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

#include <OpenMS/CHEMISTRY/ProteaseDB.h>

Inheritance diagram for ProteaseDB:

Collaboration 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...

void	writeTSV (const String &filename)
	writes the full names to a TSV file 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 &	operator= (const DigestionEnzymeDB &enzymes_db)=delete
	assignment operator 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 (const String &db_file="")

	DigestionEnzymeDB (const DigestionEnzymeDB &enzymes_db)=delete
	copy constructor 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

◆ writeTSV()

void writeTSV ( const String & filename )

writes the full names to a TSV file

Friends And Related Function Documentation

◆ DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >

friend class DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >

friend

Public Member Functions

Protected Member Functions

Friends

Additional Inherited Members