IMSElement Class Reference

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

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

List of all members.

Public Types
typedef std::string	name_type
	Type of element's name.
typedef IMSIsotopeDistribution	isotopes_type
	Type of element's isotope distribution.
typedef isotopes_type::mass_type	mass_type
	Type of isotope mass.
typedef isotopes_type::nominal_mass_type	nominal_mass_type
	Type of distribution nominal mass.
typedef isotopes_type::size_type	size_type
	Type of isotopes size.
Public Member Functions
	IMSElement ()
	Empty constructor.
	IMSElement (const IMSElement &element)
	Copy constructor.
	IMSElement (const name_type &name, const isotopes_type &isotopes)
	Constructor with name and isotope distribution.
	IMSElement (const name_type &name, mass_type mass)
	Constructor with name and mass of single isotope.
	IMSElement (const name_type &name, nominal_mass_type nominal_mass=0)
	Constructor with name and nominal mass.
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.
Static Public Attributes
static const mass_type	ELECTRON_MASS_IN_U
	Mass of electron.
Private Attributes
name_type	name_
	Element's name.
name_type	sequence_
	Element's sequence.
isotopes_type	isotopes_
	Element's isotope distribution.

---

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.Pervukhin@CeBiTec.Uni-Bielefeld.DE>

---

Member Typedef Documentation

typedef IMSIsotopeDistribution isotopes_type

Type of element's isotope distribution.

typedef isotopes_type::mass_type mass_type

Type of isotope mass.

typedef std::string name_type

Type of element's name.

typedef isotopes_type::nominal_mass_type nominal_mass_type

Type of distribution nominal mass.

typedef isotopes_type::size_type size_type

Type of isotopes size.

---

Constructor & Destructor Documentation

IMSElement

(

)

[inline]

Empty constructor.

IMSElement

(

const IMSElement &

element

)

[inline]

Copy constructor.

IMSElement	(	const name_type &	name,
		const isotopes_type &	isotopes
	)			[inline]

Constructor with name and isotope distribution.

IMSElement	(	const name_type &	name,
		mass_type	mass
	)			[inline]

Constructor with name and mass of single isotope.

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

Constructor with name and nominal mass.

virtual ~IMSElement

(

)

[inline, virtual]

Default destructor.

---

Member Function Documentation

mass_type getAverageMass

(

)

const [inline]

Gets element's average mass.

Returns:

An average mass of element.

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.

const IMSIsotopeDistribution& getIsotopeDistribution

(

)

const [inline]

Gets element's isotope distribution.

Returns:

Element's isotope distribution.

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()().

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.

nominal_mass_type getNominalMass

(

)

const [inline]

Gets element's nominal mass.

Returns:

A nominal mass of element.

const name_type& getSequence

(

)

const [inline]

Gets element's sequence.

Returns:

Sequence of element.

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.

IMSElement& operator=

(

const IMSElement &

element

)

Assignment operator.

Parameters:

element

Element to be assigned to this one.

Returns:

Reference to this object.

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

void setIsotopeDistribution

(

const IMSIsotopeDistribution &

isotopes

)

[inline]

Sets element's isotope distribution.

Parameters:

isotopes

A new isotope distribution to be set for element.

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.

void setSequence

(

const name_type &

sequence

)

[inline]

Sets element's sequence.

Parameters:

sequence

A new sequence to be set for element.

---

Member Data Documentation

const mass_type ELECTRON_MASS_IN_U [static]

Mass of electron.

isotopes_type isotopes_ [private]

Element's isotope distribution.

name_type name_ [private]

Element's name.

name_type sequence_ [private]

Element's sequence.