A ChemicalGroup instance contains the properties of a group of atoms. More...

#include <chemicalgroup.h>

Public Member Functions
	ChemicalGroup (std::string name="", std::string label="", double bindEnergy=0.0, double averageMass=0.0, double monoisotopicMass=0.0, double bindArea=1.0)
	Constructs a chemical group with the given parameters.

std::string	name () const
	Returns the full name of the chemical group.

std::string	label () const
	Returns the brief code of the group used in peptide sequence notation.

double	averageMass () const
	Returns the average mass of the chemical group.

double	monoisotopicMass () const
	Returns the monoisotopic mass of the chemical group.

double	bindEnergy () const
	Returns the energy of binding to the surface of a solid phase.

double	bindArea () const
	Returns the area of the contact with the surface of a solid phase.

bool	isNTerminal () const
	Shows whether the group is N-Terminal.

bool	isCTerminal () const
	Shows whether the group is C-Terminal.

bool	isAminoAcid () const
	Shows whether the group is an amino acid.

void	setName (std::string newName)
	Sets the full name of the chemical group.

void	setBindEnergy (double newBindEnergy)
	Sets the binding energy value.

void	setBindArea (double newBindArea)
	Sets the binding energy value.

void	setAverageMass (double newAverageMass)
	Sets the average mass of the chemical group.

void	setMonoisotopicMass (double newMonoisotopicMass)
	Sets the monoisotopic mass of the chemical group.

Detailed Description

A ChemicalGroup instance contains the properties of a group of atoms.

An instance of ChemicalGroup contains the physical properties of a group of atoms inside a protein molecule.

This group can be an amino acid residue or a terminal group, depending on its label.

Please, see the "Peptide sequence notation" for the following help on labels.

Constructor & Destructor Documentation

◆ ChemicalGroup()

BioLCCC::ChemicalGroup::ChemicalGroup	(	std::string	name = `""`,
		std::string	label = `""`,
		double	bindEnergy = `0.0`,
		double	averageMass = `0.0`,
		double	monoisotopicMass = `0.0`,
		double	bindArea = `1.0`
	)

Constructs a chemical group with the given parameters.

Parameters

name	The full name of the chemical group.
label	The label of the chemical group used in sequence notation.
bindEnergy	The energy of binding to the surface of a solid phase measured in kT.
averageMass	The average mass of the group in Da.
monoisotopicMass	The monoisotopic mass of the group in Da.
bindArea	The area of the contact between the group and the surface.

Member Function Documentation

◆ averageMass()

double BioLCCC::ChemicalGroup::averageMass ( ) const

Returns the average mass of the chemical group.

The average mass of an amino acid is measured for R-CH(NH-)-CO- structure WITHOUT terminal H- and -OH (equals to the average mass of a whole amino acid molecule minus 18.01528).

◆ bindArea()

double BioLCCC::ChemicalGroup::bindArea ( ) const

Returns the area of the contact with the surface of a solid phase.

The unit of the bind area is the area of ACN contact. The bind area of a terminal group is added to the area of the corresponding terminal amino acid.

◆ bindEnergy()

double BioLCCC::ChemicalGroup::bindEnergy ( ) const

Returns the energy of binding to the surface of a solid phase.

The bind energy of water is zero and unit is kT. The bind energy of a terminal group is added to the binding group of the corresponding terminal amino acid.

◆ label()

std::string BioLCCC::ChemicalGroup::label ( ) const

Returns the brief code of the group used in peptide sequence notation.

Examples:

M
pT
Ac-

◆ monoisotopicMass()

double BioLCCC::ChemicalGroup::monoisotopicMass ( ) const

Returns the monoisotopic mass of the chemical group.

The monoisotopic mass of an amino acid is measured for R-CH(NH-)-CO- structure WITHOUT terminal H- and -OH (equals to the monoisotopic mass of a whole amino acid molecule minus 18.010565).

◆ name()

std::string BioLCCC::ChemicalGroup::name ( ) const

Returns the full name of the chemical group.