mmdb::Residue Class Reference

#include <mmdb_atom.h>

Inheritance diagram for mmdb::Residue:

List of all members.

Public Member Functions
	Residue ()
	Residue (PChain Chain_Owner)
	Residue (PChain Chain_Owner, const ResName resName, int sqNum, const InsCode ins)
	Residue (io::RPStream Object)
	~Residue ()
void	SetChain (PChain Chain_Owner)
void	SetResID (const ResName resName, int sqNum, const InsCode ins)
void	SetChainID (const ChainID chID)
void	PDBASCIIAtomDump (io::RFile f)
void	MakeAtomCIF (mmcif::PData CIF)
PChain	GetChain ()
PModel	GetModel ()
int	GetModelNum ()
pstr	GetChainID ()
pstr	GetLabelAsymID ()
pstr	GetResName ()
pstr	GetLabelCompID ()
int	GetAASimilarity (const ResName resName)
int	GetAASimilarity (PResidue res)
realtype	GetAAHydropathy ()
void	SetResName (const ResName resName)
int	GetSeqNum ()
int	GetLabelSeqID ()
int	GetLabelEntityID ()
pstr	GetInsCode ()
int	GetResidueNo ()
int	GetCenter (realtype &x, realtype &y, realtype &z)
void *	GetCoordHierarchy ()
void	GetAtomStatistics (RAtomStat AS)
void	CalAtomStatistics (RAtomStat AS)
pstr	GetResidueID (pstr ResidueID)
void	GetAltLocations (int &nAltLocs, PAltLoc &aLoc, rvector &occupancy, int &alflag)
int	GetNofAltLocations ()
bool	isAminoacid ()
bool	isNucleotide ()
int	isDNARNA ()
bool	isSugar ()
bool	isSolvent ()
bool	isModRes ()
bool	isInSelection (int selHnd)
bool	isNTerminus ()
bool	isCTerminus ()
int	CheckID (int *snum, const InsCode inscode=pstr(""), const ResName resname=NULL)
int	CheckIDS (cpstr ID)
int	GetNumberOfAtoms ()
int	GetNumberOfAtoms (bool countTers)
PAtom	GetAtom (const AtomName aname, const Element elname=NULL, const AltLoc aloc=cpstr(""))
PAtom	GetAtom (int atomNo)
void	GetAtomTable (PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (PPAtom &atomTable, int &NumberOfAtoms)
int	DeleteAtom (const AtomName aname, const Element elname=NULL, const AltLoc aloc=cpstr(""))
int	DeleteAtom (int atomNo)
int	DeleteAllAtoms ()
int	DeleteAltLocs ()
void	TrimAtomTable ()
int	AddAtom (PAtom atm)
int	InsertAtom (PAtom atm, int position)
int	InsertAtom (PAtom atm, const AtomName aname)
void	ApplyTransform (mat44 &TMatrix)
void	MaskAtoms (PMask Mask)
void	UnmaskAtoms (PMask Mask)
int	PutUDData (int UDDhandle, int iudd)
int	PutUDData (int UDDhandle, realtype rudd)
int	PutUDData (int UDDhandle, cpstr sudd)
int	GetUDData (int UDDhandle, int &iudd)
int	GetUDData (int UDDhandle, realtype &rudd)
int	GetUDData (int UDDhandle, pstr sudd, int maxLen)
int	GetUDData (int UDDhandle, pstr &sudd)
bool	isMainchainHBond (PResidue res)
void	Copy (PResidue res)
void	write (io::RFile f)
void	read (io::RFile f)
Public Attributes
ResName	name
	residue name - all spaces cut
ResName	label_comp_id
	assigned residue name
ChainID	label_asym_id
	assigned chain Id
InsCode	insCode
	residue insertion code
PChain	chain
	reference to chain
PPAtom	atom
	array of atoms
int	seqNum
	residue sequence number
int	label_seq_id
	assigned residue sequence number
int	label_entity_id
	assigned entity id
int	index
	index in the chain
int	nAtoms
	number of atoms in the residue
byte	SSE
	SSE type.
Protected Member Functions
void	InitResidue ()
void	FreeMemory ()
int	_AddAtom (PAtom atm)
int	_ExcludeAtom (int kndex)
void	_copy (PResidue res)
void	_copy (PResidue res, PPAtom atm, int &atom_index)
void	ExpandAtomArray (int nAdd)
void	CheckInAtoms ()
Protected Attributes
int	AtmLen
bool	Exclude
Friends
class	Atom
class	Chain
class	Root

---

Constructor & Destructor Documentation

mmdb::Residue::Residue

(

)

mmdb::Residue::Residue

(

PChain

Chain_Owner )

mmdb::Residue::Residue	(	PChain	Chain_Owner,
		const ResName	resName,
		int	sqNum,
		const InsCode	ins
	)

mmdb::Residue::Residue

(

io::RPStream

Object )

mmdb::Residue::~Residue

(

)

---

Member Function Documentation

int mmdb::Residue::_AddAtom

(

PAtom

atm )

[protected]

void mmdb::Residue::_copy

(

PResidue

res )

[protected]

void mmdb::Residue::_copy	(	PResidue	res,
		PPAtom	atm,
		int &	atom_index
	)		[protected]

int mmdb::Residue::_ExcludeAtom

(

int

kndex )

[protected]

int mmdb::Residue::AddAtom

(

PAtom

atm )

void mmdb::Residue::ApplyTransform

(

mat44 &

TMatrix )

void mmdb::Residue::CalAtomStatistics

(

RAtomStat

AS )

int mmdb::Residue::CheckID	(	int *	snum,
		const InsCode	inscode = pstr(""),
		const ResName	resname = NULL
	)

int mmdb::Residue::CheckIDS

(

cpstr

ID )

void mmdb::Residue::CheckInAtoms

(

)

[protected]

void mmdb::Residue::Copy

(

PResidue

res )

int mmdb::Residue::DeleteAllAtoms

(

)

int mmdb::Residue::DeleteAltLocs

(

)

int mmdb::Residue::DeleteAtom	(	const AtomName	aname,
		const Element	elname = NULL,
		const AltLoc	aloc = cpstr("")
	)

int mmdb::Residue::DeleteAtom

(

int

atomNo )

void mmdb::Residue::ExpandAtomArray

(

int

nAdd )

[protected]

void mmdb::Residue::FreeMemory

(

)

[protected]

realtype mmdb::Residue::GetAAHydropathy

(

)

int mmdb::Residue::GetAASimilarity

(

const ResName

resName )

int mmdb::Residue::GetAASimilarity

(

PResidue

res )

void mmdb::Residue::GetAltLocations	(	int &	nAltLocs,
		PAltLoc &	aLoc,
		rvector &	occupancy,
		int &	alflag
	)

PAtom mmdb::Residue::GetAtom

(

int

atomNo )

PAtom mmdb::Residue::GetAtom	(	const AtomName	aname,
		const Element	elname = NULL,
		const AltLoc	aloc = cpstr("")
	)

void mmdb::Residue::GetAtomStatistics

(

RAtomStat

AS )

void mmdb::Residue::GetAtomTable	(	PPAtom &	atomTable,
		int &	NumberOfAtoms
	)

void mmdb::Residue::GetAtomTable1	(	PPAtom &	atomTable,
		int &	NumberOfAtoms
	)

int mmdb::Residue::GetCenter	(	realtype &	x,
		realtype &	y,
		realtype &	z
	)

PChain mmdb::Residue::GetChain

(

)

pstr mmdb::Residue::GetChainID

(

)

void * mmdb::Residue::GetCoordHierarchy

(

)

pstr mmdb::Residue::GetInsCode

(

)

pstr mmdb::Residue::GetLabelAsymID

(

)

pstr mmdb::Residue::GetLabelCompID

(

)

int mmdb::Residue::GetLabelEntityID

(

)

int mmdb::Residue::GetLabelSeqID

(

)

PModel mmdb::Residue::GetModel

(

)

int mmdb::Residue::GetModelNum

(

)

int mmdb::Residue::GetNofAltLocations

(

)

int mmdb::Residue::GetNumberOfAtoms

(

)

int mmdb::Residue::GetNumberOfAtoms

(

bool

countTers )

pstr mmdb::Residue::GetResidueID

(

pstr

ResidueID )

int mmdb::Residue::GetResidueNo

(

)

pstr mmdb::Residue::GetResName

(

)

int mmdb::Residue::GetSeqNum

(

)

int mmdb::Residue::GetUDData	(	int	UDDhandle,
		pstr &	sudd
	)

int mmdb::Residue::GetUDData	(	int	UDDhandle,
		realtype &	rudd
	)

int mmdb::Residue::GetUDData	(	int	UDDhandle,
		int &	iudd
	)

int mmdb::Residue::GetUDData	(	int	UDDhandle,
		pstr	sudd,
		int	maxLen
	)

void mmdb::Residue::InitResidue

(

)

[protected]

int mmdb::Residue::InsertAtom	(	PAtom	atm,
		int	position
	)

int mmdb::Residue::InsertAtom	(	PAtom	atm,
		const AtomName	aname
	)

bool mmdb::Residue::isAminoacid

(

)

bool mmdb::Residue::isCTerminus

(

)

int mmdb::Residue::isDNARNA

(

)

bool mmdb::Residue::isInSelection

(

int

selHnd )

bool mmdb::Residue::isMainchainHBond

(

PResidue

res )

bool mmdb::Residue::isModRes

(

)

bool mmdb::Residue::isNTerminus

(

)

bool mmdb::Residue::isNucleotide

(

)

bool mmdb::Residue::isSolvent

(

)

bool mmdb::Residue::isSugar

(

)

void mmdb::Residue::MakeAtomCIF

(

mmcif::PData

CIF )

void mmdb::Residue::MaskAtoms

(

PMask

Mask )

void mmdb::Residue::PDBASCIIAtomDump

(

io::RFile

f )

int mmdb::Residue::PutUDData	(	int	UDDhandle,
		cpstr	sudd
	)

int mmdb::Residue::PutUDData	(	int	UDDhandle,
		int	iudd
	)

int mmdb::Residue::PutUDData	(	int	UDDhandle,
		realtype	rudd
	)

void mmdb::Residue::read

(

io::RFile

f )

Reimplemented from mmdb::UDData.

void mmdb::Residue::SetChain

(

PChain

Chain_Owner )

void mmdb::Residue::SetChainID

(

const ChainID

chID )

void mmdb::Residue::SetResID	(	const ResName	resName,
		int	sqNum,
		const InsCode	ins
	)

void mmdb::Residue::SetResName

(

const ResName

resName )

void mmdb::Residue::TrimAtomTable

(

)

void mmdb::Residue::UnmaskAtoms

(

PMask

Mask )

void mmdb::Residue::write

(

io::RFile

f )

Reimplemented from mmdb::UDData.

---

Friends And Related Function Documentation

friend class Atom [friend]

friend class Chain [friend]

friend class Root [friend]

---

Member Data Documentation

int mmdb::Residue::AtmLen [protected]

PPAtom mmdb::Residue::atom

array of atoms

PChain mmdb::Residue::chain

reference to chain

bool mmdb::Residue::Exclude [protected]

int mmdb::Residue::index

index in the chain

InsCode mmdb::Residue::insCode

residue insertion code

ChainID mmdb::Residue::label_asym_id

assigned chain Id

ResName mmdb::Residue::label_comp_id

assigned residue name

int mmdb::Residue::label_entity_id

assigned entity id

int mmdb::Residue::label_seq_id

assigned residue sequence number

ResName mmdb::Residue::name

residue name - all spaces cut

int mmdb::Residue::nAtoms

number of atoms in the residue

int mmdb::Residue::seqNum

residue sequence number

byte mmdb::Residue::SSE

SSE type.

---

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

• src/mmdb_atom.h
• src/mmdb_atom.cpp