Public Member Functions
BioLCCC::ChemicalGroup Class Reference

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

#include <chemicalgroup.h>

List of all members.

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.

Definition at line 20 of file chemicalgroup.h.


Constructor & Destructor Documentation

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:
nameThe full name of the chemical group.
labelThe label of the chemical group used in sequence notation.
bindEnergyThe energy of binding to the surface of a solid phase measured in kT.
averageMassThe average mass of the group in Da.
monoisotopicMassThe monoisotopic mass of the group in Da.
bindAreaThe area of the contact between the group and the surface.

Definition at line 6 of file chemicalgroup.cpp.


Member Function Documentation

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).

Definition at line 42 of file chemicalgroup.cpp.

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.

Definition at line 37 of file chemicalgroup.cpp.

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.

Definition at line 32 of file chemicalgroup.cpp.

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

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

Examples:

  • M
  • pT
  • Ac-

Definition at line 27 of file chemicalgroup.cpp.

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).

Definition at line 47 of file chemicalgroup.cpp.

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

Returns the full name of the chemical group.

Examples:

  • Methionine
  • Phosphorylated threonine
  • C-Terminal amidation

Definition at line 22 of file chemicalgroup.cpp.


The documentation for this class was generated from the following files:
 All Classes Namespaces Functions Variables Enumerations Enumerator