ChainHandle Class Reference

#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)
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
bool	InSequence () const
bool	operator== (const ChainHandle &ref) const
bool	operator!= (const ChainHandle &ref) const
void	SetInSequence (const int index)
Single item addressing
ResidueHandle	FindResidue (const ResNum &num) const
AtomHandle	FindAtom (const ResNum &num, const String &atom_name) const
ResidueHandle	GetResidueByIndex (int index) 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 ()
	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	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

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.

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Constructor & Destructor Documentation

ChainHandle

(

)

ChainHandle

(

const impl::ChainImplPtr &

impl

)

---

Member Function Documentation

void Apply

(

EntityVisitor &

visitor

)

Apply visitor.

Parameters:

visitor

is the visitor to apply

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

assign secondary structure to the inclusive residue range start, end

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

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

int GetAtomCount

(

)

const

Get number of atoms of this chain.

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

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

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)

EntityHandle GetEntity

(

)

const

Get parent entity.

ChainHandle GetHandle

(

)

const

get this handle

Useful for duck-typing in Python and in templates

Real GetMass

(

)

const

Get entity's mass.

ResidueHandle GetNext

(

const ResidueHandle &

rh

)

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.

ResidueHandle GetResidueByIndex

(

int

index

)

const

Get residue by index.

Indices are start at zero

int GetResidueCount

(

)

const

Get number of residues of this chain.

See also:

EntityHandle::GetResidueCount()

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

bool InSequence

(

)

const

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

bool operator!=

(

const ChainHandle &

ref

)

const

bool operator==

(

const ChainHandle &

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

void SetInSequence

(

const int

index

)

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

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

• stage/include/ost/mol/chain_handle.hh