CandidateSearch.util.Peptide Class Reference

Simplified peptide class that stores peptide/peptidoform information. More...

Public Member Functions
	Peptide (string Sequence, double Mass, Dictionary< int, double > Modifications, Settings IonSettings, bool IsDecoy)
	Constructor for a new peptide/pepidoform.
int[]	getEnconding (int massRange=5000, int massMultiplier=100)
	Get the encoding vector of the peptide.
override string	ToString ()
	Constructs a string representation of the peptide.
bool	addModification (int position, double mass)
	Adds a modification to the peptide if the peptide isn't already modified at that position.

Properties
string	sequence [get]
	Amino acid sequence of the peptide.
double	mass [get]
	Mass of the unmodified peptide.
Dictionary< int, double >	modifications [get]
	Dictionary mapping residue positions (0 based) to modification masses.
bool	isDecoy [get]
	Is the peptide a decoy peptide or target peptide.
List< double >	ions [get]
	List of theoretical ion m/z values.

Detailed Description

Simplified peptide class that stores peptide/peptidoform information.

Definition at line 8 of file Database.cs.

Constructor & Destructor Documentation

Peptide()

CandidateSearch.util.Peptide.Peptide	(	string	Sequence,
		double	Mass,
		Dictionary< int, double >	Modifications,
		Settings	IonSettings,
		bool	IsDecoy
	)

Constructor for a new peptide/pepidoform.

Parameters

Sequence	Sequence of amino acids.
Mass	Mass of the unmodified peptide.
Modifications	Dictionary that maps amino acid positions (0 based) to modification masses.
IonSettings	Settings used for ion calculation.
IsDecoy	Whether or not the peptide is a decoy peptide.

Definition at line 39 of file Database.cs.

Member Function Documentation

addModification()

bool CandidateSearch.util.Peptide.addModification	(	int	position,
		double	mass
	)

Adds a modification to the peptide if the peptide isn't already modified at that position.

Parameters

position	The position (0 based) of the modification.
mass	The modification mass.

Returns

True if the modification was added, false if there is already a modification on the specified residue.

Definition at line 97 of file Database.cs.

getEnconding()

int[] CandidateSearch.util.Peptide.getEnconding	(	int	massRange = 5000,
		int	massMultiplier = 100
	)

Get the encoding vector of the peptide.

Parameters

massRange	Maximum m/z that should be considered while encoding. Has to match the specifications of VectorSearch.
massMultiplier	Precision of the encoding. Has to match the specifications of VectorSearch.

Returns

The encoding vector as an integer array.

Definition at line 54 of file Database.cs.

ToString()

override string CandidateSearch.util.Peptide.ToString

(

)

Constructs a string representation of the peptide.

Returns

The string representation of the peptide.

Definition at line 73 of file Database.cs.

Property Documentation

ions

List<double> CandidateSearch.util.Peptide.ions

get

List of theoretical ion m/z values.

Definition at line 29 of file Database.cs.

isDecoy

bool CandidateSearch.util.Peptide.isDecoy

get

Is the peptide a decoy peptide or target peptide.

Definition at line 25 of file Database.cs.

mass

double CandidateSearch.util.Peptide.mass

get

Mass of the unmodified peptide.

Definition at line 17 of file Database.cs.

modifications

Dictionary<int, double> CandidateSearch.util.Peptide.modifications

get

Dictionary mapping residue positions (0 based) to modification masses.

Definition at line 21 of file Database.cs.

sequence

string CandidateSearch.util.Peptide.sequence

get

Amino acid sequence of the peptide.

Definition at line 13 of file Database.cs.

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The documentation for this class was generated from the following file:

• C:/Users/P42587/Documents/GitHub/CandidateSearch/util/Database.cs