ms_linker_site Class Reference [Mascot results file module]

Position of an intact link between alpha and beta peptide or a looplink. More...

#include <ms_linker_site.hpp>

List of all members.

Public Member Functions
	ms_linker_site ()
	Create a nil linker site.
	ms_linker_site (ms_peptide::PSM linkFrom, ms_peptide::PSM linkTo, int siteFrom, int siteTo, int varModIdxFrom, int varModIdxTo, double linkerMass)
	Create a linker site.
	ms_linker_site (const ms_linker_site &src)
	Copying constructor.
	~ms_linker_site ()
	Destructor.
void	copyFrom (const ms_linker_site *right)
	Copies all content from another instance of this class.
double	getLinkerMass () const
	Linker mass (Mr).
ms_peptide::PSM	getLinkFrom () const
	Source peptide type.
ms_peptide::PSM	getLinkTo () const
	Target peptide type.
int	getSiteFrom () const
	Linker site index in source peptide.
int	getSiteTo () const
	Linker site index in target peptide.
int	getVarModIdxFrom () const
	Varmod index at the source site.
int	getVarModIdxTo () const
	Varmod index at the target site.
ms_linker_site &	operator= (const ms_linker_site &right)
	C++ assignment operator.

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Detailed Description

Position of an intact link between alpha and beta peptide or a looplink.

The ms_linker_site class encapsulates the position of an intact link between the alpha and beta peptides, and looplinks in general. The link end points ("from" and "to") may have different variable mod numbers if the sites require different specificities. For example, one end could be a lysine with Xlink:DSS (K) and the other could be N-term with Xlink:DSS (Protein N-term).

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Member Function Documentation

double getLinkerMass

(

)

const

Linker mass (Mr).

Returns:

Mass of the linker molecule. There is only one mass even if getVarModIdxFrom() and getVarModIdxTo() differ.

ms_peptide::PSM getLinkFrom

(

)

const

Source peptide type.

Returns:

ms_peptide::PSM_CROSSLINK_ALPHA or ms_peptide::PSM_CROSSLINK_BETA

ms_peptide::PSM getLinkTo

(

)

const

Target peptide type.

Returns:

ms_peptide::PSM_CROSSLINK_ALPHA or ms_peptide::PSM_CROSSLINK_BETA

int getSiteFrom

(

)

const

Linker site index in source peptide.

Returns:

Integer index between 0 and n+1, where n is the source peptide sequence length.

int getSiteTo

(

)

const

Linker site index in target peptide.

Returns:

Integer index between 0 and m+1, where m is the target peptide sequence length.

int getVarModIdxFrom

(

)

const

Varmod index at the source site.

The variable mods index could be different between the from and to ends of the link if they have different specificities. For example, getVarModIdxFrom() could be index 1 (Xlink:DSS (K)) and getVarModIdxTo() could be index 3 (Xlink:DSS (Protein N-term)).

Returns:

Varmod index of the linker at the source site.

int getVarModIdxTo

(

)

const

Varmod index at the target site.

The variable mods index could be different between the from and to ends of the link if they have different specificities. For example, getVarModIdxFrom() could be index 1 (Xlink:DSS (K)) and getVarModIdxTo() could be index 3 (Xlink:DSS (Protein N-term)).

Returns:

Varmod index of the linker at the target site.

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

• ms_linker_site.hpp
• ms_linker_site.cpp