ChainImpl Class Reference

#include <chain_impl.hh>

Inherits GenericPropContainerImpl, and enable_shared_from_this< ChainImpl >.

Public Member Functions
	ChainImpl (const EntityImplPtr &e, const String &name)
void	SetName (const String &new_name)
String	GetName () const
void	SetType (const ChainType type)
ChainType	GetType () const
bool	IsPolymer () const
bool	IsPolysaccharide () const
bool	IsOligosaccharide () const
bool	IsPolypeptide () const
bool	IsPolynucleotide () const
void	SetDescription (const String desc)
String	GetDescription () const
ResidueImplPtr	AppendResidue (const ResidueImplPtr &res, bool deep)
ResidueImplPtr	InsertResidueBefore (int index, const ResNum &n, const ResidueKey &k)
ResidueImplPtr	InsertResidueAfter (int index, const ResNum &n, const ResidueKey &k)
ResidueImplPtr	AppendResidue (const ResidueKey &k)
ResidueImplPtr	AppendResidue (const ResidueKey &k, const ResNum &n)
ResidueImplPtr	GetPrev (const ResidueImplPtr &r) const
ResidueImplPtr	GetNext (const ResidueImplPtr &r) const
const ResidueImplList &	GetResidueList () const
bool	InSequence () const
ResidueImplList &	GetResidueList ()
Real	GetMass () const
geom::Vec3	GetCenterOfMass () const
geom::Vec3	GetCenterOfAtoms () const
geom::AlignedCuboid	GetBounds () const
ResidueImplPtr	FindResidue (const ResNum &number) const
AtomImplPtr	FindAtom (const ResNum &number, const String &atom_name) const
int	GetResidueCount () const
int	GetAtomCount () const
int	GetBondCount () const
void	Apply (EntityVisitor &v)
EntityImplPtr	GetEntity () const
void	DeleteResidue (const ResNum &number)
void	DeleteResidue (const ResidueImplPtr &residue)
void	DeleteAllResidues ()
void	ReorderResidues ()
void	RenumberAllResidues (int start, bool keep_spacing)
void	RenumberAllResidues (const ResNumList &new_numbers)
int	GetIndex (const ResidueImplPtr &res) const
void	AssignSecondaryStructure (SecStructure ss, const ResNum &start, const ResNum &end)
int	GetIndexForResNum (const ResNum &number) const
void	SetInSequence (int index)
void	UpdateTransformedPos ()
Public Member Functions inherited from GenericPropContainerImpl
	GenericPropContainerImpl ()
	~GenericPropContainerImpl ()
	GenericPropContainerImpl (const GenericPropContainerImpl &rhs)
GenericPropContainerImpl &	operator= (const GenericPropContainerImpl &r)
GenericPropValue &	GenericProp (const String &key)
const GenericPropValue &	GenericProp (const String &key) const
bool	HasProp (const String &key) const
void	ClearProps ()
void	RemoveProp (const String &key)
void	Assign (const GenericPropContainerImpl &impl)
PropertyMap	GetPropMap () const
std::vector< String >	GetPropList () const

Detailed Description

Definition at line 42 of file chain_impl.hh.

Constructor & Destructor Documentation

ChainImpl()

ChainImpl	(	const EntityImplPtr &	e,
		const String &	name
	)

Member Function Documentation

AppendResidue() [1/3]

ResidueImplPtr AppendResidue	(	const ResidueImplPtr &	res,
		bool	deep
	)

append new residue with exactly the same parameters as res, but no atoms and bonds

AppendResidue() [2/3]

ResidueImplPtr AppendResidue

(

const ResidueKey &

k

)

Append residue at end of chain.

Residue number will be automatically set to last+1. The first residue will have the number 1. insertion code from a previous residue are copied.

AppendResidue() [3/3]

ResidueImplPtr AppendResidue	(	const ResidueKey &	k,
		const ResNum &	n
	)

Append residue at end of chain.

Apply()

void Apply

(

EntityVisitor &

v

)

AssignSecondaryStructure()

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

DeleteAllResidues()

void DeleteAllResidues

(

)

DeleteResidue() [1/2]

void DeleteResidue

(

const ResidueImplPtr &

residue

)

DeleteResidue() [2/2]

void DeleteResidue

(

const ResNum &

number

)

FindAtom()

AtomImplPtr FindAtom	(	const ResNum &	number,
		const String &	atom_name
	)		const

FindResidue()

ResidueImplPtr FindResidue

(

const ResNum &

number

)

const

Get residue by number. Returns a invalid pointer if the chain does not have any residue with this number.

GetAtomCount()

int GetAtomCount

(

)

const

Get number of atoms of this chain.

GetBondCount()

int GetBondCount

(

)

const

Get number of bonds of this chain.

GetBounds()

geom::AlignedCuboid GetBounds

(

)

const

returns the axis-aligned bounding box of the entity

GetCenterOfAtoms()

geom::Vec3 GetCenterOfAtoms

(

)

const

GetCenterOfMass()

geom::Vec3 GetCenterOfMass

(

)

const

GetDescription()

String GetDescription ( ) const

inline

Get information about a chain.

Returns

description

Definition at line 110 of file chain_impl.hh.

GetEntity()

EntityImplPtr GetEntity

(

)

const

GetIndex()

int GetIndex

(

const ResidueImplPtr &

res

)

const

GetIndexForResNum()

int GetIndexForResNum

(

const ResNum &

number

)

const

GetMass()

Real GetMass

(

)

const

GetName()

String GetName

(

)

const

GetNext()

ResidueImplPtr GetNext

(

const ResidueImplPtr &

r

)

const

previous residue, not necessarily in sequence

GetPrev()

ResidueImplPtr GetPrev

(

const ResidueImplPtr &

r

)

const

GetResidueCount()

int GetResidueCount

(

)

const

Get number of residues of this chain.

GetResidueList() [1/2]

ResidueImplList& GetResidueList ( )

inline

Definition at line 145 of file chain_impl.hh.

GetResidueList() [2/2]

const ResidueImplList& GetResidueList

(

)

const

GetType()

ChainType GetType ( ) const

inline

Get the type of a chain.

Returns

chain type of ChainType

Definition at line 62 of file chain_impl.hh.

InSequence()

bool InSequence

(

)

const

whether the residue numbers are in ascending order

InsertResidueAfter()

ResidueImplPtr InsertResidueAfter	(	int	index,
		const ResNum &	n,
		const ResidueKey &	k
	)

InsertResidueBefore()

ResidueImplPtr InsertResidueBefore	(	int	index,
		const ResNum &	n,
		const ResidueKey &	k
	)

IsOligosaccharide()

bool IsOligosaccharide ( ) const

inline

whether the chain is a polysaccharide

Definition at line 82 of file chain_impl.hh.

IsPolymer()

bool IsPolymer ( ) const

inline

whether the chain is a polymer

Definition at line 68 of file chain_impl.hh.

IsPolynucleotide()

bool IsPolynucleotide ( ) const

inline

whether the chain is a polynucleotide

Definition at line 93 of file chain_impl.hh.

IsPolypeptide()

bool IsPolypeptide ( ) const

inline

whether the chain is a polypeptide

Definition at line 87 of file chain_impl.hh.

IsPolysaccharide()

bool IsPolysaccharide ( ) const

inline

whether the chain is a polysaccharide

Definition at line 76 of file chain_impl.hh.

RenumberAllResidues() [1/2]

void RenumberAllResidues

(

const ResNumList &

new_numbers

)

RenumberAllResidues() [2/2]

void RenumberAllResidues	(	int	start,
		bool	keep_spacing
	)

ReorderResidues()

void ReorderResidues

(

)

SetDescription()

void SetDescription ( const String  desc )

inline

Assign a description to a chain.

Parameters

desc	description

Definition at line 102 of file chain_impl.hh.

SetInSequence()

void SetInSequence

(

int

index

)

checks if the residue with that index breaks the in_sequence property and updates it accordingly

SetName()

void SetName

(

const String &

new_name

)

SetType()

void SetType ( const ChainType  type )

inline

Assign a type to a chain.

Parameters

type	chain type of ChainType

Definition at line 54 of file chain_impl.hh.

UpdateTransformedPos()

void UpdateTransformedPos

(

)

---

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

• build-dev-doc/stage/include/ost/mol/impl/chain_impl.hh