| OpenMS 2.5.0

Classes | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
EnzymaticDigestionLogModel Class Reference
Chemistry

Class for the Log L model of enzymatic digestion of proteins. More...

`#include <OpenMS/CHEMISTRY/EnzymaticDigestionLogModel.h>`

## Classes

struct | BindingSite_
struct | CleavageModel_

## Public Member Functions

| EnzymaticDigestionLogModel ()
| Default constructor. More...
| EnzymaticDigestionLogModel (const EnzymaticDigestionLogModel &rhs)
| Copy constructor. More...
EnzymaticDigestionLogModel & | operator= (const EnzymaticDigestionLogModel &rhs)
| Assignment operator. More...
String | getEnzymeName () const
| Returns the enzyme for the digestion. More...
void | setEnzyme (const String name)
| Sets the enzyme for the digestion. More...
void | digest (const AASequence &protein, std::vector< AASequence > &output) const
| Performs the enzymatic digestion of a protein. More...
Size | peptideCount (const AASequence &protein)
| Returns the number of peptides a digestion of `protein` would yield under the current enzyme and missed cleavage settings. More...
double | getLogThreshold () const
| Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data) More...
void | setLogThreshold (double threshold)

## Protected Member Functions

void | nextCleavageSite_ (const AASequence &sequence, AASequence::ConstIterator &p) const
| Moves the iterator `p` behind (i.e., C-term) the next cleavage site of the `sequence`. More...
bool | isCleavageSite_ (const AASequence &sequence, const AASequence::ConstIterator &p) const
| Tests if position pointed to by `p` (N-term side) is a valid cleavage site. More...

## Protected Attributes

const DigestionEnzyme * | enzyme_
| Used enzyme. More...
double | log_model_threshold_
| Threshold to decide if position is cleaved or missed (only for the model) More...
Map< BindingSite_, CleavageModel_ > | model_data_
| Holds the cleavage model. More...

## Detailed Description

Class for the Log L model of enzymatic digestion of proteins.

An alternative model for tryptic digestion. where the protein is cleaved only at positions where a cleavage model trained on real data, exceeds a certain threshold. The model is published in Siepen et al. (2007), "Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.", doi: 10.1021/pr060507u The model is only available for trypsin and ignores the missed cleavage setting. You should however use setLogThreshold() to adjust FP vs FN rates. A higher threshold increases the number of cleavages predicted.

## Constructor & Destructor Documentation

## ◆ EnzymaticDigestionLogModel() [1/2]

EnzymaticDigestionLogModel | ( |  | ) |

Default constructor.

## ◆ EnzymaticDigestionLogModel() [2/2]

EnzymaticDigestionLogModel | ( | const EnzymaticDigestionLogModel & | rhs | ) |

Copy constructor.

## Member Function Documentation

## ◆ digest()

void digest | ( | const AASequence & | protein,
|  | std::vector< AASequence > & | output
| ) |  | const

Performs the enzymatic digestion of a protein.

## ◆ getEnzymeName()

String getEnzymeName | ( |  | ) | const

Returns the enzyme for the digestion.

## ◆ getLogThreshold()

double getLogThreshold | ( |  | ) | const

Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data)

## ◆ isCleavageSite_()

bool isCleavageSite_ | ( | const AASequence & | sequence,
|  | const AASequence::ConstIterator & | p
| ) |  | const

protected

Tests if position pointed to by `p` (N-term side) is a valid cleavage site.

## ◆ nextCleavageSite_()

void nextCleavageSite_ | ( | const AASequence & | sequence,
|  | AASequence::ConstIterator & | p
| ) |  | const

protected

Moves the iterator `p` behind (i.e., C-term) the next cleavage site of the `sequence`.

## ◆ operator=()

EnzymaticDigestionLogModel& operator= | ( | const EnzymaticDigestionLogModel & | rhs | ) |

Assignment operator.

## ◆ peptideCount()

Size peptideCount | ( | const AASequence & | protein | ) |

Returns the number of peptides a digestion of `protein` would yield under the current enzyme and missed cleavage settings.

## ◆ setEnzyme()

void setEnzyme | ( | const String | name | ) |

Sets the enzyme for the digestion.

## ◆ setLogThreshold()

void setLogThreshold | ( | double | threshold | ) |

Sets the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data) Default is 0.25

## Member Data Documentation

## ◆ enzyme_

const DigestionEnzyme* enzyme_

protected

Used enzyme.

## ◆ log_model_threshold_

double log_model_threshold_

protected

Threshold to decide if position is cleaved or missed (only for the model)

## ◆ model_data_

Map<BindingSite_, CleavageModel_> model_data_

protected

Holds the cleavage model.