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core::chemical::MMAtomTypeSet Class Reference

A set of MMAtomTypes. More...

#include <MMAtomTypeSet.hh>

Inheritance diagram for core::chemical::MMAtomTypeSet:
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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< MMAtomTypeOPatoms_
 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().

Member Data Documentation

std::map< std::string, int > core::chemical::MMAtomTypeSet::atom_type_index_
private

atom_type_index_ lookup map

atom_type_index_ allows lookup of the atom type index by a string

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

utility::vector1< MMAtomTypeOP > core::chemical::MMAtomTypeSet::atoms_
private

a collection of MMAtomTypes,

MMAtomType has data of atom properties, and it can be looked up by atom_type_index.

Referenced by n_atomtypes(), operator[](), and read_file().

std::string core::chemical::MMAtomTypeSet::name_
private

What the ChemicalManager knows this as, if relevant.

Referenced by name().


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