A set of MMAtomTypes. More...

#include <MMAtomTypeSet.hh>

Inheritance diagram for core::chemical::MMAtomTypeSet:

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

	~MMAtomTypeSet () override

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

core::Size	n_atomtypes () const
	Number of MM 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...

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

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

void	print_all_types ()
	Print all of the names of all of the MMAtomTypes in the set. Usefull for debuging. More...

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

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

utility::vector1< MMAtomTypeOP >	atoms_
	a collection of MMAtomTypes, More...

Detailed Description

A set of MMAtomTypes.

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

Constructor & Destructor Documentation

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

core::chemical::MMAtomTypeSet::~MMAtomTypeSet ( )

overridedefault

Member Function Documentation

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

inline

Lookup the atom_type by the atom_type_name string.

References atom_type_index_.

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

inline

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

References atom_type_index_.

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

inline

Number of MM atom types in the set.

References atoms_.

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

inline

What the ChemicalManager knows this as, if relevant.

References name_.

MMAtomType const& core::chemical::MMAtomTypeSet::operator[] ( core::Size const index ) const

inline

Lookup an MMAtomType by 1-based indexing.

References atoms_.

void core::chemical::MMAtomTypeSet::print_all_types ( )

Print all of the names of all of the MMAtomTypes in the set. Usefull for debuging.

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

References atom_type_index_.

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

Load the MMAtomTypeSet from a file.

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

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

Referenced by core::chemical::add_mm_atom_type_set_parameters_from_command_line().