inherited from ResidueBase
	ResidueBase ()

	ResidueBase (const impl::ResidueImplPtr &impl)

	ResidueBase (const ResidueBase &rhs)

	operator bool () const

bool	IsValid () const

const ResNum &	GetNumber () const

const ResidueKey &	GetKey () const

const String &	GetName () const

String	GetQualifiedName () const

AtomHandle	GetCentralAtom () const

void	SetCentralAtom (const AtomHandle &a)

geom::Vec3	GetCentralNormal () const

bool	IsPeptideLinking () const

bool	IsNucleotideLinking () const

ChemClass	GetChemClass () const

void	SetChemClass (ChemClass cc)

ChemType	GetChemType () const

void	SetChemType (ChemType ct)

SecStructure	GetSecStructure () const

void	SetSecStructure (SecStructure ss)

TorsionHandle	GetPhiTorsion () const

TorsionHandle	GetPsiTorsion () const

TorsionHandle	GetOmegaTorsion () const

char	GetOneLetterCode () const

void	SetOneLetterCode (char olc)

String	GetStringProperty (Prop::ID prop_id) const

Real	GetFloatProperty (Prop::ID prop_id) const

int	GetIntProperty (Prop::ID prop_id) const

bool	IsProtein () const

void	SetIsProtein (bool protein)

void	SetIsLigand (bool ligand)

bool	IsLigand () const

impl::ResidueImplPtr &	Impl ()

const impl::ResidueImplPtr &	Impl () const

Public Member Functions inherited from GenericPropContainer< ResidueBase >
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< ResidueBase >
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

Protected Member Functions
void	SetIndex (int index)

Protected Member Functions inherited from ResidueBase
GenericPropContainerImpl *	GpImpl ()

const GenericPropContainerImpl *	GpImpl () const

void	CheckValidity () const

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

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

GenericPropContainerImpl *	GetImpl ()

const GenericPropContainerImpl *	GetImpl () const

Friends
class	ChainView

Detailed Description

residue view

Atoms are added with ResidueView::AddAtom() and removed with ResidueView::RemoveAtom(). Like other view operations, these operations only affect the view and do not alter the structure and topology of the underlying residue.

Definition at line 39 of file residue_view.hh.

Constructor & Destructor Documentation

ResidueView ( )

Create invalid ResidueView.

ResidueView	(	const ChainView &	chain,
		const ResidueHandle &	residue
	)

Create new residue view.

Parameters

chain	is the parent chain view to insert into
residue	is residue handle this view points to.

Note: For better readability consider using ChainView::AddResidue()

ResidueView	(	const ResidueViewDataPtr &	data,
		const impl::ResidueImplPtr &	impl
	)

construct new view from view data and impl.

This has the same effect as using the default copy constructor of the view.

Member Function Documentation

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

Add atom to view.

If ViewAddFlag::CHECK_DUPLICATES is set, the method will ensure that the view is not already included in this view. This method is an alias for residue_view.AddAtom(atom_view.GetHandle())

Parameters

atom_view	is the atom view 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 view.

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

Add atom to view.

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

Parameters

atom_handle	the atom handle 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.

void Apply ( EntityVisitor & visitor )

Apply entity visitor to whole chain.

void Apply ( EntityViewVisitor & visitor )

AtomView FindAtom ( const String & atom_name ) const

Find atom by name.

AtomView FindAtom ( const AtomHandle & handle ) const

int GetAtomCount ( ) const

return number of atoms in this residue view.

const AtomViewList& GetAtomList ( ) const

get list of atoms in this view

geom::AlignedCuboid GetBounds ( ) const

Get residue's axis-aligned bounding box.

geom::Vec3 GetCenterOfAtoms ( ) const

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

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

geom::Vec3 GetCenterOfMass ( ) const

Get residue's center of mass (mass weighted)

ChainView GetChain ( ) const

get parent chain view.

EntityView GetEntity ( ) const

get entity

ResidueHandle GetHandle ( ) const

get handle this view points to

int GetIndex ( ) const

get index of residue view in chain

double GetMass ( ) const

Get residue's mass.

bool HasAtoms ( ) const

bool IsAtomIncluded ( const AtomHandle & handle ) const

Check whether the view includes the the given atom.

bool IsValid ( ) const

inline

check validity of handle

See Also: operator bool()

Definition at line 68 of file residue_view.hh.

operator bool ( ) const

inline

check validity of view

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

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 65 of file residue_view.hh.

bool operator!= ( const ResidueView & rhs ) const

bool operator== ( const ResidueView & rhs ) const

void RemoveAtom ( AtomView view )

remove given atom from view

all bonds involving this atom will be removed from the view as well.

void RemoveAtoms ( )

remove all atoms

all bonds involving one of the atoms will be removed from the view as well.

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

void SetIndex ( int index )

protected

set the index of residiue view in chain should be called from chainview whenever indexes change

const ResidueViewDataPtr& ViewData ( ) const

inline

Get internal view data.

Definition at line 80 of file residue_view.hh.

ResidueViewDataPtr& ViewData ( )

inline

Get internal view data.

Definition at line 84 of file residue_view.hh.

AtomView ViewForHandle ( const AtomHandle & handle ) const

Find residue by residue handle.

Friends And Related Function Documentation

friend class ChainView

friend

Definition at line 41 of file residue_view.hh.

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

stage/include/ost/mol/residue_view.hh

Public Member Functions

Protected Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation