| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Attributes | Private Attributes | List of all members
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 | ( |  | ) |

inline virtual

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.

## ◆ 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.