core::chemical::Element Class Reference

stores element properties More...

#include <Element.hh>

Inheritance diagram for core::chemical::Element:

Public Types
enum	Properties { Mass, CovalentRadius, VDWaalsRadius, NumberOfProperties }
	enum properties for element types More...

Public Member Functions
	Element ()
	construct undefined element More...
	Element (const core::Size ATOMIC_NUMBER, const core::Size PERIOD, const core::Size MAIN_GROUP, std::string const &CHEMICAL_SYMBOL, std::string const &CHEMICAL_NAME, const core::Real MASS, const core::Real COVALENT_RADIUS, const core::Real VDW_RADIUS, ElectronConfiguration const &ELECTRON_CONFIGURATION)
	construct element from all its data More...
ElementOP	Clone () const
	virtual copy constructor More...
void	set_index (core::Size setting)
core::Size	get_index () const
	Get the index of this element in the parent Element set Will be zero if it's not a member. More...
core::chemical::element::Elements	element () const
	The element enumeration. More...
core::Size	get_atomic_number () const
	atomic number More...
core::Size	get_period () const
core::Size	get_main_group () const
const std::string &	get_chemical_symbol () const
	GetChemicalSymbol. More...
const std::string &	get_chemical_name () const
	GetChemicalName. More...
core::Real	get_property (const Element::Properties &PROPERTY) const
	element type property as core::Real More...
const ElectronConfiguration &	get_electron_configuration () const
	electron configuration More...
bool	is_conjugatable () const
	tell whether this element type can participate in a conjugated system More...
Real	weight () const
	Return the full name of the Element. More...
bool	is_fake () const
	Return true unless the element actually exists in the periodic table. More...
std::istream &	read (std::istream &ISTREAM)
	read from std::istream More...
std::ostream &	write (std::ostream &OSTREAM) const
	write to std::ostream More...

Static Public Member Functions
static const std::string &	get_property_name (const Properties &PROPERTY)
	element type property as string More...

Private Attributes
core::Size	index_
	The index of this Element in the parent typeset. More...
core::chemical::element::Elements	element_
	Element enum. More...
core::Size	atomic_number_
	atomic number More...
core::Size	period_
	Period. More...
core::Size	main_group_
	Group # in the main group (1-8) such as transistion metals. More...
std::string	chemical_symbol_
	ChemicalSymbol. More...
std::string	chemical_name_
	ChemicalName. More...
ElectronConfiguration	electron_configuration_
	electron configuration More...
utility::vector0< core::Real >	properties_
	real-valued properties More...

Detailed Description

stores element properties

This is a low level helper class to store element properties

See also

example_chemistry_element_type_data.cpp

Author

meilerj, woetzen, mendenjl

Date

08/31/2005

Member Enumeration Documentation

enum core::chemical::Element::Properties

enum properties for element types

Enumerator
Mass	Mass.
CovalentRadius	CovalentRadius.
VDWaalsRadius	VdWaalsRadius.
NumberOfProperties	Number of properties.

Constructor & Destructor Documentation

core::chemical::Element::Element

(

)

construct undefined element

core::chemical::Element::Element	(	const core::Size	ATOMIC_NUMBER,
		const core::Size	PERIOD,
		const core::Size	MAIN_GROUP,
		std::string const &	CHEMICAL_SYMBOL,
		std::string const &	CHEMICAL_NAME,
		const core::Real	MASS,
		const core::Real	COVALENT_RADIUS,
		const core::Real	VDW_RADIUS,
		ElectronConfiguration const &	ELECTRON_CONFIGURATION
	)

construct element from all its data

Parameters

ATOMIC_NUMBER	- number in the PSE
PERIOD	- in which period is the element
MAIN_GROUP	- in which of the main groups does the element belong (0 for transition metals)
CHEMICAL_SYMBOL	- one or two letters as in international PSE, first letter capital
CHEMICAL_NAME	- full international name (first letter capital)
MASS	- the atomic mass as a weighted avergage of all isotopes
COVALENT_RADIUS	- radius of atom with electrons
VDW_RADIUS	- vdw radius
ELECTRON_CONFIGURATION	- the electron configuration

References core::chemical::element::elements_from_name().

Member Function Documentation

ElementOP core::chemical::Element::Clone

(

)

const

virtual copy constructor

core::chemical::element::Elements core::chemical::Element::element ( ) const

inline

The element enumeration.

References element_.

core::Size core::chemical::Element::get_atomic_number ( ) const

inline

atomic number

Returns

atomic number

References atomic_number_.

const std::string& core::chemical::Element::get_chemical_name ( ) const

inline

GetChemicalName.

Returns

full chemical name

References chemical_name_.

Referenced by core::chemical::gasteiger::PossibleAtomTypesForAtom::FindPossibleAtomTypesForAtom().

const std::string& core::chemical::Element::get_chemical_symbol ( ) const

inline

GetChemicalSymbol.

Returns

chemical symbol one or two letters as AtomName

References chemical_symbol_.

Referenced by core::chemical::gasteiger::PossibleAtomTypesForAtom::FindPossibleAtomTypesForAtom().

const ElectronConfiguration& core::chemical::Element::get_electron_configuration ( ) const

inline

electron configuration

Returns

the ElectronConfiguration

References electron_configuration_.

core::Size core::chemical::Element::get_index ( ) const

inline

Get the index of this element in the parent Element set Will be zero if it's not a member.

References index_.

core::Size core::chemical::Element::get_main_group ( ) const

inline

Returns

main Group #

References main_group_.

core::Size core::chemical::Element::get_period ( ) const

inline

Returns

Period

References period_.

core::Real core::chemical::Element::get_property ( const Element::Properties &  PROPERTY ) const

inline

element type property as core::Real

Parameters

PROPERTY

the property desired

Returns

the property as core::Real

References properties_.

const std::string & core::chemical::Element::get_property_name ( const Properties &  PROPERTY )

static

element type property as string

Parameters

PROPERTY

the property desired

Returns

the property as string

bool core::chemical::Element::is_conjugatable ( ) const

inline

tell whether this element type can participate in a conjugated system

Returns

true if this element can participate in a common conjugated system Specifically tests if the element has 1-4 valence electrons in P orbitals

References electron_configuration_, and core::chemical::ElectronConfiguration::valence_electrons_p().

bool core::chemical::Element::is_fake ( ) const

inline

Return true unless the element actually exists in the periodic table.

References atomic_number_.

std::istream & core::chemical::Element::read

(

std::istream &

ISTREAM

)

read from std::istream

Parameters

ISTREAM

input stream

Returns

istream which was read from

References core::pose::motif::a(), atomic_number_, chemical_name_, chemical_symbol_, electron_configuration_, element_, core::chemical::element::elements_from_name(), main_group_, NumberOfProperties, period_, properties_, and core::chemical::gasteiger::safe_read().

Referenced by core::chemical::operator>>().

void core::chemical::Element::set_index ( core::Size  setting )

inline

References index_.

Real core::chemical::Element::weight ( ) const

inline

Return the full name of the Element.

This is legacy code from old element set

References Mass, and properties_.

std::ostream & core::chemical::Element::write

(

std::ostream &

OSTREAM

)

const

write to std::ostream

Parameters

OSTREAM

output stream

Returns

ostream which was written to

Parameters

OSTREAM	output stream
INDENT	number of indentations

Returns

ostream which was written to

References core::pose::motif::a(), atomic_number_, chemical_name_, chemical_symbol_, electron_configuration_, main_group_, NumberOfProperties, period_, properties_, and core::chemical::gasteiger::safe_write().

Referenced by core::chemical::operator<<().

Member Data Documentation

core::Size core::chemical::Element::atomic_number_

private

atomic number

Referenced by get_atomic_number(), is_fake(), read(), and write().

std::string core::chemical::Element::chemical_name_

private

ChemicalName.

Referenced by get_chemical_name(), read(), and write().

std::string core::chemical::Element::chemical_symbol_

private

ChemicalSymbol.

Referenced by get_chemical_symbol(), read(), and write().

ElectronConfiguration core::chemical::Element::electron_configuration_

private

electron configuration

Referenced by get_electron_configuration(), is_conjugatable(), read(), and write().

core::chemical::element::Elements core::chemical::Element::element_

private

Element enum.

Referenced by element(), and read().

core::Size core::chemical::Element::index_

private

The index of this Element in the parent typeset.

Referenced by get_index(), and set_index().

core::Size core::chemical::Element::main_group_

private

Group # in the main group (1-8) such as transistion metals.

Referenced by get_main_group(), read(), and write().

core::Size core::chemical::Element::period_

private

Period.

Referenced by get_period(), read(), and write().

utility::vector0< core::Real > core::chemical::Element::properties_

private

real-valued properties

Referenced by get_property(), read(), weight(), and write().

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

• src/core/chemical/Element.hh
• src/core/chemical/Element.cc