IMSElement Class Reference

Represents a chemical atom with name and isotope distribution. More...

#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSElement.h>

Public Types
typedef std::string	name_type
	Type of element's name. More...
typedef IMSIsotopeDistribution	isotopes_type
	Type of element's isotope distribution. More...
typedef isotopes_type::mass_type	mass_type
	Type of isotope mass. More...
typedef isotopes_type::nominal_mass_type	nominal_mass_type
	Type of distribution nominal mass. More...
typedef isotopes_type::size_type	size_type
	Type of isotopes size. More...

Public Member Functions
	IMSElement ()
	Empty constructor. More...
	IMSElement (const IMSElement &element)
	Copy constructor. More...
	IMSElement (const name_type &name, const isotopes_type &isotopes)
	Constructor with name and isotope distribution. More...
	IMSElement (const name_type &name, mass_type mass)
	Constructor with name and mass of single isotope. More...
	IMSElement (const name_type &name, nominal_mass_type nominal_mass=0)
	Constructor with name and nominal mass. More...
const name_type &	getName () const
void	setName (const name_type &name)
const name_type &	getSequence () const
void	setSequence (const name_type &sequence)
nominal_mass_type	getNominalMass () const
mass_type	getMass (size_type index=0) const
mass_type	getAverageMass () const
mass_type	getIonMass (int electrons_number=1) const
const IMSIsotopeDistribution &	getIsotopeDistribution () const
void	setIsotopeDistribution (const IMSIsotopeDistribution &isotopes)
IMSElement &	operator= (const IMSElement &element)
bool	operator== (const IMSElement &element) const
bool	operator!= (const IMSElement &element) const
virtual	~IMSElement ()
	Default destructor. More...

Static Public Attributes
static const mass_type	ELECTRON_MASS_IN_U
	Mass of electron. More...

Private Attributes
name_type	name_
	Element's name. More...
name_type	sequence_
	Element's sequence. More...
isotopes_type	isotopes_
	Element's isotope distribution. More...

Detailed Description

Represents a chemical atom with name and isotope distribution.

Simulates a chemical atom with name and isotope distribution and can be used as a base class for more complex structures that simulate non-trivial bio-chemical molecules. Element 's name represents the atom's symbol in a periodical table. Sequence is by default equal to name and introduced for more complex molecules.

Author

Anton Pervukhin Anton.nosp@m..Per.nosp@m.vukhi.nosp@m.n@Ce.nosp@m.BiTec.nosp@m..Uni.nosp@m.-Biel.nosp@m.efel.nosp@m.d.DE

Member Typedef Documentation

isotopes_type

typedef IMSIsotopeDistribution isotopes_type

Type of element's isotope distribution.

mass_type

typedef isotopes_type::mass_type mass_type

Type of isotope mass.

name_type

typedef std::string name_type

Type of element's name.

nominal_mass_type

typedef isotopes_type::nominal_mass_type nominal_mass_type

Type of distribution nominal mass.

size_type

typedef isotopes_type::size_type size_type

Type of isotopes size.

Constructor & Destructor Documentation

IMSElement() [1/5]

IMSElement ( )

inline

Empty constructor.

IMSElement() [2/5]

IMSElement ( const IMSElement &  element )

inline

Copy constructor.

IMSElement() [3/5]

IMSElement ( const name_type &  name, const isotopes_type &  isotopes  )

inline

Constructor with name and isotope distribution.

IMSElement() [4/5]

IMSElement ( const name_type &  name, mass_type  mass  )

inline

Constructor with name and mass of single isotope.

IMSElement() [5/5]

IMSElement ( const name_type &  name, nominal_mass_type  nominal_mass = 0  )

inline

Constructor with name and nominal mass.

~IMSElement()

virtual ~IMSElement ( )

inlinevirtual

Default destructor.

Member Function Documentation

getAverageMass()

mass_type getAverageMass ( ) const

inline

Gets element's average mass.

Returns

An average mass of element.

getIonMass()

mass_type getIonMass ( int  electrons_number = 1 ) const

inline

Gets ion mass of element. By default ion lacks 1 electron, but this can be changed by setting other electrons_number.

Parameters

electrons_number

Number of electrons lacking in ion.

getIsotopeDistribution()

const IMSIsotopeDistribution& getIsotopeDistribution ( ) const

inline

Gets element's isotope distribution.

Returns

Element's isotope distribution.

getMass()

mass_type getMass ( size_type  index = 0 ) const

inline

Gets mass of element's isotope index.

Parameters

index

Index of element's isotope.

Returns

mass of element's isotope with a given index.

Referenced by IMSAlphabet::MassSortingCriteria_::operator()().

getName()

const name_type& getName ( ) const

inline

Gets element's name.

Note

Name represents a symbol of element/atom in a periodical table.

Returns

Name of element.

getNominalMass()

nominal_mass_type getNominalMass ( ) const

inline

Gets element's nominal mass.

Returns

A nominal mass of element.

getSequence()

const name_type& getSequence ( ) const

inline

Gets element's sequence.

Returns

Sequence of element.

operator!=()

bool operator!=

(

const IMSElement &

element

)

const

Inequality operator. Returns true, if a given element is unequal to this one, false - otherwise.

Returns

true, if a given element is unequal to this one, false - otherwise.

operator=()

IMSElement& operator=

(

const IMSElement &

element

)

Assignment operator.

Parameters

element

Element to be assigned to this one.

Returns

Reference to this object.

operator==()

bool operator==

(

const IMSElement &

element

)

const

Equality operator. Returns true, if a given element is equal to this one, false - otherwise.

Returns

true, if a given element is equal to this one, false - otherwise

setIsotopeDistribution()

void setIsotopeDistribution ( const IMSIsotopeDistribution &  isotopes )

inline

Sets element's isotope distribution.

Parameters

isotopes

A new isotope distribution to be set for element.

References KDTree::operator!=(), and KDTree::operator==().

setName()

void setName ( const name_type &  name )

inline

Sets element's name.

Note

Name represents a symbol of element/atom in a periodical table.

Parameters

name	A new name to be set for element.

setSequence()

void setSequence ( const name_type &  sequence )

inline

Sets element's sequence.

Parameters

sequence

A new sequence to be set for element.

Member Data Documentation

ELECTRON_MASS_IN_U

const mass_type ELECTRON_MASS_IN_U

static

Mass of electron.

isotopes_

isotopes_type isotopes_

private

Element's isotope distribution.

name_

name_type name_

private

Element's name.

sequence_

name_type sequence_

private

Element's sequence.