A set of CSDAtomTypes. More...

#include <CSDAtomTypeSet.hh>

Inheritance diagram for core::chemical::CSDAtomTypeSet:

Collaboration diagram for core::chemical::CSDAtomTypeSet:

Public Member Functions
	CSDAtomTypeSet ()

	~CSDAtomTypeSet ()

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

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

int	atom_type_index (std::string const &atom_type_name) const
	Lookup the atom_type by the atom_type_name string. More...

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

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

void	print_all_types ()
	Print all of the names of all of the CSDAtomTypes in the set. Useful for debugging. More...

Private Attributes
std::map< std::string, int >	atom_type_index_
	atom_type_index_ lookup map More...

utility::vector1< CSDAtomType * >	atoms_
	a collection of CSDAtomTypes, More...

Detailed Description

A set of CSDAtomTypes.

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

Definition at line 41 of file CSDAtomTypeSet.hh.

Constructor & Destructor Documentation

core::chemical::CSDAtomTypeSet::CSDAtomTypeSet ( )

Definition at line 33 of file CSDAtomTypeSet.cc.

core::chemical::CSDAtomTypeSet::~CSDAtomTypeSet ( )

Definition at line 39 of file CSDAtomTypeSet.cc.

Member Function Documentation

int core::chemical::CSDAtomTypeSet::atom_type_index ( std::string const & atom_type_name) const

Lookup the atom_type by the atom_type_name string.

Definition at line 98 of file CSDAtomTypeSet.cc.

References atom_type_index_.

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

Check if there is an atom_type associated with an atom_type_name string.

Size core::chemical::CSDAtomTypeSet::n_atomtypes ( ) const

Number of atom types in the set.

CSDAtomType const & core::chemical::CSDAtomTypeSet::operator[] ( Size const index) const

Lookup an CSDAtomType by 1-based indexing.

Definition at line 109 of file CSDAtomTypeSet.cc.

References atoms_.

void core::chemical::CSDAtomTypeSet::print_all_types ( )

Print all of the names of all of the CSDAtomTypes in the set. Useful for debugging.

This function iterates over each element in the atom_type_index_ map and prints both keys. It is only used for debugging.

Definition at line 90 of file CSDAtomTypeSet.cc.

References atom_type_index_.

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

Load the CSDAtomTypeSet from a file.

Initialize an CSDAtomTypeSet from an external file "filename", and set parameters and properties for each CSDAtomType. Refer to minirosetta_database_stock/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt for file format

Definition at line 59 of file CSDAtomTypeSet.cc.

References atom_type_index_, atoms_, and core::chemical::tr().