digest

Documentation

Index

• func ChymoTrypsin(seq string, i int) bool
• func LysC(seq string, i int) bool
• func PepsinA(seq string, i int) bool
• func Trypsin(seq string, i int) bool
• func TrypsinP(seq string, i int) bool
• func TrypsinSimple(seq string, i int) bool
• type Digestor
  • func New(minMissedCleavage int, maxMissedCleavage int, filter Filter, enzyme Enzyme) *Digestor
  • func (d *Digestor) Cut(seq string) []string
• type Enzyme
  • func NamedEnzyme(e string) (Enzyme, error)
• type EnzymeInf
  • func Enzymes() []EnzymeInf
• type Filter

Functions

func ChymoTrypsin

func ChymoTrypsin(seq string, i int) bool

func LysC

func LysC(seq string, i int) bool

func PepsinA

func PepsinA(seq string, i int) bool

func Trypsin

func Trypsin(seq string, i int) bool

Trypsin cleaving according to https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

func TrypsinP

func TrypsinP(seq string, i int) bool

func TrypsinSimple

func TrypsinSimple(seq string, i int) bool

TrypsinSimple cuts according to [KR] not followed by P

Types

type Digestor

type Digestor struct {
	// contains filtered or unexported fields
}

func New

func New(minMissedCleavage int, maxMissedCleavage int, filter Filter, enzyme Enzyme) *Digestor

New returns a new Digestor. Parameters specify number of missed cleavages, enzyme,

func (*Digestor) Cut

func (d *Digestor) Cut(seq string) []string

type Enzyme

type Enzyme func(seq string, pos int) bool

Enzyme must return "true" if enzyme cuts at position pos in sequence seq

func NamedEnzyme

func NamedEnzyme(e string) (Enzyme, error)

NamedEnzyme takes an enzyme name and returns the corresponding cutter function

type EnzymeInf

type EnzymeInf struct {
	Name        string
	Description string
	Func        Enzyme
}

EnzymeInf contains info of cutting enzymes

func Enzymes

func Enzymes() []EnzymeInf

Enzymes returns the build-in enzymes

type Filter

type Filter func(seq string) bool

Filter must return "true" if peptide fullfils creteria (e.g. length)