Simulates protein digestion. More...
#include <OpenMS/SIMULATION/DigestSimulation.h>
Inheritance diagram for DigestSimulation:
Public Member Functions | |
| DigestSimulation & | operator= (const DigestSimulation &source) |
| Assignment operator. | |
| void | digest (FeatureMapSim &feature_map) |
| Digest a set of proteins into peptides. | |
Constructors and Destructors | |
| DigestSimulation () | |
| Default constructor. | |
| DigestSimulation (const DigestSimulation &source) | |
| Copy constructor. | |
| virtual | ~DigestSimulation () |
| Destructor. | |
Private Member Functions | |
| void | setDefaultParams_ () |
| set defaults | |
Detailed Description
Simulates protein digestion.
Supports all enzymes supported by EnzymaticDigestion.h and additionally incorporates abundance values, which are distributed evenly among digestion products of each protein.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| enzyme | string | Trypsin | Trypsin, none | Enzyme to use for digestion (select 'none' to skip digestion) |
| model | string | naive | trained, naive | The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u). |
| min_peptide_length | int | 3 | min: 1 | Minimum peptide length after digestion (shorter ones will be discarded) |
| model_trained:threshold | float | 0.5 | min: -2 max: 4 | Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage. |
| model_naive:missed_cleavages | int | 1 | min: 0 | Maximum number of missed cleavages considered. All possible resulting peptides will be created. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
| DigestSimulation | ( | ) |
Default constructor.
| DigestSimulation | ( | const DigestSimulation & | source | ) |
Copy constructor.
| virtual ~DigestSimulation | ( | ) | [virtual] |
Destructor.
Member Function Documentation
| void digest | ( | FeatureMapSim & | feature_map | ) |
Digest a set of proteins into peptides.
Digest proteins to peptides, with protein abundance distributes equally among created sibling peptides (this also applies for peptides with missed cleavages). Should a peptide be non-unique the abundances of its instances from proteins are summed up.
- Parameters:
-
feature_map Input FeatureMap containing the proteins that should be digested as ProteinIdentification
| DigestSimulation& operator= | ( | const DigestSimulation & | source | ) |
Assignment operator.
| void setDefaultParams_ | ( | ) | [private] |
set defaults
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1 |