Compound Class Reference

Represents a compound (small molecule) More...

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

Inheritance diagram for Compound:

Collaboration diagram for Compound:

Public Member Functions
	Compound ()
	Compound (const Compound &)=default
	Compound (Compound &&) noexcept=default
Compound &	operator= (const Compound &) &=default
Compound &	operator= (Compound &&) &=default
bool	operator== (const Compound &rhs) const
Public Member Functions inherited from PeptideCompound
	PeptideCompound ()=default
	PeptideCompound (const PeptideCompound &)=default
	PeptideCompound (PeptideCompound &&) noexcept=default
PeptideCompound &	operator= (const PeptideCompound &) &=default
PeptideCompound &	operator= (PeptideCompound &&) &=default
bool	operator== (const PeptideCompound &rhs) const
void	setChargeState (int charge)
	Set the peptide or compound charge state.
bool	hasCharge () const
	Whether peptide or compound has set charge state.
int	getChargeState () const
	Return the peptide or compound charge state.
void	setDriftTime (double dt)
	Set the peptide or compound ion mobility drift time.
double	getDriftTime () const
	Return the peptide or compound ion mobility drift time.
bool	hasRetentionTime () const
	Check whether compound or peptide has an annotated retention time.
double	getRetentionTime () const
	Gets compound or peptide retention time.
RetentionTime::RTType	getRetentionTimeType () const
	Get compound or peptide retentiontime type.
RetentionTime::RTUnit	getRetentionTimeUnit () const
	Get compound or peptide retentiontime unit (minute/seconds)
Public Member Functions inherited from CVTermList
	CVTermList ()=default
	Defaults constructor.
	CVTermList (const CVTermList &)=default
	Copy constructor.
	CVTermList (CVTermList &&) noexcept
	Move constructor.
virtual	~CVTermList ()
	Destructor.
CVTermList &	operator= (const CVTermList &rhs) &=default
	Assignment operator.
CVTermList &	operator= (CVTermList &&) &=default
	Move assignment operator.
void	setCVTerms (const std::vector< CVTerm > &terms)
	sets the CV terms
void	replaceCVTerm (const CVTerm &cv_term)
	replaces the specified CV term
void	replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession)
	replaces the specified CV terms using the given accession number
void	replaceCVTerms (const std::map< String, std::vector< CVTerm > > &cv_term_map)
	replaces all cv terms with a map (can be obtained via getCVTerms)
void	consumeCVTerms (const std::map< String, std::vector< CVTerm > > &cv_term_map)
	merges the given map into the member map, no duplicate checking
const std::map< String, std::vector< CVTerm > > &	getCVTerms () const
	returns the accession string of the term
void	addCVTerm (const CVTerm &term)
	adds a CV term
bool	operator== (const CVTermList &cv_term_list) const
	equality operator
bool	operator!= (const CVTermList &cv_term_list) const
	inequality operator
bool	hasCVTerm (const String &accession) const
	checks whether the term has a value
bool	empty () const
	return true if no terms are available
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.
	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.
	~MetaInfoInterface ()
	Destructor.
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator.
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.
void	swap (MetaInfoInterface &rhs)
	Swap contents.
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator.
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator.
const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found.
DataValue	getMetaValue (const String &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.
DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found
bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists.
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name.
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.
void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to name if it exists.
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists.
void	addMetaValues (const MetaInfoInterface &from)
void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.
void	clearMetaInfo ()
	Removes all meta values.

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.
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.
Protected Attributes inherited from PeptideCompound
int	charge_ {0}
bool	charge_set_ {false}
double	drift_time_ {-1}
Protected Attributes inherited from CVTermList
std::map< String, std::vector< CVTerm > >	cv_terms_
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_ = nullptr
	Pointer to the MetaInfo object.

Detailed Description

Represents a compound (small molecule)

Also stores its theoretical mass, SMILES string and molecular formula

Constructor & Destructor Documentation

Compound() [1/3]

Compound ( )

inline

Compound() [2/3]

Compound ( const Compound &  )

default

Compound() [3/3]

Compound ( Compound &&  )

defaultnoexcept

Member Function Documentation

operator=() [1/2]

Compound & operator= ( Compound &&  ) &

default

operator=() [2/2]

Compound & operator= ( const Compound &  ) &

default

operator==()

bool operator== ( const Compound &  rhs ) const

inline

References Compound::molecular_formula.

Member Data Documentation

molecular_formula

String molecular_formula

Referenced by Compound::operator==().

smiles_string

String smiles_string

theoretical_mass

double theoretical_mass