#include <HBondDatabase.hh>

Public Member Functions
virtual	~HBondDatabase ()

void	initialize ()

bool	initialized () const

void	initialize_HBPoly1D ()
	read one dimensional polynomial definitions file More...

void	initialize_HBEval ()
	read table of evaluation types More...

void	initialize_don_strength ()
	read table of donor bonding strengths More...

void	initialize_acc_strength ()
	read table of acceptor bonding strengths More...

void	initialize_HBFadeInterval ()
	read table of fade intervals More...

FadeIntervalCOP	HBFadeInterval_from_name (std::string const name) const
	find polynomial function given name More...

FadeIntervalCOP	AHdist_short_fade_lookup (Size const hb_eval_type) const
	find fading function for hbgd_AHdist sort More...

FadeIntervalCOP	AHdist_long_fade_lookup (Size const hb_eval_type) const
	find fading function for hbgd_AHdist long More...

FadeIntervalCOP	cosBAH_fade_lookup (Size const hb_eval_type) const
	find fading function for hbgd_cosBAH More...

FadeIntervalCOP	cosAHD_fade_lookup (Size const hb_eval_type) const
	find fading function for hbgd_cosAHD More...

Polynomial_1dCOP	HBPoly1D_from_name (std::string const name) const
	find polynomial function given name More...

Polynomial_1dCOP	AHdist_poly_lookup (Size const hb_eval_type) const
	find polynomial to hbgd_AHdist dimension More...

Polynomial_1dCOP	cosBAH_short_poly_lookup (Size const hb_eval_type) const
	find polynomial to hbgd_cosBAH dimension when hbgd_AHdist is short More...

Polynomial_1dCOP	cosBAH_long_poly_lookup (Size const hb_eval_type) const
	find polynomial to hbgd_cosBAH dimension when hbgd_AHdist is long More...

Polynomial_1dCOP	cosAHD_short_poly_lookup (Size const hb_eval_type) const
	find polynomial to hbgd_cosAHD dimension when hbgd_AHdist is short More...

Polynomial_1dCOP	cosAHD_long_poly_lookup (Size const hb_eval_type) const
	find polynomial to hbgd_cosAHD dimension when hbgd_AHdist is long More...

Polynomial_1dCOP	chi_poly_lookup (Size const hb_eval_type) const
	find polynomial to hbgd_chi dimension More...

Real	don_strength (HBDonChemType const don_chem_type) const
	get the bonding strength of a donor group More...

Real	acc_strength (HBAccChemType const ac_chem_type) const
	get the bonding strength of an acceptor group More...

HBondWeightType	weight_type_lookup (Size const hb_eval_type) const
	find weight type for evaluation type More...

bool	use_incorrect_deriv () const

void	report_parameter_features_schema_to_db (utility::sql_database::sessionOP db_session) const

core::Size	report_parameter_features (utility::sql_database::sessionOP db_session) const

Static Public Member Functions
static HBondDatabaseCOP	get_database ()
	only public way to create an HBondDatabase More...

static HBondDatabaseCOP	get_database (std::string const &)
	only public way to create an HBondDatabase More...

Private Member Functions
	HBondDatabase ()

	HBondDatabase (std::string const &hbond_params_database_tag)

	HBondDatabase (const HBondDatabase &src)

void	write_hbond_fade_interval_table_schema (utility::sql_database::sessionOP db_session) const

void	write_hbond_polynomial_1d_table_schema (utility::sql_database::sessionOP db_session) const

void	write_hbond_evaluation_types_table_schema (utility::sql_database::sessionOP db_session) const

Private Attributes
bool	initialized_

std::string	params_database_tag_

std::map< const std::string, FadeIntervalCOP >	HBFadeInterval_lookup_by_name_

utility::vector1< FadeIntervalCOP >	HBFadeInterval_lookup_

utility::vector1< FadeIntervalCOP >	AHdist_short_fade_lookup_

utility::vector1< FadeIntervalCOP >	AHdist_long_fade_lookup_

utility::vector1< FadeIntervalCOP >	cosBAH_fade_lookup_

utility::vector1< FadeIntervalCOP >	cosAHD_fade_lookup_

std::map< const std::string, Polynomial_1dCOP >	HBPoly1D_lookup_by_name_

utility::vector1 < Polynomial_1dCOP >	HBPoly1D_lookup_

utility::vector1 < Polynomial_1dCOP >	AHdist_poly_lookup_

utility::vector1 < Polynomial_1dCOP >	cosBAH_short_poly_lookup_

utility::vector1 < Polynomial_1dCOP >	cosBAH_long_poly_lookup_

utility::vector1 < Polynomial_1dCOP >	cosAHD_short_poly_lookup_

utility::vector1 < Polynomial_1dCOP >	cosAHD_long_poly_lookup_

utility::vector1 < Polynomial_1dCOP >	chi_poly_lookup_

utility::vector1< Real >	don_strength_lookup_

utility::vector1< Real >	acc_strength_lookup_

utility::vector1< HBondWeightType >	weight_type_lookup_

Static Private Attributes
static std::map< const std::string, HBondDatabaseCOP >	initialized_databases_

Constructor & Destructor Documentation

core::scoring::hbonds::HBondDatabase::HBondDatabase ( )

private

References initialize(), core::scoring::hbonds::HBondOptions::params_database_tag(), and params_database_tag_.

Referenced by get_database().

core::scoring::hbonds::HBondDatabase::HBondDatabase ( std::string const & hbond_params_database_tag )

private

References initialize().

core::scoring::hbonds::HBondDatabase::HBondDatabase ( const HBondDatabase & src )

private

core::scoring::hbonds::HBondDatabase::~HBondDatabase ( )

virtual

Member Function Documentation

Real core::scoring::hbonds::HBondDatabase::acc_strength ( HBAccChemType const ac_chem_type ) const

get the bonding strength of an acceptor group

References acc_strength_lookup_, and core::scoring::hbonds::hbacc_MAX.

Referenced by core::scoring::hbonds::hbond_compute_energy().

FadeIntervalCOP core::scoring::hbonds::HBondDatabase::AHdist_long_fade_lookup ( Size const hb_eval_type ) const

find fading function for hbgd_AHdist long

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References AHdist_long_fade_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

Polynomial_1dCOP core::scoring::hbonds::HBondDatabase::AHdist_poly_lookup ( Size const hb_eval_type ) const

find polynomial to hbgd_AHdist dimension

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References AHdist_poly_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

FadeIntervalCOP core::scoring::hbonds::HBondDatabase::AHdist_short_fade_lookup ( Size const hb_eval_type ) const

find fading function for hbgd_AHdist sort

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References AHdist_short_fade_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

Polynomial_1dCOP core::scoring::hbonds::HBondDatabase::chi_poly_lookup ( Size const hb_eval_type ) const

find polynomial to hbgd_chi dimension

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References chi_poly_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

FadeIntervalCOP core::scoring::hbonds::HBondDatabase::cosAHD_fade_lookup ( Size const hb_eval_type ) const

find fading function for hbgd_cosAHD

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References cosAHD_fade_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

Polynomial_1dCOP core::scoring::hbonds::HBondDatabase::cosAHD_long_poly_lookup ( Size const hb_eval_type ) const

find polynomial to hbgd_cosAHD dimension when hbgd_AHdist is long

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References cosAHD_long_poly_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

Polynomial_1dCOP core::scoring::hbonds::HBondDatabase::cosAHD_short_poly_lookup ( Size const hb_eval_type ) const

find polynomial to hbgd_cosAHD dimension when hbgd_AHdist is short

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References cosAHD_short_poly_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

FadeIntervalCOP core::scoring::hbonds::HBondDatabase::cosBAH_fade_lookup ( Size const hb_eval_type ) const

find fading function for hbgd_cosBAH

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References cosBAH_fade_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

Polynomial_1dCOP core::scoring::hbonds::HBondDatabase::cosBAH_long_poly_lookup ( Size const hb_eval_type ) const

find polynomial to hbgd_cosBAH dimension when hbgd_AHdist is long

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References cosBAH_long_poly_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

Polynomial_1dCOP core::scoring::hbonds::HBondDatabase::cosBAH_short_poly_lookup ( Size const hb_eval_type ) const

find polynomial to hbgd_cosBAH dimension when hbgd_AHdist is short

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References cosBAH_short_poly_lookup_, core::scoring::hbonds::HB_EVAL_TYPE_COUNT, and utility_exit_with_message.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and report_parameter_features().

Real core::scoring::hbonds::HBondDatabase::don_strength ( HBDonChemType const don_chem_type ) const

get the bonding strength of a donor group

References don_strength_lookup_, and core::scoring::hbonds::hbdon_MAX.

Referenced by core::scoring::hbonds::hbond_compute_energy().

HBondDatabaseCOP core::scoring::hbonds::HBondDatabase::get_database ( )

static

only public way to create an HBondDatabase

References HBondDatabase(), initialized_databases_, and core::scoring::hbonds::HBondOptions::params_database_tag().

HBondDatabaseCOP core::scoring::hbonds::HBondDatabase::get_database ( std::string const & tag )

static

only public way to create an HBondDatabase

References HBondDatabase(), and initialized_databases_.

FadeIntervalCOP core::scoring::hbonds::HBondDatabase::HBFadeInterval_from_name ( std::string const name ) const

find polynomial function given name

References HBFadeInterval_lookup_by_name_, and utility_exit_with_message.

Referenced by initialize_HBEval().

Polynomial_1dCOP core::scoring::hbonds::HBondDatabase::HBPoly1D_from_name ( std::string const name ) const

find polynomial function given name

References HBPoly1D_lookup_by_name_, and utility_exit_with_message.

Referenced by initialize_HBEval().

void core::scoring::hbonds::HBondDatabase::initialize ( )

initialize hydrogen bond parameters

References initialize_acc_strength(), initialize_don_strength(), initialize_HBEval(), initialize_HBFadeInterval(), initialize_HBPoly1D(), initialized_, and core::scoring::hbonds::tr.

Referenced by HBondDatabase().

void core::scoring::hbonds::HBondDatabase::initialize_acc_strength ( )

read table of acceptor bonding strengths

References core::scoring::hbonds::HBondTypeManager::acc_chem_type_from_name(), acc_strength_lookup_, file_exists(), full_name(), getline(), open(), params_database_tag_, s, string_split(), and utility_exit_with_message.

Referenced by initialize().

void core::scoring::hbonds::HBondDatabase::initialize_don_strength ( )

read table of donor bonding strengths

References core::scoring::hbonds::HBondTypeManager::don_chem_type_from_name(), don_strength_lookup_, file_exists(), full_name(), getline(), open(), params_database_tag_, s, string_split(), and utility_exit_with_message.

Referenced by initialize().

void core::scoring::hbonds::HBondDatabase::initialize_HBEval ( )

read table of evaluation types

read one dimensional polynomial definition file

Referenced by initialize().

void core::scoring::hbonds::HBondDatabase::initialize_HBFadeInterval ( )

read table of fade intervals

References getline(), HBFadeInterval_lookup_, HBFadeInterval_lookup_by_name_, open(), params_database_tag_, s, string_split(), and utility_exit_with_message.

Referenced by initialize().

void core::scoring::hbonds::HBondDatabase::initialize_HBPoly1D ( )

read one dimensional polynomial definitions file

read one dimensional polynomial definition file

References core::pack::dunbrack::c, core::scoring::hbonds::HBondTypeManager::geo_dim_type_from_name(), getline(), HBPoly1D_lookup_, HBPoly1D_lookup_by_name_, open(), params_database_tag_, s, string_split(), and utility_exit_with_message.

Referenced by initialize().

bool core::scoring::hbonds::HBondDatabase::initialized ( ) const

has the database already been initialized?

References initialized_.

Size core::scoring::hbonds::HBondDatabase::report_parameter_features ( utility::sql_database::sessionOP db_session ) const

void core::scoring::hbonds::HBondDatabase::report_parameter_features_schema_to_db ( utility::sql_database::sessionOP db_session ) const

References write_hbond_evaluation_types_table_schema(), write_hbond_fade_interval_table_schema(), and write_hbond_polynomial_1d_table_schema().

bool core::scoring::hbonds::HBondDatabase::use_incorrect_deriv ( ) const

inline

Signal to use deprecated derivitive calculation in core::scoring::hbonds::hb_energy_deriv_u2(). Once old code has been modified to support the new behavior, remove this option. Since the options are not passe directly to to hb_energy_deriv_u2, access it through the HBondDatabase, rather then messing with the interfaces for the hb_energy_deriv functions.

HBondWeightType core::scoring::hbonds::HBondDatabase::weight_type_lookup ( Size const hb_eval_type ) const

find weight type for evaluation type

use get_hbond_evaluation_type(...) or HBEval_lookup(...) determine hb_eval_type.

References core::scoring::hbonds::HB_EVAL_TYPE_COUNT, core::scoring::hbonds::hbw_NONE, utility_exit_with_message, and weight_type_lookup_.

Referenced by report_parameter_features().

void core::scoring::hbonds::HBondDatabase::write_hbond_evaluation_types_table_schema ( utility::sql_database::sessionOP db_session ) const

private

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Referenced by report_parameter_features_schema_to_db().

void core::scoring::hbonds::HBondDatabase::write_hbond_fade_interval_table_schema ( utility::sql_database::sessionOP db_session ) const

private

References basic::database::schema_generator::Schema::add_column(), table, and basic::database::schema_generator::Schema::write().

Referenced by report_parameter_features_schema_to_db().

void core::scoring::hbonds::HBondDatabase::write_hbond_polynomial_1d_table_schema ( utility::sql_database::sessionOP db_session ) const

private

References basic::database::schema_generator::Schema::add_column(), table, and basic::database::schema_generator::Schema::write().

Referenced by report_parameter_features_schema_to_db().

Member Data Documentation

utility::vector1< Real > core::scoring::hbonds::HBondDatabase::acc_strength_lookup_

private

Referenced by acc_strength(), and initialize_acc_strength().

utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::AHdist_long_fade_lookup_

private

Referenced by AHdist_long_fade_lookup(), and initialize_HBEval().

utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::AHdist_poly_lookup_

private

Referenced by AHdist_poly_lookup(), and initialize_HBEval().

utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::AHdist_short_fade_lookup_

private

Referenced by AHdist_short_fade_lookup(), and initialize_HBEval().

utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::chi_poly_lookup_

private

Referenced by chi_poly_lookup().

utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::cosAHD_fade_lookup_

private

Referenced by cosAHD_fade_lookup(), and initialize_HBEval().

utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosAHD_long_poly_lookup_

private

Referenced by cosAHD_long_poly_lookup(), and initialize_HBEval().

utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosAHD_short_poly_lookup_

private

Referenced by cosAHD_short_poly_lookup(), and initialize_HBEval().

utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::cosBAH_fade_lookup_

private

Referenced by cosBAH_fade_lookup(), and initialize_HBEval().

utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosBAH_long_poly_lookup_

private

Referenced by cosBAH_long_poly_lookup(), and initialize_HBEval().

utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosBAH_short_poly_lookup_

private

Referenced by cosBAH_short_poly_lookup(), and initialize_HBEval().

utility::vector1< Real > core::scoring::hbonds::HBondDatabase::don_strength_lookup_

private

Referenced by don_strength(), and initialize_don_strength().

utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::HBFadeInterval_lookup_

private

Referenced by initialize_HBFadeInterval().

std::map< const std::string, FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::HBFadeInterval_lookup_by_name_

private

Referenced by HBFadeInterval_from_name(), initialize_HBFadeInterval(), and report_parameter_features().

utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::HBPoly1D_lookup_

private

Referenced by initialize_HBPoly1D().

std::map< const std::string, Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::HBPoly1D_lookup_by_name_

private

Referenced by HBPoly1D_from_name(), initialize_HBPoly1D(), and report_parameter_features().

bool core::scoring::hbonds::HBondDatabase::initialized_

private

Referenced by initialize(), and initialized().

map< const string, HBondDatabaseCOP > core::scoring::hbonds::HBondDatabase::initialized_databases_

staticprivate

Referenced by get_database().

std::string core::scoring::hbonds::HBondDatabase::params_database_tag_

private

Referenced by HBondDatabase(), initialize_acc_strength(), initialize_don_strength(), initialize_HBEval(), initialize_HBFadeInterval(), initialize_HBPoly1D(), and report_parameter_features().

utility::vector1< HBondWeightType > core::scoring::hbonds::HBondDatabase::weight_type_lookup_

private

Referenced by initialize_HBEval(), and weight_type_lookup().

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

symlinks/rosetta/src/core/scoring/hbonds/HBondDatabase.hh
symlinks/rosetta/src/core/scoring/hbonds/HBondDatabase.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation