mmdb::Model Class Reference

#include <mmdb_model.h>

Inheritance diagram for mmdb::Model:

List of all members.

Public Member Functions
	Model ()
	Model (PManager MMDBF, int serialNum)
	Model (io::RPStream Object)
	~Model ()
void	SetMMDBManager (PManager MMDBM, int serialNum)
PManager	GetCoordHierarchy ()
PChain	GetChainCreate (const ChainID chID, bool enforceUniqueChainID)
PChain	CreateChain (const ChainID chID)
cpstr	GetEntryID ()
void	SetEntryID (const IDCode idCode)
int	GetSerNum ()
cpstr	GetModelID (pstr modelID)
int	GetNumberOfModels ()
int	GetNumberOfAtoms (bool countTers)
int	GetNumberOfResidues ()
int	GetNumberOfChains ()
bool	GetNewChainID (ChainID chID, int length=1)
PChain	GetChain (const ChainID chID)
PChain	GetChain (int chainNo)
void	GetChainTable (PPChain &chainTable, int &NumberOfChains)
int	DeleteChain (const ChainID chID)
int	DeleteChain (int chainNo)
int	DeleteAllChains ()
int	DeleteSolventChains ()
void	TrimChainTable ()
int	AddChain (PChain chn)
void	SortChains (int sortKey)
int	GetNumberOfResidues (const ChainID chainID)
int	GetNumberOfResidues (int chainNo)
PResidue	GetResidue (const ChainID chainID, int seqNo, const InsCode insCode)
PResidue	GetResidue (const ChainID chainID, int resNo)
PResidue	GetResidue (int chainNo, int seqNo, const InsCode insCode)
PResidue	GetResidue (int chainNo, int resNo)
int	GetResidueNo (const ChainID chainID, int seqNo, const InsCode insCode)
int	GetResidueNo (int chainNo, int seqNo, const InsCode insCode)
void	GetResidueTable (PPResidue &resTable, int &NumberOfResidues)
void	GetResidueTable (const ChainID chainID, PPResidue &resTable, int &NumberOfResidues)
void	GetResidueTable (int chainNo, PPResidue &resTable, int &NumberOfResidues)
int	DeleteResidue (const ChainID chainID, int seqNo, const InsCode insCode)
int	DeleteResidue (const ChainID chainID, int resNo)
int	DeleteResidue (int chainNo, int seqNo, const InsCode insCode)
int	DeleteResidue (int chainNo, int resNo)
int	DeleteAllResidues (const ChainID chainID)
int	DeleteAllResidues (int chainNo)
int	DeleteSolvent ()
int	DeleteAllResidues ()
int	AddResidue (const ChainID chainID, PResidue res)
int	AddResidue (int chainNo, PResidue res)
int	GetNumberOfAllAtoms ()
PPAtom	GetAllAtoms ()
int	GetNumberOfAtoms (const ChainID chainID, int seqNo, const InsCode insCode)
int	GetNumberOfAtoms (int chainNo, int seqNo, const InsCode insCode)
int	GetNumberOfAtoms (const ChainID chainID, int resNo)
int	GetNumberOfAtoms (int chainNo, int resNo)
PAtom	GetAtom (const ChainID chID, int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (const ChainID chID, int seqNo, const InsCode insCode, int atomNo)
PAtom	GetAtom (const ChainID chID, int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (const ChainID chID, int resNo, int atomNo)
PAtom	GetAtom (int chNo, int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (int chNo, int seqNo, const InsCode insCode, int atomNo)
PAtom	GetAtom (int chNo, int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (int chNo, int resNo, int atomNo)
void	GetAtomTable (const ChainID chainID, int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (int chainNo, int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (const ChainID chainID, int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (int chainNo, int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (const ChainID chainID, int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (int chainNo, int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (const ChainID chainID, int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (int chainNo, int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomStatistics (RAtomStat AS)
void	CalAtomStatistics (RAtomStat AS)
int	DeleteAtom (const ChainID chID, int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (const ChainID chID, int seqNo, const InsCode insCode, int atomNo)
int	DeleteAtom (const ChainID chID, int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (const ChainID chID, int resNo, int atomNo)
int	DeleteAtom (int chNo, int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (int chNo, int seqNo, const InsCode insCode, int atomNo)
int	DeleteAtom (int chNo, int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (int chNo, int resNo, int atomNo)
int	DeleteAllAtoms (const ChainID chID, int seqNo, const InsCode insCode)
int	DeleteAllAtoms (const ChainID chID, int resNo)
int	DeleteAllAtoms (const ChainID chID)
int	DeleteAllAtoms (int chNo, int seqNo, const InsCode insCode)
int	DeleteAllAtoms (int chNo, int resNo)
int	DeleteAllAtoms (int chNo)
int	DeleteAllAtoms ()
int	DeleteAltLocs ()
int	AddAtom (const ChainID chID, int seqNo, const InsCode insCode, PAtom atom)
int	AddAtom (const ChainID chID, int resNo, PAtom atom)
int	AddAtom (int chNo, int seqNo, const InsCode insCode, PAtom atom)
int	AddAtom (int chNo, int resNo, PAtom atom)
ERROR_CODE	ConvertPDBString (pstr PDBString)
void	PDBASCIIDumpPS (io::RFile f)
void	PDBASCIIDumpCP (io::RFile f)
void	PDBASCIIDump (io::RFile f)
void	MakeAtomCIF (mmcif::PData CIF)
void	MakePSCIF (mmcif::PData CIF)
ERROR_CODE	GetCIF (mmcif::PData CIF)
void	MoveChain (PChain &m_chain, PPAtom m_atom, PPAtom atom, int &atom_index, int chain_ext)
void	GetAIndexRange (int &i1, int &i2)
void	MaskAtoms (PMask mask)
void	MaskResidues (PMask mask)
void	MaskChains (PMask mask)
void	UnmaskAtoms (PMask mask)
void	UnmaskResidues (PMask mask)
void	UnmaskChains (PMask mask)
int	GetNumberOfHelices ()
int	GetNumberOfSheets ()
PHelix	GetHelix (int serialNum)
void	GetSheetID (int serialNum, SheetID sheetID)
PSheet	GetSheet (int serialNum)
PSheet	GetSheet (const SheetID sheetID)
int	GetNumberOfStrands (int sheetSerNum)
int	GetNumberOfStrands (const SheetID sheetID)
PStrand	GetStrand (int sheetSerNum, int strandSerNum)
PStrand	GetStrand (const SheetID sheetID, int strandSerNum)
PSSContainer	GetHelices ()
PSheets	GetSheets ()
void	RemoveSecStructure ()
int	CalcSecStructure (bool flagBulge=true, int aminoSelHnd=-1)
PHetCompounds	GetHetInfo ()
void	RemoveHetInfo ()
int	GetNumberOfLinks ()
PLink	GetLink (int serialNum)
PLinkContainer	GetLinks ()
void	RemoveLinks ()
void	AddLink (PLink link)
int	GetNumberOfLinkRs ()
PLinkR	GetLinkR (int serialNum)
PLinkRContainer	GetLinkRs ()
void	RemoveLinkRs ()
void	AddLinkR (PLinkR linkR)
int	GetNumberOfCisPeps ()
PCisPep	GetCisPep (int CisPepNum)
PCisPepContainer	GetCisPeps ()
void	RemoveCisPeps ()
void	AddCisPep (PCisPep cisPep)
void	ApplyTransform (mat44 &TMatrix)
bool	isInSelection (int selHnd)
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 (PModel model)
void	CopyHets (PModel model)
void	CopySecStructure (PModel model)
void	CopyLinks (PModel model)
void	CopyLinkRs (PModel model)
void	CopyCisPeps (PModel model)
void	write (io::RFile f)
void	read (io::RFile f)
Protected Member Functions
void	InitModel ()
void	FreeMemory ()
void	ExpandChainArray (int nOfChains)
ERROR_CODE	GetCIFPSClass (mmcif::PData CIF, int ClassID)
int	_ExcludeChain (const ChainID chainID)
void	_copy (PModel Model)
void	_copy (PModel Model, PPAtom atom, int &atom_index)
void	CheckInAtoms ()
Protected Attributes
int	serNum
PManager	manager
HetCompounds	hetCompounds
SSContainer	helices
Sheets	sheets
SSContainer	turns
LinkContainer	links
LinkRContainer	linkRs
CisPepContainer	cisPeps
int	nChains
int	nChainsAlloc
PPChain	chain
bool	Exclude
Friends
class	Manager
class	BondManager
class	SelManager
class	CoorManager
class	Root
class	Chain
class	Residue
class	Atom

---

Constructor & Destructor Documentation

mmdb::Model::Model

(

)

mmdb::Model::Model	(	PManager	MMDBF,
		int	serialNum
	)

mmdb::Model::Model

(

io::RPStream

Object )

mmdb::Model::~Model

(

)

---

Member Function Documentation

void mmdb::Model::_copy

(

PModel

Model )

[protected]

void mmdb::Model::_copy	(	PModel	Model,
		PPAtom	atom,
		int &	atom_index
	)		[protected]

int mmdb::Model::_ExcludeChain

(

const ChainID

chainID )

[protected, virtual]

Reimplemented from mmdb::ProModel.

int mmdb::Model::AddAtom	(	const ChainID	chID,
		int	seqNo,
		const InsCode	insCode,
		PAtom	atom
	)

int mmdb::Model::AddAtom	(	const ChainID	chID,
		int	resNo,
		PAtom	atom
	)

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

int mmdb::Model::AddAtom	(	int	chNo,
		int	resNo,
		PAtom	atom
	)

int mmdb::Model::AddChain

(

PChain

chn )

[virtual]

Reimplemented from mmdb::ProModel.

void mmdb::Model::AddCisPep

(

PCisPep

cisPep )

void mmdb::Model::AddLink

(

PLink

link )

void mmdb::Model::AddLinkR

(

PLinkR

linkR )

int mmdb::Model::AddResidue	(	const ChainID	chainID,
		PResidue	res
	)

int mmdb::Model::AddResidue	(	int	chainNo,
		PResidue	res
	)

void mmdb::Model::ApplyTransform

(

mat44 &

TMatrix )

void mmdb::Model::CalAtomStatistics

(

RAtomStat

AS )

int mmdb::Model::CalcSecStructure	(	bool	flagBulge = true,
		int	aminoSelHnd = -1
	)

void mmdb::Model::CheckInAtoms

(

)

[protected]

ERROR_CODE mmdb::Model::ConvertPDBString

(

pstr

PDBString )

void mmdb::Model::Copy

(

PModel

model )

void mmdb::Model::CopyCisPeps

(

PModel

model )

void mmdb::Model::CopyHets

(

PModel

model )

void mmdb::Model::CopyLinkRs

(

PModel

model )

void mmdb::Model::CopyLinks

(

PModel

model )

void mmdb::Model::CopySecStructure

(

PModel

model )

PChain mmdb::Model::CreateChain

(

const ChainID

chID )

int mmdb::Model::DeleteAllAtoms	(	const ChainID	chID,
		int	seqNo,
		const InsCode	insCode
	)

int mmdb::Model::DeleteAllAtoms

(

const ChainID

chID )

int mmdb::Model::DeleteAllAtoms	(	const ChainID	chID,
		int	resNo
	)

int mmdb::Model::DeleteAllAtoms	(	int	chNo,
		int	resNo
	)

int mmdb::Model::DeleteAllAtoms

(

int

chNo )

int mmdb::Model::DeleteAllAtoms

(

)

int mmdb::Model::DeleteAllAtoms	(	int	chNo,
		int	seqNo,
		const InsCode	insCode
	)

int mmdb::Model::DeleteAllChains

(

)

int mmdb::Model::DeleteAllResidues

(

const ChainID

chainID )

int mmdb::Model::DeleteAllResidues

(

int

chainNo )

int mmdb::Model::DeleteAllResidues

(

)

int mmdb::Model::DeleteAltLocs

(

)

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

int mmdb::Model::DeleteAtom	(	const ChainID	chID,
		int	seqNo,
		const InsCode	insCode,
		int	atomNo
	)

int mmdb::Model::DeleteAtom	(	const ChainID	chID,
		int	resNo,
		const AtomName	aname,
		const Element	elmnt,
		const AltLoc	aloc
	)

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

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

int mmdb::Model::DeleteAtom	(	int	chNo,
		int	resNo,
		int	atomNo
	)

int mmdb::Model::DeleteAtom	(	const ChainID	chID,
		int	resNo,
		int	atomNo
	)

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

int mmdb::Model::DeleteChain

(

int

chainNo )

int mmdb::Model::DeleteChain

(

const ChainID

chID )

int mmdb::Model::DeleteResidue	(	int	chainNo,
		int	seqNo,
		const InsCode	insCode
	)

int mmdb::Model::DeleteResidue	(	const ChainID	chainID,
		int	seqNo,
		const InsCode	insCode
	)

int mmdb::Model::DeleteResidue	(	const ChainID	chainID,
		int	resNo
	)

int mmdb::Model::DeleteResidue	(	int	chainNo,
		int	resNo
	)

int mmdb::Model::DeleteSolvent

(

)

int mmdb::Model::DeleteSolventChains

(

)

void mmdb::Model::ExpandChainArray

(

int

nOfChains )

[protected]

void mmdb::Model::FreeMemory

(

)

[protected]

void mmdb::Model::GetAIndexRange	(	int &	i1,
		int &	i2
	)

PAtom * mmdb::Model::GetAllAtoms

(

)

[virtual]

Reimplemented from mmdb::ProModel.

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

PAtom mmdb::Model::GetAtom	(	const ChainID	chID,
		int	seqNo,
		const InsCode	insCode,
		int	atomNo
	)

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

PAtom mmdb::Model::GetAtom	(	const ChainID	chID,
		int	resNo,
		int	atomNo
	)

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

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

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

PAtom mmdb::Model::GetAtom	(	int	chNo,
		int	resNo,
		int	atomNo
	)

void mmdb::Model::GetAtomStatistics

(

RAtomStat

AS )

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

void mmdb::Model::GetAtomTable	(	const ChainID	chainID,
		int	resNo,
		PPAtom &	atomTable,
		int &	NumberOfAtoms
	)

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

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

void mmdb::Model::GetAtomTable1	(	const ChainID	chainID,
		int	resNo,
		PPAtom &	atomTable,
		int &	NumberOfAtoms
	)

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

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

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

PChain mmdb::Model::GetChain

(

const ChainID

chID )

PChain mmdb::Model::GetChain

(

int

chainNo )

PChain mmdb::Model::GetChainCreate	(	const ChainID	chID,
		bool	enforceUniqueChainID
	)

void mmdb::Model::GetChainTable	(	PPChain &	chainTable,
		int &	NumberOfChains
	)

ERROR_CODE mmdb::Model::GetCIF

(

mmcif::PData

CIF )

ERROR_CODE mmdb::Model::GetCIFPSClass	(	mmcif::PData	CIF,
		int	ClassID
	)		[protected]

PCisPep mmdb::Model::GetCisPep

(

int

CisPepNum )

PCisPepContainer mmdb::Model::GetCisPeps

(

)

[inline]

PManager mmdb::Model::GetCoordHierarchy

(

)

[inline, virtual]

Reimplemented from mmdb::ProModel.

cpstr mmdb::Model::GetEntryID

(

)

[virtual]

Reimplemented from mmdb::ProModel.

PSSContainer mmdb::Model::GetHelices

(

)

[inline]

PHelix mmdb::Model::GetHelix

(

int

serialNum )

PHetCompounds mmdb::Model::GetHetInfo

(

)

[inline]

PLink mmdb::Model::GetLink

(

int

serialNum )

PLinkR mmdb::Model::GetLinkR

(

int

serialNum )

PLinkRContainer mmdb::Model::GetLinkRs

(

)

[inline]

PLinkContainer mmdb::Model::GetLinks

(

)

[inline]

cpstr mmdb::Model::GetModelID

(

pstr

modelID )

bool mmdb::Model::GetNewChainID	(	ChainID	chID,
		int	length = 1
	)

int mmdb::Model::GetNumberOfAllAtoms

(

)

[virtual]

Reimplemented from mmdb::ProModel.

int mmdb::Model::GetNumberOfAtoms

(

bool

countTers )

int mmdb::Model::GetNumberOfAtoms	(	const ChainID	chainID,
		int	seqNo,
		const InsCode	insCode
	)

int mmdb::Model::GetNumberOfAtoms	(	const ChainID	chainID,
		int	resNo
	)

int mmdb::Model::GetNumberOfAtoms	(	int	chainNo,
		int	seqNo,
		const InsCode	insCode
	)

int mmdb::Model::GetNumberOfAtoms	(	int	chainNo,
		int	resNo
	)

int mmdb::Model::GetNumberOfChains

(

)

int mmdb::Model::GetNumberOfCisPeps

(

)

int mmdb::Model::GetNumberOfHelices

(

)

int mmdb::Model::GetNumberOfLinkRs

(

)

int mmdb::Model::GetNumberOfLinks

(

)

int mmdb::Model::GetNumberOfModels

(

)

[virtual]

Reimplemented from mmdb::ProModel.

int mmdb::Model::GetNumberOfResidues

(

)

int mmdb::Model::GetNumberOfResidues

(

const ChainID

chainID )

int mmdb::Model::GetNumberOfResidues

(

int

chainNo )

int mmdb::Model::GetNumberOfSheets

(

)

int mmdb::Model::GetNumberOfStrands

(

const SheetID

sheetID )

int mmdb::Model::GetNumberOfStrands

(

int

sheetSerNum )

PResidue mmdb::Model::GetResidue	(	const ChainID	chainID,
		int	seqNo,
		const InsCode	insCode
	)

PResidue mmdb::Model::GetResidue	(	int	chainNo,
		int	resNo
	)

PResidue mmdb::Model::GetResidue	(	const ChainID	chainID,
		int	resNo
	)

PResidue mmdb::Model::GetResidue	(	int	chainNo,
		int	seqNo,
		const InsCode	insCode
	)

int mmdb::Model::GetResidueNo	(	int	chainNo,
		int	seqNo,
		const InsCode	insCode
	)

int mmdb::Model::GetResidueNo	(	const ChainID	chainID,
		int	seqNo,
		const InsCode	insCode
	)

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

void mmdb::Model::GetResidueTable	(	const ChainID	chainID,
		PPResidue &	resTable,
		int &	NumberOfResidues
	)

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

int mmdb::Model::GetSerNum

(

)

[virtual]

Reimplemented from mmdb::ProModel.

PSheet mmdb::Model::GetSheet

(

int

serialNum )

PSheet mmdb::Model::GetSheet

(

const SheetID

sheetID )

void mmdb::Model::GetSheetID	(	int	serialNum,
		SheetID	sheetID
	)

PSheets mmdb::Model::GetSheets

(

)

[inline]

PStrand mmdb::Model::GetStrand	(	int	sheetSerNum,
		int	strandSerNum
	)

PStrand mmdb::Model::GetStrand	(	const SheetID	sheetID,
		int	strandSerNum
	)

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

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

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

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

void mmdb::Model::InitModel

(

)

[protected]

bool mmdb::Model::isInSelection

(

int

selHnd )

void mmdb::Model::MakeAtomCIF

(

mmcif::PData

CIF )

void mmdb::Model::MakePSCIF

(

mmcif::PData

CIF )

void mmdb::Model::MaskAtoms

(

PMask

mask )

void mmdb::Model::MaskChains

(

PMask

mask )

void mmdb::Model::MaskResidues

(

PMask

mask )

void mmdb::Model::MoveChain	(	PChain &	m_chain,
		PPAtom	m_atom,
		PPAtom	atom,
		int &	atom_index,
		int	chain_ext
	)

void mmdb::Model::PDBASCIIDump

(

io::RFile

f )

void mmdb::Model::PDBASCIIDumpCP

(

io::RFile

f )

void mmdb::Model::PDBASCIIDumpPS

(

io::RFile

f )

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

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

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

void mmdb::Model::read

(

io::RFile

f )

Reimplemented from mmdb::UDData.

void mmdb::Model::RemoveCisPeps

(

)

void mmdb::Model::RemoveHetInfo

(

)

void mmdb::Model::RemoveLinkRs

(

)

void mmdb::Model::RemoveLinks

(

)

void mmdb::Model::RemoveSecStructure

(

)

void mmdb::Model::SetEntryID

(

const IDCode

idCode )

[virtual]

Reimplemented from mmdb::ProModel.

void mmdb::Model::SetMMDBManager	(	PManager	MMDBM,
		int	serialNum
	)

void mmdb::Model::SortChains

(

int

sortKey )

void mmdb::Model::TrimChainTable

(

)

void mmdb::Model::UnmaskAtoms

(

PMask

mask )

void mmdb::Model::UnmaskChains

(

PMask

mask )

void mmdb::Model::UnmaskResidues

(

PMask

mask )

void mmdb::Model::write

(

io::RFile

f )

Reimplemented from mmdb::UDData.

---

Friends And Related Function Documentation

friend class Atom [friend]

friend class BondManager [friend]

friend class Chain [friend]

Reimplemented from mmdb::ProModel.

friend class CoorManager [friend]

friend class Manager [friend]

friend class Residue [friend]

friend class Root [friend]

friend class SelManager [friend]

Reimplemented from mmdb::UDData.

---

Member Data Documentation

PPChain mmdb::Model::chain [protected]

CisPepContainer mmdb::Model::cisPeps [protected]

bool mmdb::Model::Exclude [protected]

SSContainer mmdb::Model::helices [protected]

HetCompounds mmdb::Model::hetCompounds [protected]

LinkRContainer mmdb::Model::linkRs [protected]

LinkContainer mmdb::Model::links [protected]

PManager mmdb::Model::manager [protected]

int mmdb::Model::nChains [protected]

int mmdb::Model::nChainsAlloc [protected]

int mmdb::Model::serNum [protected]

Sheets mmdb::Model::sheets [protected]

SSContainer mmdb::Model::turns [protected]

---

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

• src/mmdb_model.h
• src/mmdb_model.cpp