magnes::Atom Class Reference

representation of an atom More...

#include <atom.h>

Classes
class	AtomData
	basic atomic data (Z, mass, electronegativity...) More...
class	IsotopeData

Public Types
enum	hybridization { UNKNOWN =0, SP, SP2, SP3 }

Public Member Functions
	Atom (const std::string &symbol)
	Atom (int z)
double	AtomicMass () const
void	Color (float *r, float *g, float *b) const
int	Z () const
double	VdW () const
double	CovalentRadius () const
double	PaulingElectronegativity () const
const std::string &	Symbol () const
void	SetSymbol (const std::string &symbol)
void	SetZ (int z)
void	SetPDBResidue (PDBResidue *r)
PDBResidue *	Residue ()
const PDBResidue *	Residue () const
void	SetPDBName (const std::string &name)
const std::string &	PDBName () const
const std::pair< const int, const IsotopeData > *	NMRIsotope () const
void	SetCurrentNMRIsotope (int m)
const std::map< const int, const IsotopeData > &	NMRIsotopes () const
size_t	MMType () const
void	SetMMType (size_t mmtype)

Detailed Description

representation of an atom

This class stores basic info about an atom such its atomic number, mass, default color to be drawn and Pauling electronegativity

Member Enumeration Documentation

hybridization

enum magnes::Atom::hybridization

hybridization of the atom

Constructor & Destructor Documentation

Atom() [1/2]

magnes::Atom::Atom ( const std::string &  symbol )

inline

Construct atom with atomic symbol

Parameters

symbol

This functions setup all atomic data adequately

Atom() [2/2]

magnes::Atom::Atom ( int  z )

inline

Construct atom with atomic number

Parameters

z	This functions setup all atomic data adequately

Member Function Documentation

AtomicMass()

double magnes::Atom::AtomicMass ( ) const

inline

Return isotopically promediated atomic mass

Color()

void magnes::Atom::Color	(	float *	r,
		float *	g,
		float *	b
	)		const

fill

Parameters

r

CovalentRadius()

double magnes::Atom::CovalentRadius ( ) const

inline

Returns

covalent radium

MMType()

size_t magnes::Atom::MMType ( ) const

inline

return the molecular mechanics type index

NMRIsotope()

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

(

)

const

Get data for the active NMR isotope

NMRIsotopes()

const std::map<const int,const IsotopeData>& magnes::Atom::NMRIsotopes ( ) const

inline

return the list of atomic isotopes

PaulingElectronegativity()

double magnes::Atom::PaulingElectronegativity ( ) const

inline

Returns

Pauling Electronegativity

PDBName()

const std::string& magnes::Atom::PDBName ( ) const

inline

return the PDB name

Residue() [1/2]

PDBResidue* magnes::Atom::Residue ( )

inline

return a pointer to the PDB residue

Residue() [2/2]

const PDBResidue* magnes::Atom::Residue ( ) const

inline

return a const pointer to the PDB residue

SetCurrentNMRIsotope()

void magnes::Atom::SetCurrentNMRIsotope

(

int

m

)

Set the active isotope to that of mass number m

SetMMType()

void magnes::Atom::SetMMType ( size_t  mmtype )

inline

Set the molecular type index;

References magnes::DefaultNMRProperties(), magnes::GetPeriodicTable(), magnes::SymbolFromZ(), and magnes::ZFromSymbol().

SetPDBName()

void magnes::Atom::SetPDBName ( const std::string &  name )

inline

Set the PDB Name

SetPDBResidue()

void magnes::Atom::SetPDBResidue ( PDBResidue *  r )

inline

Set a pointer to the molecule pdb residues table

SetSymbol()

void magnes::Atom::SetSymbol

(

const std::string &

symbol

)

Set the atomic symbol to

Parameters

symbol

and change Z

SetZ()

void magnes::Atom::SetZ

(

int

z

)

Set the atomic number to

Parameters

z	and set symbol

Symbol()

const std::string& magnes::Atom::Symbol ( ) const

inline

Returns

the atomic symbol (uppercase)

VdW()

double magnes::Atom::VdW ( ) const

inline

Returns

Van der Waals radium

Z()

int magnes::Atom::Z ( ) const

inline

Returns

atomic number

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

• /Users/armando/worksrc/magnes-code/trunk/magnes/core/atom.h