#include <chain_handle.hh>

Inherits ChainBase.

Public Member Functions
	ChainHandle ()

	ChainHandle (const impl::ChainImplPtr &impl)

EntityHandle	GetEntity () const

void	Apply (EntityVisitor &visitor)

ResidueHandle	GetPrev (const ResidueHandle &rh)

ResidueHandle	GetNext (const ResidueHandle &rh)

Single item addressing
ResidueHandle	FindResidue (const ResNum &num) const

AtomHandle	FindAtom (const ResNum &num, const String &atom_name) const

ResidueHandle	GetResidueByIndex (int index) const

int	GetAtomCount () const

int	GetBondCount () const

int	GetResidueCount () const

AtomHandleList	GetAtomList () const

ResidueHandleList	GetResidueList () const

Real	GetMass () const

geom::Vec3	GetCenterOfMass () const

geom::Vec3	GetCenterOfAtoms () const

geom::AlignedCuboid	GetBounds () const

void	AssignSecondaryStructure (SecStructure ss, const ResNum &start, const ResNum &end)

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

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

ChainHandle	GetHandle () const

unsigned long	GetHashCode () const

bool	InSequence () const

bool	operator== (const ChainHandle &ref) const

bool	operator!= (const ChainHandle &ref) const

void	SetInSequence (const int index)

Public Member Functions inherited from ChainBase
	ChainBase ()

	ChainBase (const impl::ChainImplPtr &impl)

	operator bool () const

bool	IsValid () const

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 ()

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< 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

Additional Inherited Members
Protected Member Functions inherited from ChainBase
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

linear chain of residues

In peptide chain, the residues are ordered from N- to C-terminus. To obtain the n-th residue in the chain, use GetResidueByIndex. Alternatively, the residues may be adressed by their residue number with FindResidue. Residue numbers are unique within a chain. It is however not guaranteed that the residue numbers are in ascending order.

New residues are inserted via one of the editors obtained from EntityHandle::EditXCS() or EntityHandle::EditICS(). To append a residue to the C-terminal end, use EditorBase::AppendResidue, to insert after or before a specific residue, EditorBase::InsertResidueAfter and ditorBase::InsertResidueABefore will do the job, respectively.

Definition at line 52 of file chain_handle.hh.

Constructor & Destructor Documentation

◆ ChainHandle() [1/2]

ChainHandle ( )

◆ ChainHandle() [2/2]

ChainHandle ( const impl::ChainImplPtr & impl )

Member Function Documentation

◆ Apply()

void Apply ( EntityVisitor & visitor )

Apply visitor.

Parameters

visitor is the visitor to apply

◆ AssignSecondaryStructure()

void AssignSecondaryStructure	(	SecStructure	ss,
		const ResNum &	start,
		const ResNum &	end
	)

assign secondary structure to the inclusive residue range start, end

◆ FindAtom()

AtomHandle FindAtom	(	const ResNum &	num,
		const String &	atom_name
	)		const

◆ FindResidue()

ResidueHandle FindResidue ( const ResNum & num ) const

Find residue by number. If the chain does not contain a residue with the given number, an invalid ResidueHandle will be returned.

See also: ResidueBase::IsValid, FindAtom, EntityHandle::FindResidue

◆ GetAtomCount()

int GetAtomCount ( ) const

Get number of atoms of this chain.

◆ GetAtomList()

AtomHandleList GetAtomList ( ) const

Retrieve atoms of this chain as a list.

The atoms are ordered by atom number in ascending order. If you only want to determine the number of atoms, use the dedicated ChainHandle::GetAtomCount

◆ GetBondCount()

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).

◆ 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)

◆ GetEntity()

EntityHandle GetEntity ( ) const

Get parent entity.

◆ GetHandle()

ChainHandle GetHandle ( ) const

get this handle

Useful for duck-typing in Python and in templates

◆ GetHashCode()

unsigned long GetHashCode ( ) const

◆ GetMass()

Real GetMass ( ) const

Get entity's mass.

◆ GetNext()

ResidueHandle GetNext ( const ResidueHandle & rh )

◆ GetPrev()

ResidueHandle GetPrev ( const ResidueHandle & rh )

Get residue before the given residue.

A previous residue is returned regardless whether the residues are connected by a bond.

◆ GetResidueByIndex()

ResidueHandle GetResidueByIndex ( int index ) const

Get residue by index.

Indices are start at zero

◆ GetResidueCount()

int GetResidueCount ( ) const

Get number of residues of this chain.

See also: EntityHandle::GetResidueCount()

◆ GetResidueList()

ResidueHandleList GetResidueList ( ) const

Get residues of this chain as a list.

The residues are ordered by residue number in ascending order. If you only want to determine the number of residues, use the dedicated ChainHandle::GetResidueCount

◆ InSequence()

bool InSequence ( ) const

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

◆ operator!=()

bool operator!= ( const ChainHandle & ref ) const

◆ operator==()

bool operator== ( const ChainHandle & ref ) const

◆ Select() [1/2]

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

return view based on a query object

See also: Query

◆ Select() [2/2]

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

return view based on query String.

See also: Query

◆ SetInSequence()

void SetInSequence ( const int index )

checks whether res breaks the in sequence property and updates it accordingly

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

build-2.9.0-doc/stage/include/ost/mol/chain_handle.hh

Public Member Functions

Additional Inherited Members