| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Friends | List of all members
ProteaseDB Class Reference
Chemistry

Database for enzymes that digest proteins (proteases) More...

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

Inheritance diagram for ProteaseDB:

## Public Member Functions

void | getAllXTandemNames (std::vector< String > &all_names) const
| returns all the enzyme names available for XTandem More...
void | getAllCometNames (std::vector< String > &all_names) const
| returns all the enzyme names available for Comet More...
void | getAllCruxNames (std::vector< String > &all_names) const
| returns all the enzyme names available for Crux More...
void | getAllOMSSANames (std::vector< String > &all_names) const
| returns all the enzyme names available for OMSSA More...
void | getAllMSGFNames (std::vector< String > &all_names) const
| returns all the enzyme names available for MSGFPlus More...
Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
virtual | ~DigestionEnzymeDB ()
| destructor More...
const DigestionEnzymeProtein * | getEnzyme (const String &name) const
const DigestionEnzymeProtein * | getEnzymeByRegEx (const String &cleavage_regex) const
void | getAllNames (std::vector< String > &all_names) const
| returns all the enzyme names (does NOT include synonym names) More...
bool | hasEnzyme (const String &name) const
| returns true if the db contains a enzyme with the given name (supports synonym names) More...
bool | hasEnzyme (const DigestionEnzymeProtein *enzyme) const
| returns true if the db contains the enzyme of the given pointer More...
bool | hasRegEx (const String &cleavage_regex) const
| returns true if the db contains a enzyme with the given regex More...
ConstEnzymeIterator | beginEnzyme () const
ConstEnzymeIterator | endEnzyme () const

## Protected Member Functions

| ProteaseDB ()
| constructor More...
Protected Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
| DigestionEnzymeDB (const String &db_file="")
| DigestionEnzymeDB (const DigestionEnzymeDB &enzymes_db)=delete
| copy constructor More...
void | readEnzymesFromFile_ (const String &filename)
| reads enzymes from the given file More...
const DigestionEnzymeProtein * | parseEnzyme_ (Map< String, String > &values) const
| parses an enzyme, given the key/value pairs from an XML file More...
void | addEnzyme_ (const DigestionEnzymeProtein *enzyme)
| add to internal data; also update indices for search by name and regex More...
DigestionEnzymeDB & | operator= (const DigestionEnzymeDB &enzymes_db)=delete
| assignment operator More...

## Friends

class | DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >

## Additional Inherited Members

Public Types inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
typedef std::set< const DigestionEnzymeProtein *>::const_iterator | ConstEnzymeIterator
typedef std::set< const DigestionEnzymeProtein *>::iterator | EnzymeIterator
Static Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
static ProteaseDB * | getInstance ()
| this member function serves as a replacement of the constructor More...
Protected Attributes inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
Map< String, const DigestionEnzymeProtein *> | enzyme_names_
| index by names More...
Map< String, const DigestionEnzymeProtein *> | enzyme_regex_
| index by regex More...
std::set< const DigestionEnzymeProtein *> | const_enzymes_
| set of enzymes More...

## Detailed Description

Database for enzymes that digest proteins (proteases)

The enzymes stored in this DB are defined in an XML file under share/CHEMISTRY/Enzymes.xml.

## Constructor & Destructor Documentation

## ◆ ProteaseDB()

ProteaseDB | ( |  | ) |

protected

constructor

## Member Function Documentation

## ◆ getAllCometNames()

void getAllCometNames | ( | std::vector< String > & | all_names | ) | const

returns all the enzyme names available for Comet

## ◆ getAllCruxNames()

void getAllCruxNames | ( | std::vector< String > & | all_names | ) | const

returns all the enzyme names available for Crux

## ◆ getAllMSGFNames()

void getAllMSGFNames | ( | std::vector< String > & | all_names | ) | const

returns all the enzyme names available for MSGFPlus

## ◆ getAllOMSSANames()

void getAllOMSSANames | ( | std::vector< String > & | all_names | ) | const

returns all the enzyme names available for OMSSA

## ◆ getAllXTandemNames()

void getAllXTandemNames | ( | std::vector< String > & | all_names | ) | const

returns all the enzyme names available for XTandem

## Friends And Related Function Documentation

## ◆ DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >

friend class DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >

friend