Classes
class	AlignParams
class	Alignment
class	Alignment1
class	BFGSMin
class	Vertex
class	Edge
class	Graph
class	GMatch
class	GraphMatch
class	RandomNumber
Typedefs
typedef void	BFGSMinFunc (void *UserData, int N, rvector X, realtype &F)
typedef BFGSMinFunc *	PBFGSMinFunc
typedef void	BFGSPrintFunc (void *UserData, int N, int Itn, rvector X, rvector G, realtype F)
typedef BFGSPrintFunc *	PBFGSPrintFunc
Enumerations
enum	ALIGN_METHOD { ALIGN_GLOBAL = 0, ALIGN_LOCAL = 1, ALIGN_GLOBLOC = 2, ALIGN_FREEENDS = 3 }
enum	BFGS_RC { BFGS_TooFewDigits = -2, BFGS_WrongSpaceDim = -1, BFGS_NoTermination = 0, BFGS_SmallGradient = 1, BFGS_SmallStep = 2, BFGS_LineSearchComplete = 3, BFGS_IterationLimit = 4, BFGS_LargeSteps = 5, BFGS_Stopped = 6 }
enum	GRAPH_FLAG { CHIRAL_RIGHT = 0x10000000, CHIRAL_LEFT = 0x20000000, ATOM_LEAVING = 0x40000000, HYDROGEN_BOND = 0x0F000000, SYMREL_MASK = 0x00FF0000, CHIRAL_MASK = 0xCFFFFFFF, TYPE_MASK = 0x00FFFFFF }
enum	GRAPH_BOND { BOND_SINGLE = 1, BOND_DOUBLE = 2, BOND_AROMATIC = 3, BOND_TRIPLE = 4 }
enum	GRAPH_RC { MKGRAPH_Ok = 0, MKGRAPH_NoAtoms = -1, MKGRAPH_ChangedAltLoc = 1, MKGRAPH_MaxOccupancy = 2 }
enum	GRAPH_MATCH_FLAG { GMF_UniqueMatch = 0x00000001, GMF_NoCombinations = 0x00000002 }
enum	VERTEX_EXT_TYPE { EXTTYPE_Ignore = 0, EXTTYPE_Equal = 1, EXTTYPE_AND = 2, EXTTYPE_OR = 3, EXTTYPE_XOR = 4, EXTTYPE_NotEqual = 5, EXTTYPE_NotAND = 6, EXTTYPE_NotOR = 7 }
enum	RN_MAX_SEED { _RN_MAX_IJ = 31328, _RN_MAX_KL = 30081 }
Functions
realtype	GetTorsion (rvector U, rvector W, rvector V)
realtype	GetAngle (rvector v1, rvector v2)
realtype	Combinations (int n, int m)
realtype	log1mx (realtype x)
realtype	expc (realtype x)
realtype	expc1mx (realtype x, realtype y)
double	exp10 (double x)
	MakeStreamFunctions (AlignParams) Alignment
	DefineClass (AlignParams)
	DefineStreamFunctions (AlignParams)
	DefineClass (Alignment)
	DefineClass (Alignment1)
	DefineClass (BFGSMin)
void	FFT (rvector data, int nn, bool Forward)
void	RealFFT (rvector data, int n, bool Forward)
void	TwoFFT (rvector data1, rvector data2, rvector fft1, rvector fft2, int n)
void	Convolve (rvector data, int n, rvector respns, int m, rvector ans, bool Conv)
void	mConvolve (rvector data, int n, int m)
	MakeStreamFunctions (Vertex) Edge
	MakeStreamFunctions (Edge) Graph
void	SetGraphAllocPortion (int alloc_portion)
	MakeStreamFunctions (Graph) GMatch
	MakeStreamFunctions (GMatch) GraphMatch
	DefineClass (Vertex)
	DefineStreamFunctions (Vertex)
	DefineClass (Edge)
	DefineStreamFunctions (Edge)
	DefineClass (Graph)
	DefineStreamFunctions (Graph)
	DefineClass (GMatch)
	DefineStreamFunctions (GMatch)
	DefineClass (GraphMatch)
	DefineStreamFunctions (GraphMatch)
void	Jacobi (int N, rmatrix A, rmatrix T, rvector Eigen, rvector Aik, int &Signal)
void	PbCholDecomp (int N, rvector HDiag, realtype MaxOff, realtype MachEps, rmatrix L, realtype &MaxAdd)
void	LSolve (int N, rmatrix L, rvector B, rvector Y)
void	LTSolve (int N, rmatrix L, rvector Y, rvector X)
void	ChSolve (int N, rmatrix L, rvector G, rvector S)
void	FastInverse (int N, rmatrix A, ivector J0, int &Signal)
realtype	Sign (realtype A, realtype B)
realtype	SrX2Y2 (realtype X, realtype Y)
void	SVD (int NA, int M, int N, rmatrix A, rmatrix U, rmatrix V, rvector W, rvector RV1, bool MatU, bool MatV, int &RetCode)
void	OrderSVD (int M, int N, rmatrix U, rmatrix V, rvector W, bool MatU, bool MatV)
	DefineClass (RandomNumber)
Variables
const realtype	NO_TORSION = -MaxReal
const int	ring_mask []

Typedef Documentation

typedef void mmdb::math::BFGSMinFunc(void *UserData, int N, rvector X, realtype &F)

typedef void mmdb::math::BFGSPrintFunc(void *UserData, int N, int Itn, rvector X, rvector G, realtype F)

typedef BFGSMinFunc* mmdb::math::PBFGSMinFunc

typedef BFGSPrintFunc* mmdb::math::PBFGSPrintFunc

Enumeration Type Documentation

enum mmdb::math::ALIGN_METHOD

Enumerator:

ALIGN_GLOBAL
ALIGN_LOCAL
ALIGN_GLOBLOC
ALIGN_FREEENDS

enum mmdb::math::BFGS_RC

Enumerator:

BFGS_TooFewDigits
BFGS_WrongSpaceDim
BFGS_NoTermination
BFGS_SmallGradient
BFGS_SmallStep
BFGS_LineSearchComplete
BFGS_IterationLimit
BFGS_LargeSteps
BFGS_Stopped

enum mmdb::math::GRAPH_BOND

Enumerator:

BOND_SINGLE
BOND_DOUBLE
BOND_AROMATIC
BOND_TRIPLE

enum mmdb::math::GRAPH_FLAG

Enumerator:

CHIRAL_RIGHT
CHIRAL_LEFT
ATOM_LEAVING
HYDROGEN_BOND
SYMREL_MASK
CHIRAL_MASK
TYPE_MASK

enum mmdb::math::GRAPH_MATCH_FLAG

Enumerator:

GMF_UniqueMatch
GMF_NoCombinations

enum mmdb::math::GRAPH_RC

Enumerator:

MKGRAPH_Ok
MKGRAPH_NoAtoms
MKGRAPH_ChangedAltLoc
MKGRAPH_MaxOccupancy

enum mmdb::math::RN_MAX_SEED

Enumerator:

_RN_MAX_IJ
_RN_MAX_KL

enum mmdb::math::VERTEX_EXT_TYPE

Enumerator:

EXTTYPE_Ignore
EXTTYPE_Equal
EXTTYPE_AND
EXTTYPE_OR
EXTTYPE_XOR
EXTTYPE_NotEqual
EXTTYPE_NotAND
EXTTYPE_NotOR

Function Documentation

void mmdb::math::ChSolve	(	int	N,
		rmatrix	L,
		rvector	G,
		rvector	S
	)

realtype mmdb::math::Combinations	(	int	n,
		int	m
	)

void mmdb::math::Convolve	(	rvector	data,
		int	n,
		rvector	respns,
		int	m,
		rvector	ans,
		bool	Conv
	)

mmdb::math::DefineClass ( GraphMatch )

mmdb::math::DefineClass ( AlignParams )

mmdb::math::DefineClass ( Alignment )

mmdb::math::DefineClass ( RandomNumber )

mmdb::math::DefineClass ( Alignment1 )

mmdb::math::DefineClass ( BFGSMin )

mmdb::math::DefineClass ( Vertex )

mmdb::math::DefineClass ( Edge )

mmdb::math::DefineClass ( Graph )

mmdb::math::DefineClass ( GMatch )

mmdb::math::DefineStreamFunctions ( GraphMatch )

mmdb::math::DefineStreamFunctions ( AlignParams )

mmdb::math::DefineStreamFunctions ( Vertex )

mmdb::math::DefineStreamFunctions ( Edge )

mmdb::math::DefineStreamFunctions ( Graph )

mmdb::math::DefineStreamFunctions ( GMatch )

double mmdb::math::exp10 ( double x ) [inline]

realtype mmdb::math::expc ( realtype x )

realtype mmdb::math::expc1mx	(	realtype	x,
		realtype	y
	)

void mmdb::math::FastInverse	(	int	N,
		rmatrix	A,
		ivector	J0,
		int &	Signal
	)

void mmdb::math::FFT	(	rvector	data,
		int	nn,
		bool	Forward
	)

realtype mmdb::math::GetAngle	(	rvector	v1,
		rvector	v2
	)

realtype mmdb::math::GetTorsion	(	rvector	U,
		rvector	W,
		rvector	V
	)

void mmdb::math::Jacobi	(	int	N,
		rmatrix	A,
		rmatrix	T,
		rvector	Eigen,
		rvector	Aik,
		int &	Signal
	)

Diagonalization of symmetric matrices A[1..N][1..N] by the method of Jacobi.

Parameters:

N	dimension of the matrix
A	matrix to diagonalize; the lower triangle, except the diagonal, will remain unchanged
T	eigenvectors placed as columns
Eigen	vector of eigenvalues, orderd by increasing
Aik	working array
Signal	0 <=> Ok, ItMax <=> iteration limit exchausted.

realtype mmdb::math::log1mx ( realtype x )

void mmdb::math::LSolve	(	int	N,
		rmatrix	L,
		rvector	B,
		rvector	Y
	)

void mmdb::math::LTSolve	(	int	N,
		rmatrix	L,
		rvector	Y,
		rvector	X
	)

mmdb::math::MakeStreamFunctions ( Graph )

mmdb::math::MakeStreamFunctions ( AlignParams )

mmdb::math::MakeStreamFunctions ( Edge )

mmdb::math::MakeStreamFunctions ( GMatch )

mmdb::math::MakeStreamFunctions ( Vertex )

void mmdb::math::mConvolve	(	rvector	data,
		int	n,
		int	m
	)

void mmdb::math::OrderSVD	(	int	M,
		int	N,
		rmatrix	U,
		rmatrix	V,
		rvector	W,
		bool	MatU,
		bool	MatV
	)

void mmdb::math::PbCholDecomp	(	int	N,
		rvector	HDiag,
		realtype	MaxOff,
		realtype	MachEps,
		rmatrix	L,
		realtype &	MaxAdd
	)

void mmdb::math::RealFFT	(	rvector	data,
		int	n,
		bool	Forward
	)

void mmdb::math::SetGraphAllocPortion ( int alloc_portion )

realtype mmdb::math::Sign	(	realtype	A,
		realtype	B
	)

realtype mmdb::math::SrX2Y2	(	realtype	X,
		realtype	Y
	)

void mmdb::math::SVD	(	int	NA,
		int	M,
		int	N,
		rmatrix	A,
		rmatrix	U,
		rmatrix	V,
		rvector	W,
		rvector	RV1,
		bool	MatU,
		bool	MatV,
		int &	RetCode
	)

void mmdb::math::TwoFFT	(	rvector	data1,
		rvector	data2,
		rvector	fft1,
		rvector	fft2,
		int	n
	)

Variable Documentation

const realtype mmdb::math::NO_TORSION = -MaxReal

const int mmdb::math::ring_mask[]

Initial value:

 {
      0x00000000,
      0x00000000,
      0x00000000,
      0x00000001,
      0x00000002,
      0x00000004,
      0x00000008,
      0x00000010,
      0x00000020,
      0x00000040,
      0x00000080
    }

mmdb::math Namespace Reference

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation