mmdb::Chain Class Reference

#include <mmdb_chain.h>

Inheritance diagram for mmdb::Chain:

List of all members.

Public Member Functions
	Chain ()
	Chain (PProModel model, const ChainID chID)
	Chain (io::RPStream Object)
	~Chain ()
void	FreeAnnotations ()
void	SetModel (PProModel model)
void	SetChain (const ChainID chID)
PManager	GetCoordHierarchy ()
ERROR_CODE	ConvertDBREF (cpstr PDBString)
ERROR_CODE	ConvertSEQADV (cpstr PDBString)
ERROR_CODE	ConvertSEQRES (cpstr PDBString)
ERROR_CODE	ConvertMODRES (cpstr PDBString)
ERROR_CODE	ConvertHET (cpstr PDBString)
void	PDBASCIIDump (io::RFile f)
void	PDBASCIIAtomDump (io::RFile f)
void	MakeAtomCIF (mmcif::PData CIF)
int	GetNumberOfResidues ()
PResidue	GetResidue (int resNo)
PResidue	GetResidue (int seqNum, const InsCode insCode)
int	GetResidueNo (int seqNum, const InsCode insCode)
void	GetResidueTable (PPResidue &resTable, int &NumberOfResidues)
PResidue	GetResidueCreate (const ResName resName, int seqNum, const InsCode insCode, bool Enforce)
int	DeleteResidue (int resNo)
int	DeleteResidue (int seqNum, const InsCode insCode)
int	DeleteAllResidues ()
int	DeleteSolvent ()
void	TrimResidueTable ()
int	AddResidue (PResidue res)
int	InsResidue (PResidue res, int pos)
int	InsResidue (PResidue res, int seqNum, const InsCode insCode)
int	GetNumberOfAtoms (bool countTers)
int	GetNumberOfAtoms (int seqNo, const InsCode insCode)
int	GetNumberOfAtoms (int resNo)
PAtom	GetAtom (int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (int seqNo, const InsCode insCode, int atomNo)
PAtom	GetAtom (int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (int resNo, int atomNo)
void	GetAtomTable (int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (int resNo, PPAtom &atomTable, int &NumberOfAtoms)
int	DeleteAtom (int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (int seqNo, const InsCode insCode, int atomNo)
int	DeleteAtom (int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (int resNo, int atomNo)
int	DeleteAllAtoms (int seqNo, const InsCode insCode)
int	DeleteAllAtoms (int resNo)
int	DeleteAllAtoms ()
int	DeleteAltLocs ()
int	AddAtom (int seqNo, const InsCode insCode, PAtom atom)
int	AddAtom (int resNo, PAtom atom)
void	ApplyTransform (mat44 &TMatrix)
int	GetModelNum ()
PModel	GetModel ()
cpstr	GetChainID ()
void	SetChainID (const ChainID chID)
cpstr	GetChainID (pstr ChID)
void	GetAtomStatistics (RAtomStat AS)
void	CalAtomStatistics (RAtomStat AS)
int	CheckID (const ChainID chID)
int	CheckIDS (cpstr CID)
cpstr	GetEntryID ()
void	SetEntryID (const IDCode idCode)
int	GetNumberOfDBRefs ()
PDBReference	GetDBRef (int dbRefNo)
void	MaskAtoms (PMask Mask)
void	MaskResidues (PMask Mask)
void	UnmaskAtoms (PMask Mask)
void	UnmaskResidues (PMask Mask)
void	SortResidues ()
int	GetNofModResidues ()
PModRes	GetModResidue (int modResNo)
bool	isSolventChain ()
bool	isInSelection (int selHnd)
bool	isAminoacidChain ()
bool	isNucleotideChain ()
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)
void	Copy (PChain chain)
void	CopyAnnotations (PChain chain)
void	write (io::RFile f)
void	read (io::RFile f)
Public Attributes
ChainContainer	DBRef
ChainContainer	seqAdv
SeqRes	seqRes
ChainContainer	modRes
ChainContainer	Het
Protected Member Functions
void	InitChain ()
void	FreeMemory ()
void	ExpandResidueArray (int inc)
int	_ExcludeResidue (const ResName resName, int seqNum, const InsCode insCode)
void	_copy (PChain chain)
void	_copy (PChain chain, PPAtom atom, int &atom_index)
void	CheckInAtoms ()
Protected Attributes
ChainID	chainID
ChainID	prevChainID
PProModel	model
int	nWeights
realtype	Weight
int	nResidues
PPResidue	residue
bool	Exclude
Friends
class	DBReference
class	SeqAdv
class	SeqRes
class	ModRes
class	HetRec
class	Residue
class	Atom
class	Model
class	Root
class	SelManager
class	BondManager
class	CoorManager
class	Manager

---

Constructor & Destructor Documentation

mmdb::Chain::Chain

(

)

mmdb::Chain::Chain	(	PProModel	model,
		const ChainID	chID
	)

mmdb::Chain::Chain

(

io::RPStream

Object )

mmdb::Chain::~Chain

(

)

---

Member Function Documentation

void mmdb::Chain::_copy

(

PChain

chain )

[protected]

void mmdb::Chain::_copy	(	PChain	chain,
		PPAtom	atom,
		int &	atom_index
	)		[protected]

int mmdb::Chain::_ExcludeResidue	(	const ResName	resName,
		int	seqNum,
		const InsCode	insCode
	)		[protected]

int mmdb::Chain::AddAtom	(	int	seqNo,
		const InsCode	insCode,
		PAtom	atom
	)

int mmdb::Chain::AddAtom	(	int	resNo,
		PAtom	atom
	)

int mmdb::Chain::AddResidue

(

PResidue

res )

void mmdb::Chain::ApplyTransform

(

mat44 &

TMatrix )

void mmdb::Chain::CalAtomStatistics

(

RAtomStat

AS )

int mmdb::Chain::CheckID

(

const ChainID

chID )

int mmdb::Chain::CheckIDS

(

cpstr

CID )

void mmdb::Chain::CheckInAtoms

(

)

[protected]

ERROR_CODE mmdb::Chain::ConvertDBREF

(

cpstr

PDBString )

ERROR_CODE mmdb::Chain::ConvertHET

(

cpstr

PDBString )

ERROR_CODE mmdb::Chain::ConvertMODRES

(

cpstr

PDBString )

ERROR_CODE mmdb::Chain::ConvertSEQADV

(

cpstr

PDBString )

ERROR_CODE mmdb::Chain::ConvertSEQRES

(

cpstr

PDBString )

void mmdb::Chain::Copy

(

PChain

chain )

void mmdb::Chain::CopyAnnotations

(

PChain

chain )

int mmdb::Chain::DeleteAllAtoms

(

int

resNo )

int mmdb::Chain::DeleteAllAtoms	(	int	seqNo,
		const InsCode	insCode
	)

int mmdb::Chain::DeleteAllAtoms

(

)

int mmdb::Chain::DeleteAllResidues

(

)

int mmdb::Chain::DeleteAltLocs

(

)

int mmdb::Chain::DeleteAtom	(	int	seqNo,
		const InsCode	insCode,
		const AtomName	aname,
		const Element	elmnt,
		const AltLoc	aloc
	)

int mmdb::Chain::DeleteAtom	(	int	seqNo,
		const InsCode	insCode,
		int	atomNo
	)

int mmdb::Chain::DeleteAtom	(	int	resNo,
		int	atomNo
	)

int mmdb::Chain::DeleteAtom	(	int	resNo,
		const AtomName	aname,
		const Element	elmnt,
		const AltLoc	aloc
	)

int mmdb::Chain::DeleteResidue

(

int

resNo )

int mmdb::Chain::DeleteResidue	(	int	seqNum,
		const InsCode	insCode
	)

int mmdb::Chain::DeleteSolvent

(

)

void mmdb::Chain::ExpandResidueArray

(

int

inc )

[protected]

void mmdb::Chain::FreeAnnotations

(

)

void mmdb::Chain::FreeMemory

(

)

[protected]

PAtom mmdb::Chain::GetAtom	(	int	resNo,
		const AtomName	aname,
		const Element	elmnt,
		const AltLoc	aloc
	)

PAtom mmdb::Chain::GetAtom	(	int	resNo,
		int	atomNo
	)

PAtom mmdb::Chain::GetAtom	(	int	seqNo,
		const InsCode	insCode,
		const AtomName	aname,
		const Element	elmnt,
		const AltLoc	aloc
	)

PAtom mmdb::Chain::GetAtom	(	int	seqNo,
		const InsCode	insCode,
		int	atomNo
	)

void mmdb::Chain::GetAtomStatistics

(

RAtomStat

AS )

void mmdb::Chain::GetAtomTable	(	int	seqNo,
		const InsCode	insCode,
		PPAtom &	atomTable,
		int &	NumberOfAtoms
	)

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

void mmdb::Chain::GetAtomTable1	(	int	seqNo,
		const InsCode	insCode,
		PPAtom &	atomTable,
		int &	NumberOfAtoms
	)

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

cpstr mmdb::Chain::GetChainID

(

)

[inline]

cpstr mmdb::Chain::GetChainID

(

pstr

ChID )

PManager mmdb::Chain::GetCoordHierarchy

(

)

PDBReference mmdb::Chain::GetDBRef

(

int

dbRefNo )

cpstr mmdb::Chain::GetEntryID

(

)

PModel mmdb::Chain::GetModel

(

)

[inline]

int mmdb::Chain::GetModelNum

(

)

PModRes mmdb::Chain::GetModResidue

(

int

modResNo )

int mmdb::Chain::GetNofModResidues

(

)

int mmdb::Chain::GetNumberOfAtoms

(

bool

countTers )

int mmdb::Chain::GetNumberOfAtoms	(	int	seqNo,
		const InsCode	insCode
	)

int mmdb::Chain::GetNumberOfAtoms

(

int

resNo )

int mmdb::Chain::GetNumberOfDBRefs

(

)

int mmdb::Chain::GetNumberOfResidues

(

)

PResidue mmdb::Chain::GetResidue	(	int	seqNum,
		const InsCode	insCode
	)

PResidue mmdb::Chain::GetResidue

(

int

resNo )

PResidue mmdb::Chain::GetResidueCreate	(	const ResName	resName,
		int	seqNum,
		const InsCode	insCode,
		bool	Enforce
	)

int mmdb::Chain::GetResidueNo	(	int	seqNum,
		const InsCode	insCode
	)

void mmdb::Chain::GetResidueTable	(	PPResidue &	resTable,
		int &	NumberOfResidues
	)

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

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

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

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

void mmdb::Chain::InitChain

(

)

[protected]

int mmdb::Chain::InsResidue	(	PResidue	res,
		int	pos
	)

int mmdb::Chain::InsResidue	(	PResidue	res,
		int	seqNum,
		const InsCode	insCode
	)

bool mmdb::Chain::isAminoacidChain

(

)

bool mmdb::Chain::isInSelection

(

int

selHnd )

bool mmdb::Chain::isNucleotideChain

(

)

bool mmdb::Chain::isSolventChain

(

)

void mmdb::Chain::MakeAtomCIF

(

mmcif::PData

CIF )

void mmdb::Chain::MaskAtoms

(

PMask

Mask )

void mmdb::Chain::MaskResidues

(

PMask

Mask )

void mmdb::Chain::PDBASCIIAtomDump

(

io::RFile

f )

void mmdb::Chain::PDBASCIIDump

(

io::RFile

f )

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

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

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

void mmdb::Chain::read

(

io::RFile

f )

Reimplemented from mmdb::UDData.

void mmdb::Chain::SetChain

(

const ChainID

chID )

void mmdb::Chain::SetChainID

(

const ChainID

chID )

void mmdb::Chain::SetEntryID

(

const IDCode

idCode )

void mmdb::Chain::SetModel

(

PProModel

model )

void mmdb::Chain::SortResidues

(

)

void mmdb::Chain::TrimResidueTable

(

)

void mmdb::Chain::UnmaskAtoms

(

PMask

Mask )

void mmdb::Chain::UnmaskResidues

(

PMask

Mask )

void mmdb::Chain::write

(

io::RFile

f )

Reimplemented from mmdb::UDData.

---

Friends And Related Function Documentation

friend class Atom [friend]

friend class BondManager [friend]

friend class CoorManager [friend]

friend class DBReference [friend]

friend class HetRec [friend]

friend class Manager [friend]

friend class Model [friend]

friend class ModRes [friend]

friend class Residue [friend]

friend class Root [friend]

friend class SelManager [friend]

Reimplemented from mmdb::UDData.

friend class SeqAdv [friend]

friend class SeqRes [friend]

---

Member Data Documentation

ChainID mmdb::Chain::chainID [protected]

ChainContainer mmdb::Chain::DBRef

bool mmdb::Chain::Exclude [protected]

ChainContainer mmdb::Chain::Het

PProModel mmdb::Chain::model [protected]

ChainContainer mmdb::Chain::modRes

int mmdb::Chain::nResidues [protected]

int mmdb::Chain::nWeights [protected]

ChainID mmdb::Chain::prevChainID [protected]

PPResidue mmdb::Chain::residue [protected]

ChainContainer mmdb::Chain::seqAdv

SeqRes mmdb::Chain::seqRes

realtype mmdb::Chain::Weight [protected]

---

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

• src/mmdb_chain.h
• src/mmdb_chain.cpp