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core::chemical::gasteiger::GasteigerAtomTypeSet Class Reference

A set of Bcl Atom types. More...

#include <GasteigerAtomTypeSet.hh>

Inheritance diagram for core::chemical::gasteiger::GasteigerAtomTypeSet:
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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::Sizeatom_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)
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_.

Member Data Documentation

std::map< std::string, core::Size > core::chemical::gasteiger::GasteigerAtomTypeSet::atom_type_index_
private

allows lookup of the atom type by its name

Referenced by atom_type_index(), contains_atom_type(), and read_file().

utility::vector1< GasteigerAtomTypeDataOP > core::chemical::gasteiger::GasteigerAtomTypeSet::atom_types_
private

the set of atom types,

Referenced by atom_type(), n_types(), operator[](), read_bond_file(), read_file(), and type_for_fake_atoms().

ElementSetCAP core::chemical::gasteiger::GasteigerAtomTypeSet::element_set_
private

The associated element type set.

Referenced by element_set(), and read_file().

std::string core::chemical::gasteiger::GasteigerAtomTypeSet::name_
private

What does the ChemicalManager call this TypeSet?

Referenced by name().


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