magnes Namespace Reference

the global magnes namespace More...

Classes
class	Atom
	representation of an atom More...
class	Bond
	representation of a chemical bond More...
class	CCCHEquation
	An specialized class for implementation of 3JCCCH karplus-like equations HCCHEquation implements convenient atom selection functions for 3JCHCH equations as well as a table with Huggins electronegativities. More...
class	ChemicalShift
class	Coordinate
	representaion of a 3D point More...
class	CouplingConstant
	representation of a coupling constant between nuclei More...
class	D1Array
	monodimensional dynamically allocated array More...
class	D1StaticArray
class	D2Array
	monodimensional array More...
class	Energy
	A class for storing energy values. More...
class	Error
	A general class for storing experimental errors. More...
class	Frame
	Representation of a conformer. More...
class	HCCHEquation
	An specialized class for implementation of 3JHCCH karplus-like equations HCCHEquation implements convenient atom selection functions for 3JHHCH equations as well as a table with Huggins electronegativities. Implementation of 3JHHCH equations is therefore straightforward. More...
class	JEquation
	The base class for the computation of scalar coupling constants. More...
class	Molecule
class	PDBResidue
class	QuantumCoupling
class	Quaternion
	quaternion representation More...
class	RingPerceptor
	Implementation of a ring perception algorithm. More...
class	Scalar
class	Tensor
class	Thermostat
	A class to manage thermodynamics. More...

Typedefs
typedef ChemicalShift	QuadrupolarCoupling
typedef std::vector< size_t >	Ring

Enumerations
enum	ensemble { NVE =0, NVT }

Functions
MAGNES_CORE_API const PeriodicTable &	GetPeriodicTable ()
MAGNES_CORE_API void	BuildPeriodicTable ()
MAGNES_CORE_API int	ZFromSymbol (const std::string &symbol)
MAGNES_CORE_API std::string	SymbolFromZ (int z)
MAGNES_CORE_API const std::pair< const int, const Atom::IsotopeData > *	DefaultNMRProperties (const std::string &symbol)
MAGNES_CORE_API bool	operator== (const ChemicalShift &, const ChemicalShift &)
Coordinate	operator* (float f, Coordinate a)
MAGNES_CORE_API std::ostream &	operator<< (std::ostream &s, const Coordinate &c)
MAGNES_CORE_API std::ostream &	operator<< (std::ostream &s, const Quaternion &c)
MAGNES_CORE_API bool	operator== (const CouplingConstant &, const CouplingConstant &)
MAGNES_CORE_API std::ostream &	operator<< (std::ostream &s, const CouplingConstant &c)
MAGNES_CORE_API std::ostream &	operator<< (std::ostream &s, const magnes::Frame &m)
MAGNES_CORE_API std::ostream &	operator<< (std::ostream &s, const magnes::Molecule &m)
MAGNES_CORE_API bool	CompareMolecules (const magnes::Molecule &mol1, const magnes::Molecule &mol2)
double	operator* (const D1Array< double > &a, const D1Array< double > &b)
D2Array< double >	operator* (const D2Array< double > &a, const D2Array< double > &b)
D1Array< double >	operator* (const D2Array< double > &a, const D1Array< double > &b)
int	Eigen (D2Array< double > &a, D1Array< double > &e)
void	SVDFit (const D1Array< double > &res, const D2Array< double > &modelmatrix, D1Array< double > &solution)
int	Invert (D2Array< double > &a)
std::string	MathInfo ()

Variables
MAGNES_CORE_API typedef std::map< const std::string, const magnes::Atom::AtomData >	PeriodicTable

Detailed Description

the global magnes namespace

Author

Armando Navarro Vazquez qoajn.nosp@m.v@us.nosp@m.c.es

Typedef Documentation

QuadrupolarCoupling

typedef ChemicalShift magnes::QuadrupolarCoupling

Define QuadrupolarCoupling in the same way

Function Documentation

DefaultNMRProperties()

MAGNES_CORE_API const std::pair<const int,const Atom::IsotopeData>* magnes::DefaultNMRProperties

(

const std::string &

symbol

)

return default nmr properties for atom given by atomic number z

Referenced by magnes::Atom::SetMMType().

Eigen()

int magnes::Eigen ( D2Array< double > &  a, D1Array< double > &  e  )

inline

diagonalize a symmetric matrix a, eigenvectors will be stored as a columns and eigenvalues will be stored in vector e

References magnes::D2Array< X >::NColumns(), magnes::D2Array< X >::NRows(), and magnes::D1Array< X >::size().

GetPeriodicTable()

MAGNES_CORE_API const PeriodicTable& magnes::GetPeriodicTable

(

)

Returns

a reference to the global periodic table

Referenced by magnes::Atom::SetMMType().

MathInfo()

std::string magnes::MathInfo ( )

inline

return the name of the mathetmatical library underneath and the type of storage

operator*() [1/2]

Coordinate magnes::operator* ( float  f, Coordinate  a  )

inline

scalar coordinate product

Referenced by operator*(), and magnes::D2Array< X >::Trace().

operator*() [2/2]

D2Array<double> magnes::operator* ( const D2Array< double > &  a, const D2Array< double > &  b  )

inline

specializations

References magnes::D2Array< X >::NColumns(), magnes::D2Array< X >::NRows(), operator*(), and magnes::D1Array< X >::size().

operator<<() [1/4]

MAGNES_CORE_API std::ostream& magnes::operator<<	(	std::ostream &	s,
		const magnes::Frame &	m
	)

print frame coordinates on stream s

operator<<() [2/4]

MAGNES_CORE_API std::ostream& magnes::operator<<	(	std::ostream &	s,
		const magnes::Molecule &	m
	)

print molecule frames on stream s

operator<<() [3/4]

MAGNES_CORE_API std::ostream& magnes::operator<<	(	std::ostream &	s,
		const CouplingConstant &	c
	)

print frame coordinates on stream s

operator<<() [4/4]

MAGNES_CORE_API std::ostream& magnes::operator<< ( std::ostream &  s, const Coordinate &  c  )

inline

used for debugging purposes

References magnes::Quaternion::V(), magnes::Quaternion::W(), magnes::Coordinate::x(), magnes::Coordinate::y(), and magnes::Coordinate::z().

Referenced by magnes::CouplingConstant::AveragedDistribution(), magnes::Frame::ParentMolecule(), and magnes::Molecule::Weight().

operator==() [1/2]

MAGNES_CORE_API bool magnes::operator==	(	const ChemicalShift &	,
		const ChemicalShift &
	)

Returns

true if indexes I and J are the same

Referenced by magnes::CouplingConstant::AveragedDistribution(), and magnes::ChemicalShift::StatisticalWeight().

operator==() [2/2]

MAGNES_CORE_API bool magnes::operator==	(	const CouplingConstant &	,
		const CouplingConstant &
	)

Returns

true if indexes I and J are the same

SymbolFromZ()

MAGNES_CORE_API std::string magnes::SymbolFromZ

(

int

z

)

Return the Symbol for element of atomic number z

Referenced by magnes::Atom::SetMMType().

ZFromSymbol()

MAGNES_CORE_API int magnes::ZFromSymbol

(

const std::string &

symbol

)

Return the atomic number Z for symbol

Referenced by magnes::Atom::SetMMType().