a set of AtomTypes More...

#include <AtomTypeSet.hh>

Inheritance diagram for core::chemical::AtomTypeSet:

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 More...

	AtomTypeSet (std::string const &directory, std::string const &name)

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

	~AtomTypeSet () override

std::string	name () const
	the name of the AtomTypeSet More...

TypeSetMode	mode () const
	The mode of the AtomTypeSet. More...

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

std::string const &	directory () const
	Get the source directory, eg to open an additional file in that directory. More...

bool	has_atom (std::string const &atom_type_name) const
	Check if atom is present. More...

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

AtomType const &	operator[] (Size const index) const
	[ ] operator, simulating vector index behavior More...

AtomType &	operator[] (Size const index)
	[ ] operator, simulating vector index behavior, non-const version More...

int	extra_parameter_index (std::string const &name) const
	SLOW. More...

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 More...

void	read_meta_file (std::string const &filename)
	Read in meta information from the given file Meta information is info about the AtomTypeSet as a whole. More...

void	add_parameters_from_file (std::string const &filename)
	additional file I/O More...

Private Member Functions
Real	get_default_parameter (std::string const &param_name, std::string const &atm_name) const
	Private helper fxn for performing default parameter substitutions while reading a params file. More...

AtomType &	create_atom_type_from_database (std::string const &atom_type_set_name, std::string const &atom_type_name, utility::sql_database::sessionOP db_session)
	create an atom type instance on the stack More...

void	read_atom_type_properties_table (std::string const &atom_type_set_name, chemical::AtomType &atom_type, utility::sql_database::sessionOP db_session)

void	read_atom_type_extra_parameters_table (std::string const &atom_type_set_name, chemical::AtomType &atom_type, utility::sql_database::sessionOP db_session)

void	legacy_command_line_post_processing ()
	post processing from command-line – deprecated, but here for backwards compatibility – rhiju. More...

void	clone_atom_types_from_commandline ()

Private Attributes
TypeSetMode	mode_
	The mode (fullatom/centroid/etc) of the AtomTypeSet. More...

std::map< std::string, int >	atom_type_index_
	lookup map: get atom_type_index by atom_type_name More...

utility::vector1< AtomType * >	atoms_
	a collection of AtomTypes, More...

std::map< std::string, int >	extra_parameter_indices_
	lookup map: get atom extra parameter index by atom_type_name More...

std::string	directory_
	Save the directory name for future use, eg to load associated AtomVDW data. More...

std::string	name_
	The name of the ATS. More...

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(), clone_atom_types_from_commandline(), directory_, legacy_command_line_post_processing(), name_, read_file(), and read_meta_file().

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

References name(), and name_.

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

References create_atom_type_from_database(), directory_, extra_parameter_index(), extra_parameter_indices_, name_, read_atom_type_extra_parameters_table(), and read_atom_type_properties_table().

core::chemical::AtomTypeSet::~AtomTypeSet ( )

override

References atom_type_index_, and atoms_.

Member Function Documentation

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

additional file I/O

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

Referenced by core::chemical::add_atom_type_set_parameters_from_command_line(), and AtomTypeSet().

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

lookup the atom_type by the atom_type_name string

References atom_type_index_.

Referenced by core::scoring::AtomVDW::AtomVDW(), clone_atom_types_from_commandline(), core::chemical::enlarge_h_lj_wdepth(), get_default_parameter(), core::scoring::geometric_solvation::DatabaseOccSolEne::init_acc_mapping(), core::scoring::geometric_solvation::DatabaseOccSolEne::init_atom_occ_mapping(), core::scoring::geometric_solvation::DatabaseOccSolEne::init_don_mapping(), core::chemical::modify_atom_properties_from_command_line(), core::scoring::geometric_solvation::DatabaseOccSolEne::read_datafile(), core::chemical::MutableResidueType::set_atom_type(), core::scoring::lkball::LK_BallEnergy::setup_d2_bounds(), and core::chemical::unset_acceptor_ether_oxygens().

void core::chemical::AtomTypeSet::clone_atom_types_from_commandline ( )

private

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

Referenced by AtomTypeSet().

AtomType & core::chemical::AtomTypeSet::create_atom_type_from_database	(	std::string const &	atom_type_set_name,
		std::string const &	atom_type_name,
		utility::sql_database::sessionOP	db_session
	)

private

create an atom type instance on the stack

References atom_type_index_, and atoms_.

Referenced by AtomTypeSet().

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

inline

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

References directory_.

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

int core::chemical::AtomTypeSet::extra_parameter_index ( std::string const & name ) const

inline

SLOW.

References extra_parameter_indices_.

Referenced by AtomTypeSet(), core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), get_default_parameter(), core::scoring::MultipoleElecPotential::get_effective_radii(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::init_SASA_radii_from_database(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::facts::FACTSRsdTypeInfo::initialize_parameters(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), and core::pack::interaction_graph::RotamerDotsRadiusData::RotamerDotsRadiusData().

std::map< std::string, int> const& core::chemical::AtomTypeSet::extra_parameter_indices ( ) const

inline

References extra_parameter_indices_.

Referenced by core::chemical::AtomTypeDatabaseIO::write_atom_type_extra_parameters_table().

Real core::chemical::AtomTypeSet::get_default_parameter	(	std::string const &	param_name,
		std::string const &	atm_name
	)		const

private

Private helper fxn for performing default parameter substitutions while reading a params file.

Private helper function for filling in default values in the fxn add_parameters_from_file Enables the user to specify a default parameter set to be used and then provide a few modifications.

eg in the dna_interface lj-radii parameter set we shrink the hydrogens but leave the rest unchanged.

Note: This function is very SLOW, but that should be OK we only use it a bit right at the start.

References atom_type_index(), atoms_, core::chemical::AtomType::extra_parameter(), extra_parameter_index(), has_extra_parameter(), core::chemical::AtomType::lj_radius(), core::chemical::AtomType::lj_wdepth(), core::chemical::AtomType::lk_dgfree(), core::chemical::AtomType::lk_lambda(), and core::chemical::AtomType::lk_volume().

Referenced by add_parameters_from_file().

bool core::chemical::AtomTypeSet::has_atom ( std::string const & atom_type_name ) const

inline

Check if atom is present.

References atom_type_index_.

Referenced by clone_atom_types_from_commandline(), core::chemical::make_centroid(), core::chemical::modify_atom_properties_from_command_line(), core::chemical::rosetta_retype_fullatom(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

bool core::chemical::AtomTypeSet::has_extra_parameter ( std::string const & name ) const

inline

References extra_parameter_indices_.

Referenced by get_default_parameter().

void core::chemical::AtomTypeSet::legacy_command_line_post_processing ( )

private

post processing from command-line – deprecated, but here for backwards compatibility – rhiju.

Do not add anything here. These options are largely deprecated in favor of options that fine tune score terms (EnergyMethodOptions), which are better controlled than changing AtomTypeSet, which is almost a global setting in Rosetta.

References core::chemical::enlarge_h_lj_wdepth(), and core::chemical::unset_acceptor_ether_oxygens().

Referenced by AtomTypeSet().

TypeSetMode core::chemical::AtomTypeSet::mode ( ) const

inline

The mode of the AtomTypeSet.

References mode_.

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

inline

number of atom types in the set

References atoms_.

Referenced by core::scoring::AtomVDW::AtomVDW(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::vdwaals::VDW_Energy::calculate_hydrogen_interaction_cutoff(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::chemical::enlarge_h_lj_wdepth(), core::scoring::geometric_solvation::DatabaseOccSolEne::init_acc_mapping(), core::scoring::geometric_solvation::DatabaseOccSolEne::init_atom_occ_mapping(), core::scoring::geometric_solvation::DatabaseOccSolEne::init_don_mapping(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::init_SASA_radii_from_database(), core::scoring::geometric_solvation::DatabaseOccSolEne::read_datafile(), core::scoring::AtomVDW::setup_approximate_vdw_radii(), core::scoring::lkball::LK_BallEnergy::setup_d2_bounds(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_set_to_database().

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

References name_.

Referenced by add_parameters_from_file(), AtomTypeSet(), core::scoring::vdwaals::VDW_Energy::calculate_hydrogen_interaction_cutoff(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), core::chemical::AtomTypeDatabaseIO::write_atom_type_extra_parameters_table(), 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

References atoms_.

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

inline

[ ] operator, simulating vector index behavior, non-const version

look up an AtomTypeSet by 1-based indexing

References atoms_.

void core::chemical::AtomTypeSet::read_atom_type_extra_parameters_table	(	std::string const &	atom_type_set_name,
		chemical::AtomType &	atom_type,
		utility::sql_database::sessionOP	db_session
	)

private

References core::chemical::AtomType::name(), and core::chemical::AtomType::set_extra_parameter().

Referenced by AtomTypeSet().

void core::chemical::AtomTypeSet::read_atom_type_properties_table	(	std::string const &	atom_type_set_name,
		chemical::AtomType &	atom_type,
		utility::sql_database::sessionOP	db_session
	)

private

References core::chemical::AtomType::add_property(), and core::chemical::AtomType::name().

Referenced by AtomTypeSet().

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

Referenced by core::chemical::add_atom_types_from_command_line(), and AtomTypeSet().

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

Read in meta information from the given file Meta information is info about the AtomTypeSet as a whole.

Read in meta information from the given file.

References mode_, and core::chemical::type_set_mode_from_string().

Referenced by AtomTypeSet().