mmdb::CoorManager Class Reference

#include <mmdb_coormngr.h>

Inheritance diagram for mmdb::CoorManager:

List of all members.

Public Member Functions
	CoorManager ()
	CoorManager (io::RPStream Object)
	~CoorManager ()
int	SetDefaultCoorID (cpstr CID)
void	RemoveBricks ()
bool	areBricks ()
void	MakeBricks (PPAtom atmvec, int avlen, realtype Margin, realtype BrickSize=6.0)
void	GetBrickDimension (int &nxmax, int &nymax, int &nzmax)
void	GetBrickCoor (PAtom A, int &nx, int &ny, int &nz)
void	GetBrickCoor (realtype x, realtype y, realtype z, int &nx, int &ny, int &nz)
PBrick	GetBrick (int nx, int ny, int nz)
void	RemoveMBricks ()
bool	areMBricks ()
void	MakeMBricks (PPAtom *atmvec, ivector avlen, int nStructures, realtype Margin, realtype BrickSize=6.0)
void	GetMBrickDimension (int &nxmax, int &nymax, int &nzmax)
void	GetMBrickCoor (PAtom A, int &nx, int &ny, int &nz)
void	GetMBrickCoor (realtype x, realtype y, realtype z, int &nx, int &ny, int &nz)
PMBrick	GetMBrick (int nx, int ny, int nz)
int	GetNumberOfModels ()
int	GetFirstModelNum ()
PModel	GetFirstDefinedModel ()
PModel	GetModel (int modelNo)
PModel	GetModel (cpstr CID)
void	GetModelTable (PPModel &modTable, int &NumberOfModels)
int	DeleteModel (cpstr CID)
int	DeleteModel (int modelNo)
int	AddModel (PModel mdl)
int	InsModel (PModel mdl, int modelNo)
void	RotateModels (int modelNo1, int modelNo2, int rotdir)
void	SwapModels (int modelNo1, int modelNo2)
int	GetNumberOfChains (int modelNo)
int	GetNumberOfChains (cpstr CID)
PChain	GetChain (int modelNo, const ChainID chainID)
PChain	GetChain (int modelNo, int chainNo)
PChain	GetChain (cpstr CID)
void	GetChainTable (int modelNo, PPChain &chainTable, int &NumberOfChains)
void	GetChainTable (cpstr CID, PPChain &chainTable, int &NumberOfChains)
int	DeleteChain (int modelNo, const ChainID chID)
int	DeleteChain (int modelNo, int chainNo)
int	DeleteAllChains (int modelNo)
int	DeleteAllChains ()
int	AddChain (int modelNo, PChain chain)
int	GetNumberOfResidues (int modelNo, const ChainID chainID)
int	GetNumberOfResidues (int modelNo, int chainNo)
int	GetNumberOfResidues (cpstr CID)
PResidue	GetResidue (int modelNo, const ChainID chainID, int seqNo, const InsCode insCode)
PResidue	GetResidue (int modelNo, int chainNo, int seqNo, const InsCode insCode)
PResidue	GetResidue (int modelNo, const ChainID chainID, int resNo)
PResidue	GetResidue (int modelNo, int chainNo, int resNo)
PResidue	GetResidue (cpstr CID)
int	GetResidueNo (int modelNo, const ChainID chainID, int seqNo, const InsCode insCode)
int	GetResidueNo (int modelNo, int chainNo, int seqNo, const InsCode insCode)
void	GetResidueTable (PPResidue &resTable, int &NumberOfResidues)
void	GetResidueTable (int modelNo, const ChainID chainID, PPResidue &resTable, int &NumberOfResidues)
void	GetResidueTable (int modelNo, int chainNo, PPResidue &resTable, int &NumberOfResidues)
void	GetResidueTable (cpstr CID, PPResidue &resTable, int &NumberOfResidues)
int	DeleteResidue (int modelNo, const ChainID chainID, int seqNo, const InsCode insCode)
int	DeleteResidue (int modelNo, const ChainID chainID, int resNo)
int	DeleteResidue (int modelNo, int chainNo, int seqNo, const InsCode insCode)
int	DeleteResidue (int modelNo, int chainNo, int resNo)
int	DeleteAllResidues (int modelNo, const ChainID chainID)
int	DeleteAllResidues (int modelNo, int chainNo)
int	DeleteAllResidues (int modelNo)
int	DeleteAllResidues ()
int	DeleteSolvent ()
int	AddResidue (int modelNo, const ChainID chainID, PResidue res)
int	AddResidue (int modelNo, int chainNo, PResidue res)
int	GetNumberOfAtoms ()
int	GetNumberOfAtoms (int modelNo, const ChainID chainID, int seqNo, const InsCode insCode)
int	GetNumberOfAtoms (int modelNo, int chainNo, int seqNo, const InsCode insCode)
int	GetNumberOfAtoms (int modelNo, const ChainID chainID, int resNo)
int	GetNumberOfAtoms (int modelNo, int chainNo, int resNo)
int	GetNumberOfAtoms (cpstr CID)
PAtom	GetAtom (int modelNo, const ChainID chID, int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (int modelNo, const ChainID chID, int seqNo, const InsCode insCode, int atomNo)
PAtom	GetAtom (int modelNo, const ChainID chID, int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (int modelNo, const ChainID chID, int resNo, int atomNo)
PAtom	GetAtom (int modelNo, int chNo, int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (int modelNo, int chNo, int seqNo, const InsCode insCode, int atomNo)
PAtom	GetAtom (int modelNo, int chNo, int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
PAtom	GetAtom (int modelNo, int chNo, int resNo, int atomNo)
PAtom	GetAtom (cpstr CID)
void	GetAtomTable (PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (int modelNo, const ChainID chainID, int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (int modelNo, int chainNo, int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (int modelNo, const ChainID chainID, int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (int modelNo, int chainNo, int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable (cpstr CID, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (int modelNo, const ChainID chainID, int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (int modelNo, int chainNo, int seqNo, const InsCode insCode, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (int modelNo, const ChainID chainID, int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (int modelNo, int chainNo, int resNo, PPAtom &atomTable, int &NumberOfAtoms)
void	GetAtomTable1 (cpstr CID, PPAtom &atomTable, int &NumberOfAtoms)
int	DeleteAtom (int modelNo, const ChainID chID, int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (int modelNo, const ChainID chID, int seqNo, const InsCode insCode, int atomNo)
int	DeleteAtom (int modelNo, const ChainID chID, int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (int modelNo, const ChainID chID, int resNo, int atomNo)
int	DeleteAtom (int modelNo, int chNo, int seqNo, const InsCode insCode, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (int modelNo, int chNo, int seqNo, const InsCode insCode, int atomNo)
int	DeleteAtom (int modelNo, int chNo, int resNo, const AtomName aname, const Element elmnt, const AltLoc aloc)
int	DeleteAtom (int modelNo, int chNo, int resNo, int atomNo)
int	DeleteAllAtoms (int modelNo, const ChainID chID, int seqNo, const InsCode insCode)
int	DeleteAllAtoms (int modelNo, const ChainID chID, int resNo)
int	DeleteAllAtoms (int modelNo, const ChainID chID)
int	DeleteAllAtoms (int modelNo, int chNo, int seqNo, const InsCode insCode)
int	DeleteAllAtoms (int modelNo, int chNo, int resNo)
int	DeleteAllAtoms (int modelNo, int chNo)
int	DeleteAllAtoms (int modelNo)
int	DeleteAllAtoms ()
int	DeleteAltLocs ()
int	AddAtom (int modelNo, const ChainID chID, int seqNo, const InsCode insCode, PAtom atom)
int	AddAtom (int modelNo, const ChainID chID, int resNo, PAtom atom)
int	AddAtom (int modelNo, int chNo, int seqNo, const InsCode insCode, PAtom atom)
int	AddAtom (int modelNo, int chNo, int resNo, PAtom atom)
int	GenerateSymMates (PGenSym genSym=NULL)
void	ApplyTransform (mat44 &TMatrix)
int	BringToUnitCell ()
bool	Frac2Orth (realtype xfrac, realtype yfrac, realtype zfrac, realtype &xorth, realtype &yorth, realtype &zorth)
bool	Orth2Frac (realtype xorth, realtype yorth, realtype zorth, realtype &xfrac, realtype &yfrac, realtype &zfrac)
bool	Frac2Orth (mat44 &F, mat44 &T)
bool	Orth2Frac (mat44 &T, mat44 &F)
void	SeekContacts (PPAtom AIndex, int ilen, int atomNum, realtype dist1, realtype dist2, int seqDist, RPContact contact, int &ncontacts, int maxlen=0, long group=0)
void	SeekContacts (PAtom A, PPAtom AIndex, int ilen, realtype dist1, realtype dist2, int seqDist, RPContact contact, int &ncontacts, int maxlen=0, long group=0)
void	SeekContacts (PPAtom AIndex1, int ilen1, PPAtom AIndex2, int ilen2, realtype dist1, realtype dist2, int seqDist, RPContact contact, int &ncontacts, int maxlen=0, mat44 *TMatrix=NULL, long group=0, int bricking=0, bool doSqrt=true)
void	SeekContacts (PPAtom AIndex1, int ilen1, PPAtom AIndex2, int ilen2, realtype contDist, PContact contact, int &ncontacts, int bricking=0)
void	SeekContacts (PPAtom AIndex1, int ilen1, PPAtom *AIndex2, ivector ilen2, int nStructures, realtype dist1, realtype dist2, PPMContact &contact, int bricking=0)
Public Attributes
int	CoorIDCode
Protected Member Functions
void	write (io::RFile f)
void	read (io::RFile f)
void	InitMMDBCoorManager ()
void	ApplySymTransform (int SymMatrixNo, PGenSym genSym=NULL)
void	ResetManager ()
void	FindSeqSection (PAtom atom, int seqDist, int &seq1, int &seq2)
bool	iContact (PAtom a1, PAtom a2, int seq1, int seq2, realtype dd, realtype d12, realtype d22, realtype &d2)
bool	iContact (realtype x, realtype y, realtype z, PAtom a2, realtype dd, realtype d12, realtype d22, realtype &d2)
Protected Attributes
realtype	brick_size
realtype	xbrick_0
realtype	ybrick_0
realtype	zbrick_0
int	nbrick_x
int	nbrick_y
int	nbrick_z
PPPBrick *	brick
realtype	mbrick_size
realtype	xmbrick_0
realtype	ymbrick_0
realtype	zmbrick_0
int	nmbrick_x
int	nmbrick_y
int	nmbrick_z
PPPMBrick *	mbrick

---

Constructor & Destructor Documentation

mmdb::CoorManager::CoorManager

(

)

mmdb::CoorManager::CoorManager

(

io::RPStream

Object )

mmdb::CoorManager::~CoorManager

(

)

---

Member Function Documentation

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

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

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

int mmdb::CoorManager::AddAtom	(	int	modelNo,
		int	chNo,
		int	resNo,
		PAtom	atom
	)

int mmdb::CoorManager::AddChain	(	int	modelNo,
		PChain	chain
	)

int mmdb::CoorManager::AddModel

(

PModel

mdl )

int mmdb::CoorManager::AddResidue	(	int	modelNo,
		int	chainNo,
		PResidue	res
	)

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

void mmdb::CoorManager::ApplySymTransform	(	int	SymMatrixNo,
		PGenSym	genSym = NULL
	)		[protected]

void mmdb::CoorManager::ApplyTransform

(

mat44 &

TMatrix )

bool mmdb::CoorManager::areBricks

(

)

[inline]

bool mmdb::CoorManager::areMBricks

(

)

[inline]

int mmdb::CoorManager::BringToUnitCell

(

)

int mmdb::CoorManager::DeleteAllAtoms	(	int	modelNo,
		const ChainID	chID,
		int	resNo
	)

int mmdb::CoorManager::DeleteAllAtoms	(	int	modelNo,
		const ChainID	chID
	)

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

int mmdb::CoorManager::DeleteAllAtoms	(	int	modelNo,
		int	chNo
	)

int mmdb::CoorManager::DeleteAllAtoms

(

int

modelNo )

int mmdb::CoorManager::DeleteAllAtoms

(

)

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

int mmdb::CoorManager::DeleteAllAtoms	(	int	modelNo,
		int	chNo,
		int	resNo
	)

int mmdb::CoorManager::DeleteAllChains

(

int

modelNo )

int mmdb::CoorManager::DeleteAllChains

(

)

int mmdb::CoorManager::DeleteAllResidues	(	int	modelNo,
		int	chainNo
	)

int mmdb::CoorManager::DeleteAllResidues	(	int	modelNo,
		const ChainID	chainID
	)

int mmdb::CoorManager::DeleteAllResidues

(

)

int mmdb::CoorManager::DeleteAllResidues

(

int

modelNo )

int mmdb::CoorManager::DeleteAltLocs

(

)

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

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

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

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

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

int mmdb::CoorManager::DeleteAtom	(	int	modelNo,
		int	chNo,
		int	resNo,
		int	atomNo
	)

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

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

int mmdb::CoorManager::DeleteChain	(	int	modelNo,
		int	chainNo
	)

int mmdb::CoorManager::DeleteChain	(	int	modelNo,
		const ChainID	chID
	)

int mmdb::CoorManager::DeleteModel

(

int

modelNo )

int mmdb::CoorManager::DeleteModel

(

cpstr

CID )

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

int mmdb::CoorManager::DeleteResidue	(	int	modelNo,
		const ChainID	chainID,
		int	resNo
	)

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

int mmdb::CoorManager::DeleteResidue	(	int	modelNo,
		int	chainNo,
		int	resNo
	)

int mmdb::CoorManager::DeleteSolvent

(

)

void mmdb::CoorManager::FindSeqSection	(	PAtom	atom,
		int	seqDist,
		int &	seq1,
		int &	seq2
	)		[protected]

bool mmdb::CoorManager::Frac2Orth	(	realtype	xfrac,
		realtype	yfrac,
		realtype	zfrac,
		realtype &	xorth,
		realtype &	yorth,
		realtype &	zorth
	)

bool mmdb::CoorManager::Frac2Orth	(	mat44 &	F,
		mat44 &	T
	)

int mmdb::CoorManager::GenerateSymMates

(

PGenSym

genSym = NULL )

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

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

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

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

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

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

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

PAtom mmdb::CoorManager::GetAtom	(	int	modelNo,
		int	chNo,
		int	resNo,
		int	atomNo
	)

PAtom mmdb::CoorManager::GetAtom

(

cpstr

CID )

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

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

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

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

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

void mmdb::CoorManager::GetAtomTable	(	cpstr	CID,
		PPAtom &	atomTable,
		int &	NumberOfAtoms
	)

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

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

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

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

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

void mmdb::CoorManager::GetAtomTable1	(	cpstr	CID,
		PPAtom &	atomTable,
		int &	NumberOfAtoms
	)

PBrick mmdb::CoorManager::GetBrick	(	int	nx,
		int	ny,
		int	nz
	)

void mmdb::CoorManager::GetBrickCoor	(	PAtom	A,
		int &	nx,
		int &	ny,
		int &	nz
	)

void mmdb::CoorManager::GetBrickCoor	(	realtype	x,
		realtype	y,
		realtype	z,
		int &	nx,
		int &	ny,
		int &	nz
	)

void mmdb::CoorManager::GetBrickDimension	(	int &	nxmax,
		int &	nymax,
		int &	nzmax
	)

PChain mmdb::CoorManager::GetChain

(

cpstr

CID )

PChain mmdb::CoorManager::GetChain	(	int	modelNo,
		const ChainID	chainID
	)

PChain mmdb::CoorManager::GetChain	(	int	modelNo,
		int	chainNo
	)

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

void mmdb::CoorManager::GetChainTable	(	cpstr	CID,
		PPChain &	chainTable,
		int &	NumberOfChains
	)

PModel mmdb::CoorManager::GetFirstDefinedModel

(

)

int mmdb::CoorManager::GetFirstModelNum

(

)

PMBrick mmdb::CoorManager::GetMBrick	(	int	nx,
		int	ny,
		int	nz
	)

void mmdb::CoorManager::GetMBrickCoor	(	PAtom	A,
		int &	nx,
		int &	ny,
		int &	nz
	)

void mmdb::CoorManager::GetMBrickCoor	(	realtype	x,
		realtype	y,
		realtype	z,
		int &	nx,
		int &	ny,
		int &	nz
	)

void mmdb::CoorManager::GetMBrickDimension	(	int &	nxmax,
		int &	nymax,
		int &	nzmax
	)

PModel mmdb::CoorManager::GetModel

(

int

modelNo )

PModel mmdb::CoorManager::GetModel

(

cpstr

CID )

void mmdb::CoorManager::GetModelTable	(	PPModel &	modTable,
		int &	NumberOfModels
	)

int mmdb::CoorManager::GetNumberOfAtoms	(	int	modelNo,
		const ChainID	chainID,
		int	resNo
	)

int mmdb::CoorManager::GetNumberOfAtoms

(

cpstr

CID )

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

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

int mmdb::CoorManager::GetNumberOfAtoms	(	int	modelNo,
		int	chainNo,
		int	resNo
	)

int mmdb::CoorManager::GetNumberOfAtoms

(

)

[inline]

int mmdb::CoorManager::GetNumberOfChains

(

int

modelNo )

int mmdb::CoorManager::GetNumberOfChains

(

cpstr

CID )

int mmdb::CoorManager::GetNumberOfModels

(

)

[inline]

int mmdb::CoorManager::GetNumberOfResidues

(

cpstr

CID )

int mmdb::CoorManager::GetNumberOfResidues	(	int	modelNo,
		const ChainID	chainID
	)

int mmdb::CoorManager::GetNumberOfResidues	(	int	modelNo,
		int	chainNo
	)

PResidue mmdb::CoorManager::GetResidue

(

cpstr

CID )

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

PResidue mmdb::CoorManager::GetResidue	(	int	modelNo,
		int	chainNo,
		int	resNo
	)

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

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

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

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

void mmdb::CoorManager::GetResidueTable	(	cpstr	CID,
		PPResidue &	resTable,
		int &	NumberOfResidues
	)

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

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

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

bool mmdb::CoorManager::iContact	(	realtype	x,
		realtype	y,
		realtype	z,
		PAtom	a2,
		realtype	dd,
		realtype	d12,
		realtype	d22,
		realtype &	d2
	)		[protected]

bool mmdb::CoorManager::iContact	(	PAtom	a1,
		PAtom	a2,
		int	seq1,
		int	seq2,
		realtype	dd,
		realtype	d12,
		realtype	d22,
		realtype &	d2
	)		[protected]

void mmdb::CoorManager::InitMMDBCoorManager

(

)

[protected]

int mmdb::CoorManager::InsModel	(	PModel	mdl,
		int	modelNo
	)

void mmdb::CoorManager::MakeBricks	(	PPAtom	atmvec,
		int	avlen,
		realtype	Margin,
		realtype	BrickSize = 6.0
	)

void mmdb::CoorManager::MakeMBricks	(	PPAtom *	atmvec,
		ivector	avlen,
		int	nStructures,
		realtype	Margin,
		realtype	BrickSize = 6.0
	)

bool mmdb::CoorManager::Orth2Frac	(	realtype	xorth,
		realtype	yorth,
		realtype	zorth,
		realtype &	xfrac,
		realtype &	yfrac,
		realtype &	zfrac
	)

bool mmdb::CoorManager::Orth2Frac	(	mat44 &	T,
		mat44 &	F
	)

void mmdb::CoorManager::read

(

io::RFile

f )

[protected]

Reimplemented from mmdb::Root.

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

void mmdb::CoorManager::RemoveBricks

(

)

void mmdb::CoorManager::RemoveMBricks

(

)

void mmdb::CoorManager::ResetManager

(

)

[protected, virtual]

Reimplemented from mmdb::Root.

Reimplemented in mmdb::SelManager.

void mmdb::CoorManager::RotateModels	(	int	modelNo1,
		int	modelNo2,
		int	rotdir
	)

void mmdb::CoorManager::SeekContacts	(	PPAtom	AIndex1,
		int	ilen1,
		PPAtom *	AIndex2,
		ivector	ilen2,
		int	nStructures,
		realtype	dist1,
		realtype	dist2,
		PPMContact &	contact,
		int	bricking = 0
	)

void mmdb::CoorManager::SeekContacts	(	PPAtom	AIndex1,
		int	ilen1,
		PPAtom	AIndex2,
		int	ilen2,
		realtype	contDist,
		PContact	contact,
		int &	ncontacts,
		int	bricking = 0
	)

void mmdb::CoorManager::SeekContacts	(	PPAtom	AIndex1,
		int	ilen1,
		PPAtom	AIndex2,
		int	ilen2,
		realtype	dist1,
		realtype	dist2,
		int	seqDist,
		RPContact	contact,
		int &	ncontacts,
		int	maxlen = 0,
		mat44 *	TMatrix = NULL,
		long	group = 0,
		int	bricking = 0,
		bool	doSqrt = true
	)

void mmdb::CoorManager::SeekContacts	(	PPAtom	AIndex,
		int	ilen,
		int	atomNum,
		realtype	dist1,
		realtype	dist2,
		int	seqDist,
		RPContact	contact,
		int &	ncontacts,
		int	maxlen = 0,
		long	group = 0
	)

void mmdb::CoorManager::SeekContacts	(	PAtom	A,
		PPAtom	AIndex,
		int	ilen,
		realtype	dist1,
		realtype	dist2,
		int	seqDist,
		RPContact	contact,
		int &	ncontacts,
		int	maxlen = 0,
		long	group = 0
	)

int mmdb::CoorManager::SetDefaultCoorID

(

cpstr

CID )

void mmdb::CoorManager::SwapModels	(	int	modelNo1,
		int	modelNo2
	)

void mmdb::CoorManager::write

(

io::RFile

f )

[protected]

Reimplemented from mmdb::Root.

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

---

Member Data Documentation

PPPBrick* mmdb::CoorManager::brick [protected]

realtype mmdb::CoorManager::brick_size [protected]

int mmdb::CoorManager::CoorIDCode

PPPMBrick* mmdb::CoorManager::mbrick [protected]

realtype mmdb::CoorManager::mbrick_size [protected]

int mmdb::CoorManager::nbrick_x [protected]

int mmdb::CoorManager::nbrick_y [protected]

int mmdb::CoorManager::nbrick_z [protected]

int mmdb::CoorManager::nmbrick_x [protected]

int mmdb::CoorManager::nmbrick_y [protected]

int mmdb::CoorManager::nmbrick_z [protected]

realtype mmdb::CoorManager::xbrick_0 [protected]

realtype mmdb::CoorManager::xmbrick_0 [protected]

realtype mmdb::CoorManager::ybrick_0 [protected]

realtype mmdb::CoorManager::ymbrick_0 [protected]

realtype mmdb::CoorManager::zbrick_0 [protected]

realtype mmdb::CoorManager::zmbrick_0 [protected]

---

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

• src/mmdb_coormngr.h
• src/mmdb_coormngr.cpp