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core::scoring::hbonds::HBondDatabase Class Reference

#include <HBondDatabase.hh>

Inheritance diagram for core::scoring::hbonds::HBondDatabase:
Inheritance graph
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Public Member Functions

 ~HBondDatabase () override
 
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 cosBAH2_fade_lookup (Size const hb_eval_type) const
 find fading function for hbgd_cosBAH2 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 cosBAH2_poly_lookup (Size const hb_eval_type) const
 find polynomial to hbgd_cosBAH2 dimension 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
 
HBondDatabaseoperator= (const HBondDatabase &)=delete
 in its current form HBondDatabase is not assignable due to presense of std::map< const std::string, ...> but compiler tries to generate assigment operator anyway More...
 

Private Attributes

bool initialized_
 
std::string params_database_tag_
 
std::map< const std::string,
FadeIntervalCOP
HBFadeInterval_lookup_by_name_
 
utility::vector1< FadeIntervalCOPHBFadeInterval_lookup_
 
utility::vector1< FadeIntervalCOPAHdist_short_fade_lookup_
 
utility::vector1< FadeIntervalCOPAHdist_long_fade_lookup_
 
utility::vector1< FadeIntervalCOPcosBAH_fade_lookup_
 
utility::vector1< FadeIntervalCOPcosBAH2_fade_lookup_
 
utility::vector1< FadeIntervalCOPcosAHD_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
cosBAH2_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< Realdon_strength_lookup_
 
utility::vector1< Realacc_strength_lookup_
 
utility::vector1< HBondWeightTypeweight_type_lookup_
 

Static Private Attributes

static std::map< const
std::string, HBondDatabaseCOP
initialized_databases_
 

Constructor & Destructor Documentation

core::scoring::hbonds::HBondDatabase::HBondDatabase ( )
private
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 ( )
overridedefault

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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

FadeIntervalCOP core::scoring::hbonds::HBondDatabase::cosBAH2_fade_lookup ( Size const  hb_eval_type) const

find fading function for hbgd_cosBAH2

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

References cosBAH2_fade_lookup_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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

Polynomial_1dCOP core::scoring::hbonds::HBondDatabase::cosBAH2_poly_lookup ( Size const  hb_eval_type) const

find polynomial to hbgd_cosBAH2 dimension

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

References cosBAH2_poly_lookup_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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_, and core::scoring::hbonds::HB_EVAL_TYPE_COUNT.

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
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_.

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_.

Referenced by initialize_HBEval().

void core::scoring::hbonds::HBondDatabase::initialize ( )
void core::scoring::hbonds::HBondDatabase::initialize_acc_strength ( )
void core::scoring::hbonds::HBondDatabase::initialize_don_strength ( )
void core::scoring::hbonds::HBondDatabase::initialize_HBEval ( )
void core::scoring::hbonds::HBondDatabase::initialize_HBFadeInterval ( )

read table of fade intervals

References HBFadeInterval_lookup_, HBFadeInterval_lookup_by_name_, and params_database_tag_.

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(), HBPoly1D_lookup_, HBPoly1D_lookup_by_name_, and params_database_tag_.

Referenced by initialize().

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

has the database already been initialized?

References initialized_.

HBondDatabase& core::scoring::hbonds::HBondDatabase::operator= ( const HBondDatabase )
privatedelete

in its current form HBondDatabase is not assignable due to presense of std::map< const std::string, ...> but compiler tries to generate assigment operator anyway

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

Member Data Documentation

utility::vector1< Real > core::scoring::hbonds::HBondDatabase::acc_strength_lookup_
private
utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::AHdist_long_fade_lookup_
private
utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::AHdist_poly_lookup_
private
utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::AHdist_short_fade_lookup_
private
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
utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosAHD_long_poly_lookup_
private
utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosAHD_short_poly_lookup_
private
utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::cosBAH2_fade_lookup_
private
utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosBAH2_poly_lookup_
private
utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::cosBAH_fade_lookup_
private
utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosBAH_long_poly_lookup_
private
utility::vector1< Polynomial_1dCOP > core::scoring::hbonds::HBondDatabase::cosBAH_short_poly_lookup_
private
utility::vector1< Real > core::scoring::hbonds::HBondDatabase::don_strength_lookup_
private
utility::vector1< FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::HBFadeInterval_lookup_
private
std::map< const std::string, FadeIntervalCOP > core::scoring::hbonds::HBondDatabase::HBFadeInterval_lookup_by_name_
private
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
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
utility::vector1< HBondWeightType > core::scoring::hbonds::HBondDatabase::weight_type_lookup_
private

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