ChainImpl Class Reference

#include <chain_impl.hh>

Inherits GenericPropContainerImpl.

Data Structures
struct	Shift

Public Member Functions
	ChainImpl (const EntityImplPtr &e, const String &name)
void	SetName (const String &new_name)
String	GetName () const
ResidueImplPtr	AppendResidue (const ResidueImplPtr &res)
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 ()
int	GetIndex (const ResidueImplPtr &res) const
void	AssignSecondaryStructure (SecStructure ss, const ResNum &start, const ResNum &end)
int	GetIndexForResNum (const ResNum &number) const
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 41 of file chain_impl.hh.

---

Constructor & Destructor Documentation

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

---

Member Function Documentation

ResidueImplPtr AppendResidue

(

const ResidueImplPtr &

res

)

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

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.

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

Append residue at end of chain.

void Apply

(

EntityVisitor &

v

)

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

void DeleteAllResidues

(

)

void DeleteResidue

(

const ResNum &

number

)

void DeleteResidue

(

const ResidueImplPtr &

residue

)

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

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.

int GetAtomCount

(

)

const

Get number of atoms of this chain.

int GetBondCount

(

)

const

Get number of bonds of this chain.

geom::AlignedCuboid GetBounds

(

)

const

returns the axis-aligned bounding box of the entity

geom::Vec3 GetCenterOfAtoms

(

)

const

geom::Vec3 GetCenterOfMass

(

)

const

EntityImplPtr GetEntity

(

)

const

int GetIndex

(

const ResidueImplPtr &

res

)

const

int GetIndexForResNum

(

const ResNum &

number

)

const

Real GetMass

(

)

const

String GetName

(

)

const

ResidueImplPtr GetNext

(

const ResidueImplPtr &

r

)

const

previous residue, not necessarily in sequence

ResidueImplPtr GetPrev

(

const ResidueImplPtr &

r

)

const

int GetResidueCount

(

)

const

Get number of residues of this chain.

const ResidueImplList& GetResidueList

(

)

const

ResidueImplList& GetResidueList ( )

inline

Definition at line 77 of file chain_impl.hh.

bool InSequence

(

)

const

whether the residue numbers are in ascending order

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

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

void ReorderResidues

(

)

void SetName

(

const String &

new_name

)

---

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

• stage/include/ost/mol/impl/chain_impl.hh