#include <residue_handle.hh>

Inherits ResidueBase.

Public Member Functions
	ResidueHandle ()

	ResidueHandle (const impl::ResidueImplPtr &impl)

EntityHandle	GetEntity () const

double	GetMass () const

geom::Vec3	GetCenterOfMass () const

geom::Vec3	GetCenterOfAtoms () const

geom::AlignedCuboid	GetBounds () const

ChainHandle	GetChain () const

ResidueHandle	GetPrev () const

ResidueHandle	GetNext () const

AtomHandle	FindAtom (const String &aname) const

void	Apply (EntityVisitor &visitor)

AtomHandleList	GetAtomList () const

int	GetAtomCount () const

int	GetBondCount () const

TorsionHandle	FindTorsion (const String &torsion_name) const

TorsionHandleList	GetTorsionList () const

int	GetIndex () const

ResidueHandle	GetHandle () const

unsigned long	GetHashCode () const

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

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

bool	operator== (const ResidueHandle &ref) const

bool	operator!= (const ResidueHandle &ref) const

Alternative atom positions
Alternative atom positions have traditionally been used to indicate that the position of an atom is not limited to one point, but that the atom may occur at more than one position. The following functions let you work with alternative atom locations on the level of residues.
bool	HasAltAtomGroup (const String &group) const

const String &	GetCurrentAltGroupName () const

std::vector< String >	GetAltAtomGroupNames () const

bool	HasAltAtoms () const

geom::Vec3	GetAltAtomPos (const AtomHandle &atom, const String &group) const

bool	SwitchAtomPos (const String &group)

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

Additional Inherited Members
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

Detailed Description

Residue handle.

In a polymer a residue is a single unit such as a nucleotide or an amino acid. In case of ligands, a residue ofter represents a completye molecule, such as a HEM group.

Every residue belongs to a chain and has a defined position (GetIndex) in that chain. In a peptide chain, the previous (towards N-terminus) and next (towards C-terminus) can be obtained with GetPrev() and GetNext() respectively.

A residue consist of one or more atoms. The list of atoms can be retrieved with GetAtomList(), wheras FindAtom() will locate a particular atom in the residue.

To add atoms to the residue, you have to request an editor and call EditorBase::InsertAtom() or EditorBase::InsertAltAtom()

*  XCSEditor edi=residue.GetEntity().EditXCS();
*  edi.InsertAtom(residue, "CA", geom.Vec3(1.0, 0.0, 0.0));
*  

Definition at line 54 of file residue_handle.hh.

Constructor & Destructor Documentation

ResidueHandle ( )

ResidueHandle ( const impl::ResidueImplPtr & impl )

inline

Definition at line 59 of file residue_handle.hh.

Member Function Documentation

void Apply ( EntityVisitor & visitor )

Apply entity visitor.

Parameters

visitor is the entity visitor to apply

See Also: EntityVisitor

AtomHandle FindAtom ( const String & aname ) const

Find atom by name.

Parameters

aname is the atom name

TorsionHandle FindTorsion ( const String & torsion_name ) const

Find torsion by name.

Note: For the PHI, ISP and PSI torsions of the backbone use the designated GetPhiTorsion and GetPsiTorsion methods, respectively.

Parameters

torsion_name is the name of the torsion you are looking for. Torsions are named with uppercase letters.

Returns: The torsion, or an invalid torsion handle if the residues does not have a torsion with the given name.

See Also: ResidueBase::GetPhiTorsion, ResidueBase::GetPsiTorsion

std::vector<String> GetAltAtomGroupNames ( ) const

Get names of alternative atom groups.

geom::Vec3 GetAltAtomPos	(	const AtomHandle &	atom,
		const String &	group
	)		const

Get alternative atom position for given atom.

If the atom is not in group, an IntegrityError is thrown.

int GetAtomCount ( ) const

Get number of atoms of this residue.

AtomHandleList GetAtomList ( ) const

Get number of atoms of this residue.

See Also: ResidueHandle::GetAtomCount

int GetBondCount ( ) const

Get number of bonds of this residue. This method might NOT work as expected (see warning below).

Warning: For a bond between two different residues, it is not clearly defined to which residue it belongs. Therefore, this method works only correctly if the residue has NO bonds to any other residues!

geom::AlignedCuboid GetBounds ( ) const

get axis-aligned bounding box of residue

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)

ChainHandle GetChain ( ) const

The chain this residue is attached to.

const String& GetCurrentAltGroupName ( ) const

Name of active alternative atom group.

Returns: The alternative atom group name or an empty String, if the atom does not have any alternative atoms.

EntityHandle GetEntity ( ) const

ResidueHandle GetHandle ( ) const

get this handle

This method exists as a convenience duck-typing in Python.

unsigned long GetHashCode ( ) const

int GetIndex ( ) const

Get position of residue in chain.

double GetMass ( ) const

Get residue's mass.

ResidueHandle GetNext ( ) const

Get next residue in chain.

Returns: Invalid handle, when there is no next residue.

ResidueHandle GetPrev ( ) const

Get previous residue in chain.

Returns: Invalid handle, when there is no previous residue.

TorsionHandleList GetTorsionList ( ) const

Get list of all torsion angles of this residue.

bool HasAltAtomGroup ( const String & group ) const

Test if residue has group of alternative atoms with a certain name.

bool HasAltAtoms ( ) const

Test if the residue has any alternative atom positions.

bool operator!= ( const ResidueHandle & ref ) const

bool operator== ( const ResidueHandle & ref ) const

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

bool SwitchAtomPos ( const String & group )

switch atoms that have alternative positions to the position in the group. Atoms that do not have an alternative position are left untouched.

Parameters

group is the group name to switch to.

Returns: True, if such a group exists, false if not.

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

stage/include/ost/mol/residue_handle.hh

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation