A set of Bcl Elements. More...

#include <ElementSet.hh>

Inheritance diagram for core::chemical::ElementSet:

Public Member Functions
	ElementSet (std::string const &name="")

	~ElementSet () override

std::string const &	name () const
	What the ChemicalManager knows this as, if relevant. More...

Size	n_elements () const
	Number of elements in the set. More...

bool	contains_element_type (std::string const &element_symbol) const
	Check if there is an element_type associated with an element_symbol string. More...

Size	element_index (core::chemical::element::Elements ele) const
	Lookup the element index by the element enum. More...

Size	element_index (std::string const &element_symbol) const
	Lookup the element index by the element_symbol string. More...

ElementCOP	element (core::chemical::element::Elements ele) const
	Lookup the element index by the element enum;. More...

ElementCOP	element (std::string const &element_symbol) const
	Lookup the element object by the element_symbol string. More...

ElementCOP	operator[] (Size const index) const
	Lookup an Element by 1-based indexing. More...

void	read_file (std::string const &filename)
	Load the ElementSet from a file. More...

Private Attributes
std::string	name_
	What the ChemicalManager knows this as, if relevant. More...

std::map< std::string, core::Size >	element_index_
	element_index_ lookup map More...

utility::vector1< ElementOP >	elements_
	a collection of Elements, More...

Detailed Description

A set of Bcl Elements.

This class contains a vector of pointers each of which points to an Element and the vector index is looked up by an element_name string in a map.

Constructor & Destructor Documentation

core::chemical::ElementSet::ElementSet ( std::string const & name = "" )

core::chemical::ElementSet::~ElementSet ( )

overridedefault

Member Function Documentation

bool core::chemical::ElementSet::contains_element_type ( std::string const & element_symbol ) const

Check if there is an element_type associated with an element_symbol string.

References element_index_.

ElementCOP core::chemical::ElementSet::element ( core::chemical::element::Elements ele ) const

Lookup the element index by the element enum;.

Lookup the element index by the element enum.

References element_index(), and elements_.

Referenced by read_file().

ElementCOP core::chemical::ElementSet::element ( std::string const & element_symbol ) const

Lookup the element object by the element_symbol string.

Lookup the element index by the element_symbol string.

References element_index(), and elements_.

Size core::chemical::ElementSet::element_index ( core::chemical::element::Elements ele ) const

Lookup the element index by the element enum.

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

Referenced by element(), and core::chemical::MutableResidueType::set_atom_type().

Size core::chemical::ElementSet::element_index ( std::string const & element_symbol ) const

Lookup the element index by the element_symbol string.

References element_index_.

Size core::chemical::ElementSet::n_elements ( ) const

inline

Number of elements in the set.

References elements_.

std::string const& core::chemical::ElementSet::name ( ) const

inline

What the ChemicalManager knows this as, if relevant.

References name_.

ElementCOP core::chemical::ElementSet::operator[] ( Size const index ) const

Lookup an Element by 1-based indexing.

References elements_.

void core::chemical::ElementSet::read_file ( std::string const & filename )

Load the ElementSet from a file.

Initialize an ElementSet from an external file "filename", and set parameters and properties for each Element. Refer to rosetta_database/chemical/elements/element_properties.txt for file format

References element(), element_index_, elements_, and core::chemical::tr().