potential remove Nter Methionin More...

#include <peptidemethioninremove.h>

Inheritance diagram for pappso::PeptideMethioninRemove:

Public Member Functions
	PeptideMethioninRemove (bool ism_isPotential)

virtual	~PeptideMethioninRemove ()

void	setPeptide (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const QString &peptide, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override
	function to give the products of a protein digestion by an enzyme

void	setSink (EnzymeProductInterface *sink) override

Private Attributes
EnzymeProductInterface *	m_sink = nullptr

bool	m_isPotential = true

Detailed Description

potential remove Nter Methionin

Definition at line 34 of file peptidemethioninremove.h.

Constructor & Destructor Documentation

◆ PeptideMethioninRemove()

pappso::PeptideMethioninRemove::PeptideMethioninRemove ( bool ism_isPotential )

Definition at line 27 of file peptidemethioninremove.cpp.

{
  m_isPotential = ism_isPotential;
}

References m_isPotential.

◆ ~PeptideMethioninRemove()

pappso::PeptideMethioninRemove::~PeptideMethioninRemove ( )

virtual

Definition at line 32 of file peptidemethioninremove.cpp.

33{

34}

Member Function Documentation

◆ setPeptide()

void pappso::PeptideMethioninRemove::setPeptide	(	std::int8_t	sequence_database_id,
		const ProteinSp &	protein_sp,
		bool	is_decoy,
		const QString &	peptide,
		unsigned int	start,
		bool	is_nter,
		unsigned int	missed_cleavage_number,
		bool	semi_enzyme )

overridevirtual

function to give the products of a protein digestion by an enzyme

Parameters

sequence_database_id	integer that references the sequence fatabase (file, stream, url...)
protein_sp	shared pointer on the protein that was digested
is_decoy	tell if the current protein is a decoy (true) or normal (false) protein
peptide	amino acid sequence of the peptide (string) produced by the digestion
start	the position of the first amino acid of the peptide in the original protein sequence. the first amino acid of the protein is at position 1.
is_nter	boolean to tell if the peptide is an Nter peptide (to allow Methionin Nter removal)
missed_cleavage_number	number of missed cleavage sites (that the enzyme has not cut) fot the product
semi_enzyme	boolean that tells if this peptide is the produce of a semi enzymatic lysis

Implements pappso::EnzymeProductInterface.

Definition at line 37 of file peptidemethioninremove.cpp.

{
  if(is_nter)
    {
      // Nter is often acetylated : MOD:00394
      if(peptide[0] == 'M')
        {
          if(m_isPotential)
            {
              m_sink->setPeptide(sequence_database_id,
                                 protein_sp,
                                 is_decoy,
                                 peptide,
                                 start,
                                 is_nter,
                                 missed_cleavage_number,
                                 semi_enzyme);
            }
          // peptide = peptide.right(peptide.size()-1);
          m_sink->setPeptide(sequence_database_id,
                             protein_sp,
                             is_decoy,
                             peptide.right(peptide.size() - 1),
                             start + 1,
                             is_nter,
                             missed_cleavage_number,
                             semi_enzyme);
        }
      else
        {
          m_sink->setPeptide(sequence_database_id,
                             protein_sp,
                             is_decoy,
                             peptide,
                             start,
                             is_nter,
                             missed_cleavage_number,
                             semi_enzyme);
        }
    }
  else
    {
 
      m_sink->setPeptide(sequence_database_id,
                         protein_sp,
                         is_decoy,
                         peptide,
                         start,
                         is_nter,
                         missed_cleavage_number,
                         semi_enzyme);
    }
}