A set of Bcl Atom types. More...

#include <GasteigerAtomTypeSet.hh>

Inheritance diagram for core::chemical::gasteiger::GasteigerAtomTypeSet:

Public Member Functions
	GasteigerAtomTypeSet (ElementSetCAP element_set, std::string const &name="")

	GasteigerAtomTypeSet (GasteigerAtomTypeSet const &other)

	~GasteigerAtomTypeSet () override

std::string const &	name () const
	What does the ChemicalManger call this TypeSet? More...

Size	n_types () const
	Number of atom types in the set. More...

ElementSetCAP	element_set () const
	Return the associated element type set. More...

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

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

GasteigerAtomTypeDataCOP	atom_type (std::string const &atom_type_name) const
	Lookup the element index by the element_symbol string. More...

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

GasteigerAtomTypeDataCOP	type_for_fake_atoms () const
	Return the type that's assigned for fake atoms. (Virtual atoms and the like.) More...

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

void	read_bond_file (std::string const &filename)

Private Member Functions
	GasteigerAtomTypeSet ()

Private Attributes
std::string	name_
	What does the ChemicalManager call this TypeSet? More...

ElementSetCAP	element_set_
	The associated element type set. More...

std::map< std::string, core::Size >	atom_type_index_
	allows lookup of the atom type by its name More...

utility::vector1 < GasteigerAtomTypeDataOP >	atom_types_
	the set of atom types, More...

Detailed Description

A set of Bcl Atom types.

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

Constructor & Destructor Documentation

core::chemical::gasteiger::GasteigerAtomTypeSet::GasteigerAtomTypeSet ( )

privatedefault

core::chemical::gasteiger::GasteigerAtomTypeSet::GasteigerAtomTypeSet	(	ElementSetCAP	element_set,
		std::string const &	name = `""`
	)

core::chemical::gasteiger::GasteigerAtomTypeSet::GasteigerAtomTypeSet ( GasteigerAtomTypeSet const & other )

core::chemical::gasteiger::GasteigerAtomTypeSet::~GasteigerAtomTypeSet ( )

overridedefault

Member Function Documentation

GasteigerAtomTypeDataCOP core::chemical::gasteiger::GasteigerAtomTypeSet::atom_type ( std::string const & atom_type_name ) const

Lookup the element index by the element_symbol string.

References atom_type_index(), and atom_types_.

Referenced by read_bond_file().

Size core::chemical::gasteiger::GasteigerAtomTypeSet::atom_type_index ( std::string const & atom_type_name ) const

Lookup the element index by the element_symbol string.

References atom_type_index_.

Referenced by atom_type(), and type_for_fake_atoms().

bool core::chemical::gasteiger::GasteigerAtomTypeSet::contains_atom_type ( std::string const & atom_type_name ) const

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

References atom_type_index_.

ElementSetCAP core::chemical::gasteiger::GasteigerAtomTypeSet::element_set ( ) const

Return the associated element type set.

References element_set_.

Size core::chemical::gasteiger::GasteigerAtomTypeSet::n_types ( ) const

inline

Number of atom types in the set.

References atom_types_.

std::string const& core::chemical::gasteiger::GasteigerAtomTypeSet::name ( ) const

inline

What does the ChemicalManger call this TypeSet?

References name_.

GasteigerAtomTypeDataCOP core::chemical::gasteiger::GasteigerAtomTypeSet::operator[] ( Size const index ) const

Lookup an Atom by 1-based indexing.

References atom_types_.

void core::chemical::gasteiger::GasteigerAtomTypeSet::read_bond_file ( std::string const & filename )

References atom_type(), atom_types_, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusAromaticBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusDoubleBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusSingleBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusTripleBond, core::id::to_string(), and core::chemical::gasteiger::GasteigerAtomTypeData::VdWaalsRadiusCSD.

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

Load the AtomSet from a file.

Initialize a GasteigerAtomTypeSet from an external file "filename", and set parameters and properties for each Atom. Refer to rosetta_database/chemical/gasteiger/atom_types/atom_properties.txt for file format

References atom_type_index_, atom_types_, element_set_, and core::chemical::gasteiger::tr().

GasteigerAtomTypeDataCOP core::chemical::gasteiger::GasteigerAtomTypeSet::type_for_fake_atoms ( ) const

Return the type that's assigned for fake atoms. (Virtual atoms and the like.)

References atom_type_index(), and atom_types_.