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core::chemical::CSDAtomTypeSet Class Reference

A set of CSDAtomTypes. More...

#include <CSDAtomTypeSet.hh>

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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, intatom_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.

Constructor & Destructor Documentation

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

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.

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.

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.

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

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

Member Data Documentation

std::map< std::string, int > core::chemical::CSDAtomTypeSet::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(), print_all_types(), and read_file().

utility::vector1< CSDAtomType* > core::chemical::CSDAtomTypeSet::atoms_
private

a collection of CSDAtomTypes,

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

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


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