mmdb::Cryst Class Reference

#include <mmdb_cryst.h>

Inheritance diagram for mmdb::Cryst:

List of all members.

Public Member Functions
	Cryst ()
	Cryst (io::RPStream Object)
	~Cryst ()
void	FreeMemory ()
void	Reset ()
ERROR_CODE	ConvertPDBString (pstr PDBString)
void	RWBROOKReadPrintout ()
void	SetCell (realtype cell_a, realtype cell_b, realtype cell_c, realtype cell_alpha, realtype cell_beta, realtype cell_gamma, int OrthCode)
void	PutCell (realtype cell_a, realtype cell_b, realtype cell_c, realtype cell_alpha, realtype cell_beta, realtype cell_gamma, int OrthCode)
void	GetCell (realtype &cell_a, realtype &cell_b, realtype &cell_c, realtype &cell_alpha, realtype &cell_beta, realtype &cell_gamma, realtype &vol)
void	GetRCell (realtype &cell_as, realtype &cell_bs, realtype &cell_cs, realtype &cell_alphas, realtype &cell_betas, realtype &cell_gammas, realtype &vols)
void	SetSyminfoLib (cpstr syminfoLib)
pstr	GetSyminfoLib ()
int	SetSpaceGroup (cpstr spGroup)
pstr	GetSpaceGroup ()
pstr	GetSpaceGroupFix ()
void	CalcCoordTransforms ()
void	PDBASCIIDump (io::RFile f)
ERROR_CODE	GetCIF (mmcif::PData CIF)
void	MakeCIF (mmcif::PData CIF)
bool	areMatrices ()
bool	Frac2Orth (realtype x, realtype y, realtype z, realtype &xx, realtype &yy, realtype &zz)
bool	Orth2Frac (realtype x, realtype y, realtype z, realtype &xx, realtype &yy, realtype &zz)
bool	Frac2Orth (mat44 &F, mat44 &T)
bool	Orth2Frac (mat44 &T, mat44 &F)
bool	Cryst2Orth (rvector U)
bool	Orth2Cryst (rvector U)
void	CalcOrthMatrices ()
bool	isNCSMatrix ()
bool	isScaleMatrix ()
bool	isCellParameters ()
int	GetNumberOfSymOps ()
pstr	GetSymOp (int Nop)
int	GetNumberOfNCSMatrices ()
int	GetNumberOfNCSMates ()
bool	GetNCSMatrix (int NCSMatrixNo, mat33 &ncs_m, vect3 &ncs_v)
bool	GetNCSMatrix (int NCSMatrixNo, mat44 &ncs_m, int &iGiven)
int	AddNCSMatrix (mat33 &ncs_m, vect3 &ncs_v, int iGiven)
int	GetTMatrix (mat44 &TMatrix, int Nop, int cellshift_a, int cellshift_b, int cellshift_c, PSymOps symOpers=NULL)
int	GetUCTMatrix (mat44 &TMatrix, int Nop, realtype x, realtype y, realtype z, int cellshift_a, int cellshift_b, int cellshift_c, PSymOps symOpers=NULL)
int	GetFractMatrix (mat44 &TMatrix, int Nop, int cellshift_a, int cellshift_b, int cellshift_c, PSymOps symOpers=NULL)
int	GetSymOpMatrix (mat44 &TMatrix, int Nop)
void	Copy (PCryst Cryst)
void	write (io::RFile f)
void	read (io::RFile f)
Public Attributes
realtype	a
realtype	b
realtype	c
realtype	alpha
realtype	beta
realtype	gamma
mat44	RO
mat44	RF
mat44	ROU
mat44	RFU
mat633	RR
realtype	Vol
int	NCode
SymGroup	spaceGroup
SymGroup	spaceGroupFix
int	Z
mat33	o
vect3	t
mat33	s
vect3	u
word	CellCheck
word	WhatIsSet
bool	ignoreScalei
bool	processSG
bool	fixSpaceGroup
Protected Member Functions
void	Init (bool fullInit)
int	FixSpaceGroup ()
Protected Attributes
CrystContainer	ncsMatrix
CrystContainer	tVect
realtype	as
realtype	bs
realtype	cs
realtype	alphas
realtype	betas
realtype	gammas
realtype	AC [6]
realtype	VolChk
realtype	VolErr
pstr	syminfo_lib
SymOps	symOps
Friends
class	Channel

---

Constructor & Destructor Documentation

mmdb::Cryst::Cryst

(

)

mmdb::Cryst::Cryst

(

io::RPStream

Object )

mmdb::Cryst::~Cryst

(

)

---

Member Function Documentation

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

bool mmdb::Cryst::areMatrices

(

)

void mmdb::Cryst::CalcCoordTransforms

(

)

void mmdb::Cryst::CalcOrthMatrices

(

)

ERROR_CODE mmdb::Cryst::ConvertPDBString

(

pstr

PDBString )

void mmdb::Cryst::Copy

(

PCryst

Cryst )

bool mmdb::Cryst::Cryst2Orth

(

rvector

U )

int mmdb::Cryst::FixSpaceGroup

(

)

[protected]

bool mmdb::Cryst::Frac2Orth	(	realtype	x,
		realtype	y,
		realtype	z,
		realtype &	xx,
		realtype &	yy,
		realtype &	zz
	)

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

void mmdb::Cryst::FreeMemory

(

)

void mmdb::Cryst::GetCell	(	realtype &	cell_a,
		realtype &	cell_b,
		realtype &	cell_c,
		realtype &	cell_alpha,
		realtype &	cell_beta,
		realtype &	cell_gamma,
		realtype &	vol
	)

ERROR_CODE mmdb::Cryst::GetCIF

(

mmcif::PData

CIF )

int mmdb::Cryst::GetFractMatrix	(	mat44 &	TMatrix,
		int	Nop,
		int	cellshift_a,
		int	cellshift_b,
		int	cellshift_c,
		PSymOps	symOpers = NULL
	)

bool mmdb::Cryst::GetNCSMatrix	(	int	NCSMatrixNo,
		mat33 &	ncs_m,
		vect3 &	ncs_v
	)

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

int mmdb::Cryst::GetNumberOfNCSMates

(

)

int mmdb::Cryst::GetNumberOfNCSMatrices

(

)

int mmdb::Cryst::GetNumberOfSymOps

(

)

void mmdb::Cryst::GetRCell	(	realtype &	cell_as,
		realtype &	cell_bs,
		realtype &	cell_cs,
		realtype &	cell_alphas,
		realtype &	cell_betas,
		realtype &	cell_gammas,
		realtype &	vols
	)

pstr mmdb::Cryst::GetSpaceGroup

(

)

pstr mmdb::Cryst::GetSpaceGroupFix

(

)

pstr mmdb::Cryst::GetSyminfoLib

(

)

pstr mmdb::Cryst::GetSymOp

(

int

Nop )

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

int mmdb::Cryst::GetTMatrix	(	mat44 &	TMatrix,
		int	Nop,
		int	cellshift_a,
		int	cellshift_b,
		int	cellshift_c,
		PSymOps	symOpers = NULL
	)

int mmdb::Cryst::GetUCTMatrix	(	mat44 &	TMatrix,
		int	Nop,
		realtype	x,
		realtype	y,
		realtype	z,
		int	cellshift_a,
		int	cellshift_b,
		int	cellshift_c,
		PSymOps	symOpers = NULL
	)

void mmdb::Cryst::Init

(

bool

fullInit )

[protected]

bool mmdb::Cryst::isCellParameters

(

)

bool mmdb::Cryst::isNCSMatrix

(

)

bool mmdb::Cryst::isScaleMatrix

(

)

void mmdb::Cryst::MakeCIF

(

mmcif::PData

CIF )

bool mmdb::Cryst::Orth2Cryst

(

rvector

U )

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

bool mmdb::Cryst::Orth2Frac	(	realtype	x,
		realtype	y,
		realtype	z,
		realtype &	xx,
		realtype &	yy,
		realtype &	zz
	)

void mmdb::Cryst::PDBASCIIDump

(

io::RFile

f )

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

void mmdb::Cryst::read

(

io::RFile

f )

void mmdb::Cryst::Reset

(

)

void mmdb::Cryst::RWBROOKReadPrintout

(

)

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

int mmdb::Cryst::SetSpaceGroup

(

cpstr

spGroup )

void mmdb::Cryst::SetSyminfoLib

(

cpstr

syminfoLib )

void mmdb::Cryst::write

(

io::RFile

f )

---

Friends And Related Function Documentation

friend class Channel [friend]

---

Member Data Documentation

realtype mmdb::Cryst::a

realtype mmdb::Cryst::AC[6] [protected]

realtype mmdb::Cryst::alpha

realtype mmdb::Cryst::alphas [protected]

realtype mmdb::Cryst::as [protected]

realtype mmdb::Cryst::b

realtype mmdb::Cryst::beta

realtype mmdb::Cryst::betas [protected]

realtype mmdb::Cryst::bs [protected]

realtype mmdb::Cryst::c

word mmdb::Cryst::CellCheck

realtype mmdb::Cryst::cs [protected]

bool mmdb::Cryst::fixSpaceGroup

realtype mmdb::Cryst::gamma

realtype mmdb::Cryst::gammas [protected]

bool mmdb::Cryst::ignoreScalei

int mmdb::Cryst::NCode

CrystContainer mmdb::Cryst::ncsMatrix [protected]

mat33 mmdb::Cryst::o

bool mmdb::Cryst::processSG

mat44 mmdb::Cryst::RF

mat44 mmdb::Cryst::RFU

mat44 mmdb::Cryst::RO

mat44 mmdb::Cryst::ROU

mat633 mmdb::Cryst::RR

mat33 mmdb::Cryst::s

SymGroup mmdb::Cryst::spaceGroup

SymGroup mmdb::Cryst::spaceGroupFix

pstr mmdb::Cryst::syminfo_lib [protected]

SymOps mmdb::Cryst::symOps [protected]

vect3 mmdb::Cryst::t

CrystContainer mmdb::Cryst::tVect [protected]

vect3 mmdb::Cryst::u

realtype mmdb::Cryst::Vol

realtype mmdb::Cryst::VolChk [protected]

realtype mmdb::Cryst::VolErr [protected]

word mmdb::Cryst::WhatIsSet

int mmdb::Cryst::Z

---

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

• src/mmdb_cryst.h
• src/mmdb_cryst.cpp