OpenMS
2.5.0
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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... | |
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.
Default constructor.
EnzymaticDigestionLogModel | ( | const EnzymaticDigestionLogModel & | rhs | ) |
Copy constructor.
void digest | ( | const AASequence & | protein, |
std::vector< AASequence > & | output | ||
) | const |
Performs the enzymatic digestion of a protein.
String getEnzymeName | ( | ) | const |
Returns the enzyme for the digestion.
double getLogThreshold | ( | ) | const |
Returns the threshold which needs to be exceeded to call a cleavage (only for the trained cleavage model on real data)
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protected |
Tests if position pointed to by p
(N-term side) is a valid cleavage site.
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protected |
Moves the iterator p
behind (i.e., C-term) the next cleavage site of the sequence
.
EnzymaticDigestionLogModel& operator= | ( | const EnzymaticDigestionLogModel & | rhs | ) |
Assignment operator.
Size peptideCount | ( | const AASequence & | protein | ) |
Returns the number of peptides a digestion of protein
would yield under the current enzyme and missed cleavage settings.
void setEnzyme | ( | const String | name | ) |
Sets the enzyme for the digestion.
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
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protected |
Used enzyme.
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protected |
Threshold to decide if position is cleaved or missed (only for the model)
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protected |
Holds the cleavage model.