Represents a compound (small molecule) More...

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h>

Inheritance diagram for Compound:

Public Member Functions
	Compound ()

	Compound (const Compound &rhs)

Compound &	operator= (const Compound &rhs)

bool	operator== (const Compound &rhs) const

Public Member Functions inherited from PeptideCompound
	PeptideCompound ()

	PeptideCompound (const PeptideCompound &rhs)

PeptideCompound &	operator= (const PeptideCompound &rhs)

bool	operator== (const PeptideCompound &rhs) const

void	setChargeState (int charge)
	Set the peptide or compound charge state. More...

bool	hasCharge () const
	Whether peptide or compound has set charge state. More...

int	getChargeState () const
	Return the peptide or compound charge state. More...

void	setDriftTime (double dt)
	Set the peptide or compound ion mobility drift time. More...

double	getDriftTime () const
	Return the peptide or compound ion mobility drift time. More...

bool	hasRetentionTime () const
	Check whether compound or peptide has an annotated retention time. More...

double	getRetentionTime () const
	Gets compound or peptide retention time. More...

RetentionTime::RTType	getRetentionTimeType () const
	Get compound or peptide retentiontime type. More...

RetentionTime::RTUnit	getRetentionTimeUnit () const
	Get compound or peptide retentiontime unit (minute/seconds) More...

Public Member Functions inherited from CVTermList
	CVTermList ()
	Defaults constructor. More...

	CVTermList (const CVTermList &rhs)
	Copy constructor. More...

virtual	~CVTermList ()
	Destructor. More...

CVTermList &	operator= (const CVTermList &rhs)
	Assignment operator. More...

void	setCVTerms (const std::vector< CVTerm > &terms)
	sets the CV terms More...

void	replaceCVTerm (const CVTerm &cv_term)
	replaces the specified CV term More...

void	replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession)
	replaces the specified CV terms using the given accession number More...

void	replaceCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
	replaces all cv terms with a map (can be obtained via getCVTerms) More...

void	consumeCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
	merges the given map into the member map, no duplicate checking More...

const Map< String, std::vector< CVTerm > > &	getCVTerms () const
	returns the accession string of the term More...

void	addCVTerm (const CVTerm &term)
	adds a CV term More...

bool	operator== (const CVTermList &cv_term_list) const
	equality operator More...

bool	operator!= (const CVTermList &cv_term_list) const
	inequality operator More...

bool	hasCVTerm (const String &accession) const
	checks whether the term has a value More...

bool	empty () const
	return true if no terms are available More...

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...

bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...

bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...

const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to an index (or DataValue::EMPTY if not found) More...

bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...

bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...

void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...

void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...

void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to `name` if it exists. More...

void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to `index` if it exists. More...

void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...

void	clearMetaInfo ()
	Removes all meta values. More...

Public Attributes
String	molecular_formula

String	smiles_string

double	theoretical_mass

Public Attributes inherited from PeptideCompound
String	id

std::vector< RetentionTime >	rts

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Protected Attributes inherited from PeptideCompound
int	charge_

bool	charge_set_

double	drift_time_

Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > >	cv_terms_

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Detailed Description

Represents a compound (small molecule)

Also stores its theoretical mass, SMILES string and molecular formula

Constructor & Destructor Documentation

◆ Compound() [1/2]

Compound ( )

inline

◆ Compound() [2/2]

Compound ( const Compound & rhs )

inline

Member Function Documentation

◆ operator=()

Compound& operator= ( const Compound & rhs )

inline

References Compound::molecular_formula, PeptideCompound::operator=(), Compound::smiles_string, and Compound::theoretical_mass.

◆ operator==()

bool operator== ( const Compound & rhs ) const

inline

References Compound::molecular_formula, PeptideCompound::operator==(), Compound::smiles_string, and Compound::theoretical_mass.

Member Data Documentation

◆ molecular_formula

String molecular_formula

Referenced by Compound::operator=(), and Compound::operator==().

◆ smiles_string

String smiles_string

Referenced by Compound::operator=(), and Compound::operator==().

◆ theoretical_mass

double theoretical_mass

Referenced by Compound::operator=(), and Compound::operator==().

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Compound() [1/2]

◆ Compound() [2/2]

Member Function Documentation

◆ operator=()

◆ operator==()

Member Data Documentation

◆ molecular_formula

◆ smiles_string

◆ theoretical_mass