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

#include <OpenMS/CHEMISTRY/ProteaseDB.h>

Inheritance diagram for ProteaseDB:

Collaboration diagram for ProteaseDB:

Public Member Functions
	ProteaseDB (std::vector< std::unique_ptr< DigestionEnzymeDataProvider< DigestionEnzymeProtein > > > providers)
	Construct from custom data providers (for testing / dependency injection)

void	getAllXTandemNames (std::vector< String > &all_names) const
	returns all the enzyme names available for XTandem

void	getAllCometNames (std::vector< String > &all_names) const
	returns all the enzyme names available for Comet

void	getAllOMSSANames (std::vector< String > &all_names) const
	returns all the enzyme names available for OMSSA

void	getAllMSGFNames (std::vector< String > &all_names) const
	returns all the enzyme names available for MSGFPlus

void	writeTSV (const String &filename)
	writes the full names to a TSV file

Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
virtual	~DigestionEnzymeDB ()
	destructor

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)

bool	hasEnzyme (const String &name) const
	returns true if the db contains a enzyme with the given name (supports synonym names)

bool	hasEnzyme (const DigestionEnzymeProtein *enzyme) const
	returns true if the db contains the enzyme of the given pointer

bool	hasRegEx (const String &cleavage_regex) const
	returns true if the db contains a enzyme with the given regex

ConstEnzymeIterator	beginEnzyme () const

ConstEnzymeIterator	endEnzyme () const

Protected Member Functions
	ProteaseDB ()
	default constructor: loads built-in enzymes and optional XML file

Protected Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
DigestionEnzymeDB &	operator= (const DigestionEnzymeDB &enzymes_db)=delete
	assignment operator

void	addEnzyme_ (const DigestionEnzymeProtein *enzyme)

void	loadFromProviders_ (std::vector< std::unique_ptr< DigestionEnzymeDataProvider< DigestionEnzymeProtein > > > &providers)

	DigestionEnzymeDB ()=default

	DigestionEnzymeDB (const DigestionEnzymeDB &enzymes_db)=delete
	copy constructor

Friends
class	DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >

Additional Inherited Members
Public Types inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
typedef std::set< constDigestionEnzymeType * >::const_iterator	ConstEnzymeIterator

typedef std::set< constDigestionEnzymeType * >::iterator	EnzymeIterator

Static Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
static ProteaseDB *	getInstance ()
	this member function serves as a replacement of the constructor

Protected Attributes inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
std::map< String, const DigestionEnzymeProtein * >	enzyme_names_
	index by names

std::map< String, const DigestionEnzymeProtein * >	enzyme_regex_
	index by regex

std::set< const DigestionEnzymeProtein * >	const_enzymes_
	set of enzymes

Detailed Description

Database for enzymes that digest proteins (proteases)

The enzymes stored in this DB are defined as built-in defaults. Additional user-defined enzymes can be loaded from share/CHEMISTRY/Enzymes.xml if present.

Supports dependency injection via a provider-based constructor for testing and custom enzyme sources.

Constructor & Destructor Documentation

◆ ProteaseDB() [1/2]

ProteaseDB ( )

protected

default constructor: loads built-in enzymes and optional XML file

◆ ProteaseDB() [2/2]

ProteaseDB ( std::vector< std::unique_ptr< DigestionEnzymeDataProvider< DigestionEnzymeProtein > > > providers )

explicit

Construct from custom data providers (for testing / dependency injection)

Parameters

[in] providers Data providers supplying enzyme definitions

Member Function Documentation

◆ getAllCometNames()

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

returns all the enzyme names available for Comet

◆ 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

◆ writeTSV()

void writeTSV ( const String & filename )

writes the full names to a TSV file

Friends And Related Symbol Documentation

◆ DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >

friend class DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >

friend

Public Member Functions

Protected Member Functions

Friends

Additional Inherited Members