Rosetta 3.4
Public Member Functions
core::chemical::AtomTypeSet Class Reference

a set of AtomTypes More...

#include <AtomTypeSet.hh>

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List of all members.

Public Member Functions

 AtomTypeSet (std::string const &directory)
 c-tor from directory in the rosetta_database This will go through the directory, usually "$ROSETTA3_DB/chemical/atom_type_sets/<atom_type_set_name>" and initialize all the atom types defined in atom_properties.txt and the extra parameters specified in extras.txt
 AtomTypeSet (std::string const &name, utility::sql_database::sessionOP db_session)
 ~AtomTypeSet ()
std::string name () const
 the name of the AtomTypeSet
Size n_atomtypes () const
 number of atom types in the set
std::string const & directory () const
 Get the source directory, eg to open an additional file in that directory.
int atom_type_index (std::string const &atom_type_name) const
 lookup the atom_type by the atom_type_name string
AtomType const & operator[] (Size const index) const
 [ ] operator, simulating vector index behavior
int extra_parameter_index (std::string const &name) const
 SLOW.
std::map< std::string, int >
const & 
extra_parameter_indices () const
bool has_extra_parameter (std::string const &name) const
void read_file (std::string const &filename)
 file I/O
void add_parameters_from_file (std::string const &filename)
 additional file I/O

Detailed Description

a set of AtomTypes

a vector of pointers each of which points to an AtomType and the vector index is looked up by an atom_name string in a map


Constructor & Destructor Documentation

core::chemical::AtomTypeSet::AtomTypeSet ( std::string const &  directory)

c-tor from directory in the rosetta_database This will go through the directory, usually "$ROSETTA3_DB/chemical/atom_type_sets/<atom_type_set_name>" and initialize all the atom types defined in atom_properties.txt and the extra parameters specified in extras.txt

References add_parameters_from_file(), directory(), and read_file().

core::chemical::AtomTypeSet::AtomTypeSet ( std::string const &  name,
utility::sql_database::sessionOP  db_session 
)
core::chemical::AtomTypeSet::~AtomTypeSet ( )

Member Function Documentation

void core::chemical::AtomTypeSet::add_parameters_from_file ( std::string const &  filename)

additional file I/O

References name(), and core::pack::interaction_graph::T().

Referenced by AtomTypeSet().

int core::chemical::AtomTypeSet::atom_type_index ( std::string const &  atom_type_name) const [inline]

lookup the atom_type by the atom_type_name string

Referenced by core::scoring::AtomVDW::AtomVDW().

std::string const& core::chemical::AtomTypeSet::directory ( ) const [inline]

Get the source directory, eg to open an additional file in that directory.

Referenced by AtomTypeSet(), core::scoring::AtomVDW::AtomVDW(), and core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne().

int core::chemical::AtomTypeSet::extra_parameter_index ( std::string const &  name) const [inline]
std::map< std::string, int> const& core::chemical::AtomTypeSet::extra_parameter_indices ( ) const [inline]
bool core::chemical::AtomTypeSet::has_extra_parameter ( std::string const &  name) const [inline]
Size core::chemical::AtomTypeSet::n_atomtypes ( ) const [inline]
std::string core::chemical::AtomTypeSet::name ( ) const

the name of the AtomTypeSet

The directory is like '$ROSETTA3_DB/rosetta_database/chemical/atom_type_sets/<atom_type_set_name>/' Return 'atom_type_set_name' Note: strip off the trailing slash, if it exists

Referenced by add_parameters_from_file(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_set_to_database().

AtomType const& core::chemical::AtomTypeSet::operator[] ( Size const  index) const [inline]

[ ] operator, simulating vector index behavior

look up an AtomTypeSet by 1-based indexing

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

file I/O

initialize an AtomTypeSet from an external file "filename", and set parameters and properties for each AtomType. Refer to minirosetta_database_stock/chemical/atom_type_sets/fa_standard/atom_properties.txt for file format

References core::chemical::AtomType::set_parameter(), core::chemical::AtomType::set_property(), and core::chemical::tr().

Referenced by AtomTypeSet().


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