A global dictionary for the lookup of data associated with the atom types defined in namespace Chem::AtomType. More...

#include <AtomDictionary.hpp>

Classes
class	Entry
	A single dictionary entry describing the properties of an (atom type, isotope) pair. More...

Public Types
typedef std::shared_ptr< AtomDictionary >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `AtomDictionary` instances. More...

typedef boost::transform_iterator< std::function< const Entry &(const EntryLookupTable::value_type &)>, EntryLookupTable::const_iterator >	ConstEntryIterator
	A constant iterator over the entries of the dictionary. More...

Public Member Functions
void	addEntry (const Entry &entry)
	Adds the given entry to the dictionary. Any pre-existing entry for the same (type, isotope) is replaced. More...

bool	containsEntry (unsigned int type, std::size_t isotope) const
	Tells whether the dictionary contains an entry for the given (type, isotope) pair. More...

void	removeEntry (unsigned int type, std::size_t isotope)
	Removes the entry for the given (type, isotope) pair, if present. More...

const Entry &	getEntry (unsigned int type, std::size_t isotope) const
	Returns the entry for the given (type, isotope) pair. More...

void	clear ()
	Removes all entries from the dictionary. More...

std::size_t	getNumEntries () const
	Returns the number of entries stored in the dictionary. More...

ConstEntryIterator	getEntriesBegin () const
	Returns a constant iterator pointing to the first entry. More...

ConstEntryIterator	getEntriesEnd () const
	Returns a constant iterator pointing one past the last entry. More...

ConstEntryIterator	begin () const
	Returns a constant iterator pointing to the first entry (range-based for support). More...

ConstEntryIterator	end () const
	Returns a constant iterator pointing one past the last entry (range-based for support). More...

void	loadDefaults ()
	Loads the default atom dictionary bundled with CDPKit. More...

Static Public Member Functions
static void	set (const SharedPointer &dict)
	Sets the process-wide default atom dictionary used by the static accessor methods. More...

static const SharedPointer &	get ()
	Returns the process-wide default atom dictionary. More...

static const std::string &	getSymbol (unsigned int type, std::size_t isotope=0)
	Returns the symbol that is associated with the specified atom type and isotope. More...

static const std::string &	getName (unsigned int type, std::size_t isotope=0)
	Returns the name of the chemical element that is associated with the specified atom type and isotope. More...

static unsigned int	getType (const std::string &symbol, bool strict=false)
	Returns the numeric atom type that is associated with the specified atom type symbol. More...

static std::size_t	getMostAbundantIsotope (unsigned int type)
	Returns the mass number of the most abundant isotope of the chemical element specified by type. More...

static std::size_t	getIUPACGroup (unsigned int type)
	Returns the IUPAC group of the chemical element specified by type. More...

static std::size_t	getPeriod (unsigned int type)
	Returns the period number of the chemical element specified by type. More...

static std::size_t	getNumValenceElectrons (unsigned int type)
	Returns the number of valence electrons of the chemical element specified by type. More...

static double	getAtomicWeight (unsigned int type, std::size_t isotope=0)
	Returns the standard atomic weight or the relative isotopic mass of an isotope of the chemical element specified by type. More...

static double	getVdWRadius (unsigned int type)
	Returns the Van der Waals radius of the chemical element specified by type. More...

static double	getCovalentRadius (unsigned int type, std::size_t order=1)
	Returns the covalent radius of the chemical element specified by type for the given bond order. More...

static double	getAllredRochowElectronegativity (unsigned int type)
	Returns the Allred-Rochow electronegativity of the chemical element specified by type. More...

static const Util::STArray &	getValenceStates (unsigned int type)
	Returns an array with the valence states of the chemical element specified by type. More...

static bool	isChemicalElement (unsigned int type)
	Tells whether the specified atom type represents a chemical element. More...

static bool	isMainGroupElement (unsigned int type)
	Tells whether the chemical element specified by type is a main group element. More...

static bool	isTransitionMetal (unsigned int type)
	Tells whether the chemical element specified by type is a transition metal. More...

static bool	isMetal (unsigned int type)
	Tells whether the chemical element specified by type is a metal. More...

static bool	isSemiMetal (unsigned int type)
	Tells whether the chemical element specified by type is a semi-metal. More...

static bool	isNonMetal (unsigned int type)
	Tells whether the chemical element specified by type is a non-metal. More...

static bool	isHalogen (unsigned int type)
	Tells whether the chemical element specified by type is a halogen. More...

static bool	isNobleGas (unsigned int type)
	Tells whether the chemical element specified by type is a noble gas. More...

Detailed Description

A global dictionary for the lookup of data associated with the atom types defined in namespace Chem::AtomType.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<AtomDictionary> CDPL::Chem::AtomDictionary::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated AtomDictionary instances.

◆ ConstEntryIterator

typedef boost::transform_iterator<std::function<const Entry&(const EntryLookupTable::value_type&)>, EntryLookupTable::const_iterator> CDPL::Chem::AtomDictionary::ConstEntryIterator

A constant iterator over the entries of the dictionary.

Member Function Documentation

◆ addEntry()

void CDPL::Chem::AtomDictionary::addEntry ( const Entry & entry )

Adds the given entry to the dictionary. Any pre-existing entry for the same (type, isotope) is replaced.

Parameters

entry The entry to add.

◆ containsEntry()

bool CDPL::Chem::AtomDictionary::containsEntry	(	unsigned int	type,
		std::size_t	isotope
	)		const

Tells whether the dictionary contains an entry for the given (type, isotope) pair.

Parameters

type	The atom type.
isotope	The isotope mass number.

Returns: true if the entry exists, and false otherwise.

◆ removeEntry()

void CDPL::Chem::AtomDictionary::removeEntry	(	unsigned int	type,
		std::size_t	isotope
	)

Removes the entry for the given (type, isotope) pair, if present.

Parameters

type	The atom type.
isotope	The isotope mass number.

◆ getEntry()

const Entry& CDPL::Chem::AtomDictionary::getEntry	(	unsigned int	type,
		std::size_t	isotope
	)		const

Returns the entry for the given (type, isotope) pair.

Parameters

type	The atom type.
isotope	The isotope mass number.

Returns: A const reference to the matching entry, or to an empty entry if no matching entry exists.

◆ clear()

void CDPL::Chem::AtomDictionary::clear ( )

Removes all entries from the dictionary.

◆ getNumEntries()

std::size_t CDPL::Chem::AtomDictionary::getNumEntries ( ) const

Returns the number of entries stored in the dictionary.

Returns: The number of entries.

◆ getEntriesBegin()

ConstEntryIterator CDPL::Chem::AtomDictionary::getEntriesBegin ( ) const

Returns a constant iterator pointing to the first entry.

Returns: A constant iterator pointing to the first entry.

◆ getEntriesEnd()

ConstEntryIterator CDPL::Chem::AtomDictionary::getEntriesEnd ( ) const

Returns a constant iterator pointing one past the last entry.

Returns: A constant iterator pointing one past the last entry.

◆ begin()

ConstEntryIterator CDPL::Chem::AtomDictionary::begin ( ) const

Returns a constant iterator pointing to the first entry (range-based for support).

Returns: A constant iterator pointing to the first entry.

◆ end()

ConstEntryIterator CDPL::Chem::AtomDictionary::end ( ) const

Returns a constant iterator pointing one past the last entry (range-based for support).

Returns: A constant iterator pointing one past the last entry.

◆ loadDefaults()

void CDPL::Chem::AtomDictionary::loadDefaults ( )

Loads the default atom dictionary bundled with CDPKit.

◆ set()

static void CDPL::Chem::AtomDictionary::set ( const SharedPointer & dict )

static

Sets the process-wide default atom dictionary used by the static accessor methods.

Parameters

dict	The new default atom dictionary.

◆ get()

static const SharedPointer& CDPL::Chem::AtomDictionary::get ( )

static

Returns the process-wide default atom dictionary.

Returns: The current default atom dictionary.

◆ getSymbol()

static const std::string& CDPL::Chem::AtomDictionary::getSymbol	(	unsigned int	type,
		std::size_t	isotope = `0`
	)

static

Returns the symbol that is associated with the specified atom type and isotope.

The isotope argument has only an effect for hydrogen whose isotopes have different symbols (D for Deuterium and T for Tritium).

Parameters

type	The atom type.
isotope	The mass number of the isotope, or 0 if not specified.

Returns: The atom type symbol, or an empty string if the symbol for the specified type and isotope is not available.

◆ getName()

static const std::string& CDPL::Chem::AtomDictionary::getName	(	unsigned int	type,
		std::size_t	isotope = `0`
	)

static

Returns the name of the chemical element that is associated with the specified atom type and isotope.

The isotope argument has only an effect for hydrogen whose isotopes are named differently (Deuterium and Tritium).

Parameters

type	The atom type specifying the chemical element.
isotope	The mass number of the element's isotope, or 0 if not specified.

Returns: The name of the element isotope, or an empty string if type does not specify a supported chemical element.

◆ getType()

static unsigned int CDPL::Chem::AtomDictionary::getType	(	const std::string &	symbol,
		bool	strict = `false`
	)

static

Returns the numeric atom type that is associated with the specified atom type symbol.

Parameters

symbol	The atom type symbol.
strict	If `true`, dictionary symbols strictly have to match the argument symbol. Otherwise, the symbols will be converted to upper-case before their comparison.

Returns: The numeric atom type, or AtomType::UNKNOWN if symbol does not specify a supported atom type.

◆ getMostAbundantIsotope()

static std::size_t CDPL::Chem::AtomDictionary::getMostAbundantIsotope ( unsigned int type )

static

Returns the mass number of the most abundant isotope of the chemical element specified by type.

Parameters

type	The atom type specifying the chemical element.

Returns: The mass number of the most abundant isotope of the element, or 0 if type does not specify a supported chemical element.

◆ getIUPACGroup()

static std::size_t CDPL::Chem::AtomDictionary::getIUPACGroup ( unsigned int type )

static

Returns the IUPAC group of the chemical element specified by type.

Parameters

type	The atom type specifying the chemical element.

Returns: The IUPAC group of the element, or 0 if type does not specify a supported chemical element.

◆ getPeriod()

static std::size_t CDPL::Chem::AtomDictionary::getPeriod ( unsigned int type )

static

Returns the period number of the chemical element specified by type.

Parameters

type	The atom type specifying the chemical element.

Returns: The period of the element, or 0 if type does not specify a supported chemical element.

◆ getNumValenceElectrons()

static std::size_t CDPL::Chem::AtomDictionary::getNumValenceElectrons ( unsigned int type )

static

Returns the number of valence electrons of the chemical element specified by type.

Parameters

type	The atom type specifying the chemical element.

Returns: The number of valence electrons, or 0 if type does not specify a supported chemical element.

◆ getAtomicWeight()

static double CDPL::Chem::AtomDictionary::getAtomicWeight	(	unsigned int	type,
		std::size_t	isotope = `0`
	)

static

Returns the standard atomic weight or the relative isotopic mass of an isotope of the chemical element specified by type.

If the element isotope is left unspecified, i.e. the argument isotope is zero, then the standard atomic weight of the chemical element will be returned. If an isotope is specified and the exact relative isotopic mass of the specified isotope is not available, the relative isotopic mass is approximated by the provided mass number of the isotope.

Parameters

type	The atom type specifying the chemical element.
isotope	The mass number of the element's isotope, or 0 if not specified.

Returns: The relative isotopic mass of the specified element isotope, or the standard atomic weight of the element if isotope is zero.

◆ getVdWRadius()

static double CDPL::Chem::AtomDictionary::getVdWRadius ( unsigned int type )

static

Returns the Van der Waals radius of the chemical element specified by type.

Parameters

type	The atom type specifying the chemical element.

Returns: The Van der Waals radius, or 0.0 if type does not specify a supported chemical element.

◆ getCovalentRadius()

static double CDPL::Chem::AtomDictionary::getCovalentRadius	(	unsigned int	type,
		std::size_t	order = `1`
	)

static

Returns the covalent radius of the chemical element specified by type for the given bond order.

Parameters

type	The atom type specifying the chemical element.
order	The bond order.

Returns: The covalent radius for the specified bond order, or 0.0 if type does not specify a supported chemical element, order is not valid or the radius is unknown.

◆ getAllredRochowElectronegativity()

static double CDPL::Chem::AtomDictionary::getAllredRochowElectronegativity ( unsigned int type )

static

Returns the Allred-Rochow electronegativity of the chemical element specified by type.

Parameters

type	The atom type specifying the chemical element.

Returns: The Allred-Rochow electronegativity, or 0.0 if the electronegativity of the specified element is not available.

◆ getValenceStates()

static const Util::STArray& CDPL::Chem::AtomDictionary::getValenceStates ( unsigned int type )

static

Returns an array with the valence states of the chemical element specified by type.

Parameters

type	The atom type specifying the chemical element.

Returns: An array with the valence states of the specified chemical element.

◆ isChemicalElement()

static bool CDPL::Chem::AtomDictionary::isChemicalElement ( unsigned int type )

static

Tells whether the specified atom type represents a chemical element.

Parameters

type	The atom type.

Returns: true if type specifies a chemical element, and false otherwise.

◆ isMainGroupElement()

static bool CDPL::Chem::AtomDictionary::isMainGroupElement ( unsigned int type )

static

Tells whether the chemical element specified by type is a main group element.

Parameters

type	The atom type specifying the chemical element.

Returns: true if type specifies a main group element, and false otherwise.

◆ isTransitionMetal()

static bool CDPL::Chem::AtomDictionary::isTransitionMetal ( unsigned int type )

static

Tells whether the chemical element specified by type is a transition metal.

Parameters

type	The atom type specifying the chemical element.

Returns: true if type specifies a transition metal, and false otherwise.

◆ isMetal()

static bool CDPL::Chem::AtomDictionary::isMetal ( unsigned int type )

static

Tells whether the chemical element specified by type is a metal.

Parameters

type	The atom type specifying the chemical element.

Returns: true if type specifies a metal, and false otherwise.

◆ isSemiMetal()

static bool CDPL::Chem::AtomDictionary::isSemiMetal ( unsigned int type )

static

Tells whether the chemical element specified by type is a semi-metal.

Parameters

type	The atom type specifying the chemical element.

Returns: true if type specifies a semi-metal, and false otherwise.

◆ isNonMetal()

static bool CDPL::Chem::AtomDictionary::isNonMetal ( unsigned int type )

static

Tells whether the chemical element specified by type is a non-metal.

Parameters

type	The atom type specifying the chemical element.

Returns: true if type specifies a non-metal, and false otherwise.

◆ isHalogen()

static bool CDPL::Chem::AtomDictionary::isHalogen ( unsigned int type )

static

Tells whether the chemical element specified by type is a halogen.

Parameters

type	The atom type specifying the chemical element.

Returns: true if type specifies a halogen, and false otherwise.

◆ isNobleGas()

static bool CDPL::Chem::AtomDictionary::isNobleGas ( unsigned int type )

static

Tells whether the chemical element specified by type is a noble gas.

Parameters

type	The atom type specifying the chemical element.

Returns: true if type specifies a noble gas, and false otherwise.

The documentation for this class was generated from the following file:

AtomDictionary.hpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstEntryIterator

Member Function Documentation

◆ addEntry()

◆ containsEntry()

◆ removeEntry()

◆ getEntry()

◆ clear()

◆ getNumEntries()

◆ getEntriesBegin()

◆ getEntriesEnd()

◆ begin()

◆ end()

◆ loadDefaults()

◆ set()

◆ get()

◆ getSymbol()

◆ getName()

◆ getType()

◆ getMostAbundantIsotope()

◆ getIUPACGroup()

◆ getPeriod()

◆ getNumValenceElectrons()

◆ getAtomicWeight()

◆ getVdWRadius()

◆ getCovalentRadius()

◆ getAllredRochowElectronegativity()

◆ getValenceStates()

◆ isChemicalElement()

◆ isMainGroupElement()

◆ isTransitionMetal()

◆ isMetal()

◆ isSemiMetal()

◆ isNonMetal()

◆ isHalogen()

◆ isNobleGas()