mmdb::Root Class Reference

#include <mmdb_root.h>

Inheritance diagram for mmdb::Root:

List of all members.

Public Member Functions
	Root ()
	Root (io::RPStream Object)
	~Root ()
void	FreeFileMemory ()
void	SetFlag (word Flag)
void	RemoveFlag (word Flag)
ERROR_CODE	ReadPDBASCII (cpstr PDBFileName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadPDBASCII1 (cpstr PDBLFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadPDBASCII (io::RFile f)
ERROR_CODE	ReadCIFASCII (cpstr CIFFileName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadCIFASCII1 (cpstr CIFLFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadCIFASCII (io::RFile f)
ERROR_CODE	ReadFromCIF (mmcif::PData CIFD)
ERROR_CODE	AddPDBASCII1 (cpstr PDBLFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	AddPDBASCII (cpstr PDBFileName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadCoorFile (cpstr LFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadCoorFile1 (cpstr CFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadCoorFile (io::RFile f)
ERROR_CODE	WritePDBASCII (cpstr PDBFileName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	WritePDBASCII1 (cpstr PDBLFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
void	WritePDBASCII (io::RFile f)
ERROR_CODE	WriteCIFASCII (cpstr CIFFileName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	WriteCIFASCII1 (cpstr CIFLFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadMMDBF (cpstr MMDBRootName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadMMDBF1 (cpstr MMDBLFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	ReadMMDBF (io::RFile f)
ERROR_CODE	WriteMMDBF (cpstr MMDBRootName, io::GZ_MODE gzipMode=io::GZM_CHECK)
ERROR_CODE	WriteMMDBF1 (cpstr MMDBLFName, io::GZ_MODE gzipMode=io::GZM_CHECK)
void	GetInputBuffer (pstr Line, int &count)
ERROR_CODE	PutPDBString (cpstr PDBString)
word	PDBCleanup (word CleanKey)
void	MakeHetAtoms (cpstr chainID, bool Make)
PPAtom	GetAtomArray ()
int	GetAtomArrayLength ()
PAtom	GetAtomI (int index)
int	PutAtom (int index, int serNum, const AtomName atomName, const ResName resName, const ChainID chainID, int seqNum, const InsCode insCode, const AltLoc altLoc, const SegID segID, const Element element)
int	PutAtom (int index, PAtom A, int serNum=0)
void	RemoveAtom (int index)
int	FinishStructEdit ()
void	TrimModelTable ()
int	DeleteAllModels ()
bool	GetNewChainID (int modelNo, ChainID chID, int length=1)
int	CrystReady ()
bool	isCrystInfo ()
bool	isCellInfo ()
bool	isSpaceGroup ()
bool	isTransfMatrix ()
bool	isScaleMatrix ()
bool	isNCSMatrix ()
int	GetNumberOfNCSMatrices ()
int	GetNumberOfNCSMates ()
bool	GetNCSMatrix (int NCSMatrixNo, mat44 &ncs_m, int &iGiven)
int	GetNumberOfSymOps ()
pstr	GetSymOp (int Nop)
int	RegisterUDInteger (UDR_TYPE udr_type, cpstr UDDataID)
int	RegisterUDReal (UDR_TYPE udr_type, cpstr UDDataID)
int	RegisterUDString (UDR_TYPE udr_type, cpstr UDDataID)
int	GetUDDHandle (UDR_TYPE udr_type, cpstr UDDataID)
void	SetSyminfoLib (cpstr syminfo_lib)
pstr	GetSyminfoLib ()
int	SetSpaceGroup (cpstr spGroup)
pstr	GetSpaceGroup ()
pstr	GetSpaceGroupFix ()
void	GetAtomStatistics (RAtomStat AS)
void	SetIgnoreSCALEi (bool ignoreScalei)
void	SetCell (realtype cell_a, realtype cell_b, realtype cell_c, realtype cell_alpha, realtype cell_beta, realtype cell_gamma, int OrthCode=0)
void	PutCell (realtype cell_a, realtype cell_b, realtype cell_c, realtype cell_alpha, realtype cell_beta, realtype cell_gamma, int OrthCode=0)
int	GetCell (realtype &cell_a, realtype &cell_b, realtype &cell_c, realtype &cell_alpha, realtype &cell_beta, realtype &cell_gamma, realtype &vol, int &OrthCode)
int	GetRCell (realtype &cell_as, realtype &cell_bs, realtype &cell_cs, realtype &cell_alphas, realtype &cell_betas, realtype &cell_gammas, realtype &vols, int &OrthCode)
void	GetROMatrix (mat44 &RO)
int	GetTMatrix (mat44 &TMatrix, int Nop, int cellshift_a, int cellshift_b, int cellshift_c)
int	GetUCTMatrix (mat44 &TMatrix, int Nop, realtype x, realtype y, realtype z, int cellshift_a, int cellshift_b, int cellshift_c)
int	GetFractMatrix (mat44 &TMatrix, int Nop, int cellshift_a, int cellshift_b, int cellshift_c)
int	GetSymOpMatrix (mat44 &TMatrix, int Nop)
int	AddNCSMatrix (mat33 &ncs_m, vect3 &ncs_v, int iGiven)
int	GenerateNCSMates ()
pstr	GetEntryID ()
void	SetEntryID (const IDCode idCode)
int	GetNofExpDataRecs ()
pstr	GetExpDataRec (int recNo)
int	GetNofMdlTypeRecs ()
pstr	GetMdlTypeRec (int recNo)
int	GetFileType ()
void	Copy (PRoot MMDBRoot)
void	SetShortBinary ()
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)
pstr	GetStructureTitle (pstr &L)
PCryst	GetCrystData ()
PClassContainer	GetUnparsedA ()
PClassContainer	GetUnparsedB ()
PClassContainer	GetUnparsedC ()
Protected Member Functions
void	InitMMDBRoot ()
void	FreeCoordMemory ()
void	ReadPDBLine (io::RFile f, pstr L, int maxlen)
ERROR_CODE	ReadPDBAtom (cpstr L)
ERROR_CODE	ReadCIFAtom (mmcif::PData CIFD)
ERROR_CODE	CheckAtomPlace (int index, cpstr L)
ERROR_CODE	CheckAtomPlace (int index, mmcif::PLoop Loop)
ERROR_CODE	SwitchModel (cpstr L)
ERROR_CODE	SwitchModel (int nM)
ERROR_CODE	AllocateAtom (int index, const ChainID chainID, const ChainID label_asym_id, const ResName resName, const ResName label_comp_id, int seqNum, int label_seq_id, int label_entity_id, const InsCode insCode, bool Replace)
void	ExpandAtomArray (int inc)
void	AddAtomArray (int inc)
void	ApplyNCSTransform (int NCSMatrixNo)
virtual void	ResetManager ()
void	write (io::RFile f)
void	read (io::RFile f)
int	_ExcludeModel (int serNum)
int	CheckInAtom (int index, PAtom A)
int	CheckInAtoms (int index, PPAtom A, int natms)
virtual PMask	GetSelMask (int selHnd)
Protected Attributes
word	Flags
int	FType
Title	title
Cryst	cryst
UDRegister	udRegister
int	nModels
PPModel	model
int	nAtoms
int	atmLen
PPAtom	atom
AtomPath	DefPath
ClassContainer	SA
ClassContainer	Footnote
ClassContainer	SB
ClassContainer	SC
int	lcount
char	S [500]
mmcif::PData	CIF
PModel	crModel
PChain	crChain
PResidue	crRes
bool	Exclude
bool	ignoreRemarks
bool	allowDuplChID
bool	enforceUniqueChID
Friends
class	Model
class	Chain
class	Residue
class	Atom

---

Constructor & Destructor Documentation

mmdb::Root::Root

(

)

mmdb::Root::Root

(

io::RPStream

Object )

mmdb::Root::~Root

(

)

---

Member Function Documentation

int mmdb::Root::_ExcludeModel

(

int

serNum )

[protected]

void mmdb::Root::AddAtomArray

(

int

inc )

[protected]

int mmdb::Root::AddNCSMatrix	(	mat33 &	ncs_m,
		vect3 &	ncs_v,
		int	iGiven
	)

ERROR_CODE mmdb::Root::AddPDBASCII	(	cpstr	PDBFileName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::AddPDBASCII1	(	cpstr	PDBLFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::AllocateAtom	(	int	index,
		const ChainID	chainID,
		const ChainID	label_asym_id,
		const ResName	resName,
		const ResName	label_comp_id,
		int	seqNum,
		int	label_seq_id,
		int	label_entity_id,
		const InsCode	insCode,
		bool	Replace
	)		[protected]

void mmdb::Root::ApplyNCSTransform

(

int

NCSMatrixNo )

[protected]

ERROR_CODE mmdb::Root::CheckAtomPlace	(	int	index,
		mmcif::PLoop	Loop
	)		[protected]

ERROR_CODE mmdb::Root::CheckAtomPlace	(	int	index,
		cpstr	L
	)		[protected]

int mmdb::Root::CheckInAtom	(	int	index,
		PAtom	A
	)		[protected]

int mmdb::Root::CheckInAtoms	(	int	index,
		PPAtom	A,
		int	natms
	)		[protected]

void mmdb::Root::Copy

(

PRoot

MMDBRoot )

int mmdb::Root::CrystReady

(

)

int mmdb::Root::DeleteAllModels

(

)

void mmdb::Root::ExpandAtomArray

(

int

inc )

[protected]

int mmdb::Root::FinishStructEdit

(

)

void mmdb::Root::FreeCoordMemory

(

)

[protected]

void mmdb::Root::FreeFileMemory

(

)

int mmdb::Root::GenerateNCSMates

(

)

PPAtom mmdb::Root::GetAtomArray

(

)

[inline]

int mmdb::Root::GetAtomArrayLength

(

)

[inline]

PAtom mmdb::Root::GetAtomI

(

int

index )

void mmdb::Root::GetAtomStatistics

(

RAtomStat

AS )

int mmdb::Root::GetCell	(	realtype &	cell_a,
		realtype &	cell_b,
		realtype &	cell_c,
		realtype &	cell_alpha,
		realtype &	cell_beta,
		realtype &	cell_gamma,
		realtype &	vol,
		int &	OrthCode
	)

PCryst mmdb::Root::GetCrystData

(

)

[inline]

pstr mmdb::Root::GetEntryID

(

)

pstr mmdb::Root::GetExpDataRec

(

int

recNo )

int mmdb::Root::GetFileType

(

)

[inline]

int mmdb::Root::GetFractMatrix	(	mat44 &	TMatrix,
		int	Nop,
		int	cellshift_a,
		int	cellshift_b,
		int	cellshift_c
	)

void mmdb::Root::GetInputBuffer	(	pstr	Line,
		int &	count
	)

pstr mmdb::Root::GetMdlTypeRec

(

int

recNo )

bool mmdb::Root::GetNCSMatrix	(	int	NCSMatrixNo,
		mat44 &	ncs_m,
		int &	iGiven
	)

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

int mmdb::Root::GetNofExpDataRecs

(

)

int mmdb::Root::GetNofMdlTypeRecs

(

)

int mmdb::Root::GetNumberOfNCSMates

(

)

int mmdb::Root::GetNumberOfNCSMatrices

(

)

int mmdb::Root::GetNumberOfSymOps

(

)

int mmdb::Root::GetRCell	(	realtype &	cell_as,
		realtype &	cell_bs,
		realtype &	cell_cs,
		realtype &	cell_alphas,
		realtype &	cell_betas,
		realtype &	cell_gammas,
		realtype &	vols,
		int &	OrthCode
	)

void mmdb::Root::GetROMatrix

(

mat44 &

RO )

PMask mmdb::Root::GetSelMask

(

int

selHnd )

[protected, virtual]

Reimplemented in mmdb::SelManager.

pstr mmdb::Root::GetSpaceGroup

(

)

pstr mmdb::Root::GetSpaceGroupFix

(

)

pstr mmdb::Root::GetStructureTitle

(

pstr &

L )

pstr mmdb::Root::GetSyminfoLib

(

)

pstr mmdb::Root::GetSymOp

(

int

Nop )

int mmdb::Root::GetSymOpMatrix	(	mat44 &	TMatrix,
		int	Nop
	)

int mmdb::Root::GetTMatrix	(	mat44 &	TMatrix,
		int	Nop,
		int	cellshift_a,
		int	cellshift_b,
		int	cellshift_c
	)

int mmdb::Root::GetUCTMatrix	(	mat44 &	TMatrix,
		int	Nop,
		realtype	x,
		realtype	y,
		realtype	z,
		int	cellshift_a,
		int	cellshift_b,
		int	cellshift_c
	)

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

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

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

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

int mmdb::Root::GetUDDHandle	(	UDR_TYPE	udr_type,
		cpstr	UDDataID
	)

PClassContainer mmdb::Root::GetUnparsedA

(

)

[inline]

PClassContainer mmdb::Root::GetUnparsedB

(

)

[inline]

PClassContainer mmdb::Root::GetUnparsedC

(

)

[inline]

void mmdb::Root::InitMMDBRoot

(

)

[protected]

bool mmdb::Root::isCellInfo

(

)

bool mmdb::Root::isCrystInfo

(

)

bool mmdb::Root::isNCSMatrix

(

)

bool mmdb::Root::isScaleMatrix

(

)

bool mmdb::Root::isSpaceGroup

(

)

bool mmdb::Root::isTransfMatrix

(

)

void mmdb::Root::MakeHetAtoms	(	cpstr	chainID,
		bool	Make
	)

word mmdb::Root::PDBCleanup

(

word

CleanKey )

int mmdb::Root::PutAtom	(	int	index,
		int	serNum,
		const AtomName	atomName,
		const ResName	resName,
		const ChainID	chainID,
		int	seqNum,
		const InsCode	insCode,
		const AltLoc	altLoc,
		const SegID	segID,
		const Element	element
	)

int mmdb::Root::PutAtom	(	int	index,
		PAtom	A,
		int	serNum = 0
	)

void mmdb::Root::PutCell	(	realtype	cell_a,
		realtype	cell_b,
		realtype	cell_c,
		realtype	cell_alpha,
		realtype	cell_beta,
		realtype	cell_gamma,
		int	OrthCode = 0
	)

ERROR_CODE mmdb::Root::PutPDBString

(

cpstr

PDBString )

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

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

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

void mmdb::Root::read

(

io::RFile

f )

[protected]

Reimplemented from mmdb::UDData.

Reimplemented in mmdb::BondManager, mmdb::CoorManager, mmdb::Manager, and mmdb::SelManager.

ERROR_CODE mmdb::Root::ReadCIFASCII

(

io::RFile

f )

ERROR_CODE mmdb::Root::ReadCIFASCII	(	cpstr	CIFFileName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::ReadCIFASCII1	(	cpstr	CIFLFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::ReadCIFAtom

(

mmcif::PData

CIFD )

[protected]

ERROR_CODE mmdb::Root::ReadCoorFile	(	cpstr	LFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::ReadCoorFile

(

io::RFile

f )

ERROR_CODE mmdb::Root::ReadCoorFile1	(	cpstr	CFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::ReadFromCIF

(

mmcif::PData

CIFD )

ERROR_CODE mmdb::Root::ReadMMDBF

(

io::RFile

f )

ERROR_CODE mmdb::Root::ReadMMDBF	(	cpstr	MMDBRootName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::ReadMMDBF1	(	cpstr	MMDBLFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::ReadPDBASCII	(	cpstr	PDBFileName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::ReadPDBASCII

(

io::RFile

f )

ERROR_CODE mmdb::Root::ReadPDBASCII1	(	cpstr	PDBLFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::ReadPDBAtom

(

cpstr

L )

[protected]

void mmdb::Root::ReadPDBLine	(	io::RFile	f,
		pstr	L,
		int	maxlen
	)		[protected]

int mmdb::Root::RegisterUDInteger	(	UDR_TYPE	udr_type,
		cpstr	UDDataID
	)

int mmdb::Root::RegisterUDReal	(	UDR_TYPE	udr_type,
		cpstr	UDDataID
	)

int mmdb::Root::RegisterUDString	(	UDR_TYPE	udr_type,
		cpstr	UDDataID
	)

void mmdb::Root::RemoveAtom

(

int

index )

void mmdb::Root::RemoveFlag

(

word

Flag )

void mmdb::Root::ResetManager

(

)

[protected, virtual]

Reimplemented in mmdb::CoorManager, and mmdb::SelManager.

void mmdb::Root::SetCell	(	realtype	cell_a,
		realtype	cell_b,
		realtype	cell_c,
		realtype	cell_alpha,
		realtype	cell_beta,
		realtype	cell_gamma,
		int	OrthCode = 0
	)

void mmdb::Root::SetEntryID

(

const IDCode

idCode )

void mmdb::Root::SetFlag

(

word

Flag )

void mmdb::Root::SetIgnoreSCALEi

(

bool

ignoreScalei )

void mmdb::Root::SetShortBinary

(

)

int mmdb::Root::SetSpaceGroup

(

cpstr

spGroup )

void mmdb::Root::SetSyminfoLib

(

cpstr

syminfo_lib )

ERROR_CODE mmdb::Root::SwitchModel

(

cpstr

L )

[protected]

ERROR_CODE mmdb::Root::SwitchModel

(

int

nM )

[protected]

void mmdb::Root::TrimModelTable

(

)

void mmdb::Root::write

(

io::RFile

f )

[protected]

Reimplemented from mmdb::UDData.

Reimplemented in mmdb::BondManager, mmdb::CoorManager, mmdb::Manager, and mmdb::SelManager.

ERROR_CODE mmdb::Root::WriteCIFASCII	(	cpstr	CIFFileName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::WriteCIFASCII1	(	cpstr	CIFLFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::WriteMMDBF	(	cpstr	MMDBRootName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::WriteMMDBF1	(	cpstr	MMDBLFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

void mmdb::Root::WritePDBASCII

(

io::RFile

f )

ERROR_CODE mmdb::Root::WritePDBASCII	(	cpstr	PDBFileName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

ERROR_CODE mmdb::Root::WritePDBASCII1	(	cpstr	PDBLFName,
		io::GZ_MODE	gzipMode = io::GZM_CHECK
	)

---

Friends And Related Function Documentation

friend class Atom [friend]

friend class Chain [friend]

friend class Model [friend]

friend class Residue [friend]

---

Member Data Documentation

bool mmdb::Root::allowDuplChID [protected]

int mmdb::Root::atmLen [protected]

PPAtom mmdb::Root::atom [protected]

mmcif::PData mmdb::Root::CIF [protected]

PChain mmdb::Root::crChain [protected]

PModel mmdb::Root::crModel [protected]

PResidue mmdb::Root::crRes [protected]

Cryst mmdb::Root::cryst [protected]

AtomPath mmdb::Root::DefPath [protected]

bool mmdb::Root::enforceUniqueChID [protected]

bool mmdb::Root::Exclude [protected]

word mmdb::Root::Flags [protected]

ClassContainer mmdb::Root::Footnote [protected]

int mmdb::Root::FType [protected]

bool mmdb::Root::ignoreRemarks [protected]

int mmdb::Root::lcount [protected]

PPModel mmdb::Root::model [protected]

int mmdb::Root::nAtoms [protected]

int mmdb::Root::nModels [protected]

char mmdb::Root::S[500] [protected]

ClassContainer mmdb::Root::SA [protected]

ClassContainer mmdb::Root::SB [protected]

ClassContainer mmdb::Root::SC [protected]

Title mmdb::Root::title [protected]

UDRegister mmdb::Root::udRegister [protected]

---

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

• src/mmdb_root.h
• src/mmdb_root.cpp