a set of AtomTypes More...

#include <AtomTypeSet.hh>

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 &name, utility::sql_database::sessionOP db_session)

virtual	~AtomTypeSet ()

std::string	name () const
	the name 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	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	enlarge_h_lj_wdepth ()

Private Attributes
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...

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(), utility::io::izstream::close(), directory(), directory_, basic::options::OptionKeys::chemical::enlarge_H_lj, enlarge_h_lj_wdepth(), getline(), utility::io::izstream::good(), basic::options::option, and read_file().

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_, basic::database::full_name(), read_atom_type_extra_parameters_table(), read_atom_type_properties_table(), basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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

virtual

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(), getline(), l, name(), parameters, params, runtime_assert, basic::T(), tag, tags, core::chemical::tr, utility_exit, and utility_exit_with_message.

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_, utility::trim(), and utility_exit_with_message.

Referenced by core::scoring::AtomVDW::AtomVDW(), enlarge_h_lj_wdepth(), get_default_parameter(), core::chemical::modify_atom_properties_from_command_line(), and core::scoring::geometric_solvation::DatabaseOccSolEne::read_datafile().

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_, atoms_, core::chemical::AtomType::name(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), core::chemical::AtomType::set_parameter(), and utility_exit_with_message.

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

void core::chemical::AtomTypeSet::enlarge_h_lj_wdepth ( )

private

References atom_type_index(), and atoms_.

Referenced by AtomTypeSet().

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

inline

SLOW.

References extra_parameter_indices_, and utility_exit_with_message.

Referenced by AtomTypeSet(), core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), get_default_parameter(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii(), core::pack::interaction_graph::RotamerDotsRadiusData::get_ROSETTA_SASA_radii(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::init_SASA_radii_from_database(), core::scoring::GenBornResidueInfo::initialize(), and core::scoring::FACTSRsdTypeInfo::initialize_parameters().

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(), core::chemical::AtomType::lk_volume(), and utility_exit_with_message.

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 core::chemical::modify_atom_properties_from_command_line(), 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().

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::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::vdwaals::VDW_Energy::calculate_hydrogen_interaction_cutoff(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii(), core::pack::interaction_graph::RotamerDotsRadiusData::get_ROSETTA_SASA_radii(), 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(), 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 directory_.

Referenced by add_parameters_from_file(), core::scoring::vdwaals::VDW_Energy::calculate_hydrogen_interaction_cutoff(), 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(), basic::database::safely_prepare_statement(), basic::database::safely_read_from_database(), 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(), core::chemical::AtomType::name(), basic::database::safely_prepare_statement(), and basic::database::safely_read_from_database().

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_, getline(), l, core::chemical::AtomType::set_parameter(), core::chemical::AtomType::set_property(), tag, tags, core::chemical::tr, and utility_exit_with_message.

Referenced by AtomTypeSet().