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Rosetta 3.5
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#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 |
Static Private Attributes | |
| static std::map< const std::string, HBondDatabaseCOP > | initialized_databases_ |
Definition at line 45 of file HBondDatabase.hh.
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Definition at line 79 of file HBondDatabase.cc.
References initialize(), core::scoring::hbonds::HBondOptions::params_database_tag(), and params_database_tag_.
Referenced by get_database().
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Definition at line 105 of file HBondDatabase.cc.
References initialize().
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Definition at line 133 of file HBondDatabase.cc.
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Definition at line 185 of file HBondDatabase.cc.
| Real core::scoring::hbonds::HBondDatabase::acc_strength | ( | HBAccChemType const | ac_chem_type) | const |
get the bonding strength of an acceptor group
Definition at line 991 of file HBondDatabase.cc.
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.
Definition at line 761 of file HBondDatabase.cc.
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.
Definition at line 845 of file HBondDatabase.cc.
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.
Definition at line 737 of file HBondDatabase.cc.
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.
Definition at line 960 of file HBondDatabase.cc.
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.
Definition at line 807 of file HBondDatabase.cc.
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.
Definition at line 938 of file HBondDatabase.cc.
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.
Definition at line 915 of file HBondDatabase.cc.
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::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.
Definition at line 784 of file HBondDatabase.cc.
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.
Definition at line 892 of file HBondDatabase.cc.
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.
Definition at line 868 of file HBondDatabase.cc.
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
Definition at line 982 of file HBondDatabase.cc.
References don_strength_lookup_, and core::scoring::hbonds::hbdon_MAX.
Referenced by core::scoring::hbonds::hbond_compute_energy().
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only public way to create an HBondDatabase
Definition at line 160 of file HBondDatabase.cc.
References HBondDatabase(), initialized_databases_, and core::scoring::hbonds::HBondOptions::params_database_tag().
Referenced by protocols::features::HBondParameterFeatures::report_features(), and protocols::features::HBondParameterFeatures::write_schema_to_db().
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only public way to create an HBondDatabase
Definition at line 173 of file HBondDatabase.cc.
References HBondDatabase(), and initialized_databases_.
| FadeIntervalCOP core::scoring::hbonds::HBondDatabase::HBFadeInterval_from_name | ( | std::string const | name) | const |
find polynomial function given name
Definition at line 718 of file HBondDatabase.cc.
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
Definition at line 828 of file HBondDatabase.cc.
References HBPoly1D_lookup_by_name_.
Referenced by initialize_HBEval().
| void core::scoring::hbonds::HBondDatabase::initialize | ( | ) |
initialize hydrogen bond parameters
Definition at line 190 of file HBondDatabase.cc.
References initialize_acc_strength(), initialize_don_strength(), initialize_HBEval(), initialize_HBFadeInterval(), initialize_HBPoly1D(), initialized_, initialized_databases_, and params_database_tag_.
Referenced by HBondDatabase().
| void core::scoring::hbonds::HBondDatabase::initialize_acc_strength | ( | ) |
read table of acceptor bonding strengths
Definition at line 667 of file HBondDatabase.cc.
References core::scoring::hbonds::HBondTypeManager::acc_chem_type_from_name(), acc_strength_lookup_, and params_database_tag_.
Referenced by initialize().
| void core::scoring::hbonds::HBondDatabase::initialize_don_strength | ( | ) |
read table of donor bonding strengths
Definition at line 614 of file HBondDatabase.cc.
References core::scoring::hbonds::HBondTypeManager::don_chem_type_from_name(), don_strength_lookup_, and params_database_tag_.
Referenced by initialize().
| void core::scoring::hbonds::HBondDatabase::initialize_HBEval | ( | ) |
read table of evaluation types
read one dimensional polynomial definition file
Definition at line 374 of file HBondDatabase.cc.
References core::scoring::hbonds::HBondTypeManager::acc_chem_type_from_name(), AHdist_long_fade_lookup_, AHdist_poly_lookup_, AHdist_short_fade_lookup_, cosAHD_fade_lookup_, cosAHD_long_poly_lookup_, cosAHD_short_poly_lookup_, cosBAH_fade_lookup_, cosBAH_long_poly_lookup_, cosBAH_short_poly_lookup_, core::scoring::hbonds::HBondTypeManager::don_chem_type_from_name(), core::scoring::hbonds::HB_EVAL_TYPE_COUNT, core::scoring::hbonds::hbe_MAX, core::scoring::hbonds::HBEval_lookup, HBFadeInterval_from_name(), core::scoring::hbonds::hbgd_AHD, core::scoring::hbonds::hbgd_AHdist, core::scoring::hbonds::hbgd_cosAHD, core::scoring::hbonds::hbgd_cosBAH, HBPoly1D_from_name(), core::scoring::hbonds::hbw_NONE, params_database_tag_, core::scoring::hbonds::HBondTypeManager::seq_sep_type_from_name(), core::scoring::hbonds::HBondTypeManager::weight_type_from_name(), and weight_type_lookup_.
Referenced by initialize().
| void core::scoring::hbonds::HBondDatabase::initialize_HBFadeInterval | ( | ) |
read table of fade intervals
Definition at line 219 of file HBondDatabase.cc.
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
Definition at line 294 of file HBondDatabase.cc.
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?
Definition at line 212 of file HBondDatabase.cc.
References initialized_.
| Size core::scoring::hbonds::HBondDatabase::report_parameter_features | ( | utility::sql_database::sessionOP | db_session) | const |
Definition at line 1280 of file HBondDatabase.cc.
References AHdist_long_fade_lookup(), AHdist_poly_lookup(), AHdist_short_fade_lookup(), cosAHD_fade_lookup(), cosAHD_long_poly_lookup(), cosAHD_short_poly_lookup(), cosBAH_fade_lookup(), cosBAH_long_poly_lookup(), cosBAH_short_poly_lookup(), core::scoring::hbonds::hbacc_MAX, core::scoring::hbonds::hbdon_MAX, core::scoring::hbonds::HBEval_lookup, HBFadeInterval_lookup_by_name_, HBPoly1D_lookup_by_name_, core::scoring::hbonds::HBondTypeManager::name_from_acc_chem_type(), core::scoring::hbonds::HBondTypeManager::name_from_don_chem_type(), core::scoring::hbonds::HBondTypeManager::name_from_geo_dim_type(), core::scoring::hbonds::HBondTypeManager::name_from_seq_sep_type(), core::scoring::hbonds::HBondTypeManager::name_from_weight_type(), params_database_tag_, core::scoring::hbonds::seq_sep_MAX, and weight_type_lookup().
| void core::scoring::hbonds::HBondDatabase::report_parameter_features_schema_to_db | ( | utility::sql_database::sessionOP | db_session) | const |
Definition at line 1023 of file HBondDatabase.cc.
References write_hbond_evaluation_types_table_schema(), write_hbond_fade_interval_table_schema(), and write_hbond_polynomial_1d_table_schema().
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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.
Definition at line 168 of file HBondDatabase.hh.
| 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.
Definition at line 1002 of file HBondDatabase.cc.
References core::scoring::hbonds::HB_EVAL_TYPE_COUNT, core::scoring::hbonds::hbw_NONE, and weight_type_lookup_.
Referenced by report_parameter_features().
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Definition at line 1120 of file HBondDatabase.cc.
Referenced by report_parameter_features_schema_to_db().
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Definition at line 1032 of file HBondDatabase.cc.
Referenced by report_parameter_features_schema_to_db().
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Definition at line 1062 of file HBondDatabase.cc.
Referenced by report_parameter_features_schema_to_db().
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Definition at line 215 of file HBondDatabase.hh.
Referenced by acc_strength(), and initialize_acc_strength().
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Definition at line 202 of file HBondDatabase.hh.
Referenced by AHdist_long_fade_lookup(), and initialize_HBEval().
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Definition at line 208 of file HBondDatabase.hh.
Referenced by AHdist_poly_lookup(), and initialize_HBEval().
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Definition at line 201 of file HBondDatabase.hh.
Referenced by AHdist_short_fade_lookup(), and initialize_HBEval().
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Definition at line 213 of file HBondDatabase.hh.
Referenced by chi_poly_lookup().
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Definition at line 204 of file HBondDatabase.hh.
Referenced by cosAHD_fade_lookup(), and initialize_HBEval().
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Definition at line 212 of file HBondDatabase.hh.
Referenced by cosAHD_long_poly_lookup(), and initialize_HBEval().
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Definition at line 211 of file HBondDatabase.hh.
Referenced by cosAHD_short_poly_lookup(), and initialize_HBEval().
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Definition at line 203 of file HBondDatabase.hh.
Referenced by cosBAH_fade_lookup(), and initialize_HBEval().
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Definition at line 210 of file HBondDatabase.hh.
Referenced by cosBAH_long_poly_lookup(), and initialize_HBEval().
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Definition at line 209 of file HBondDatabase.hh.
Referenced by cosBAH_short_poly_lookup(), and initialize_HBEval().
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Definition at line 214 of file HBondDatabase.hh.
Referenced by don_strength(), and initialize_don_strength().
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Definition at line 200 of file HBondDatabase.hh.
Referenced by initialize_HBFadeInterval().
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Definition at line 199 of file HBondDatabase.hh.
Referenced by HBFadeInterval_from_name(), initialize_HBFadeInterval(), and report_parameter_features().
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Definition at line 207 of file HBondDatabase.hh.
Referenced by initialize_HBPoly1D().
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Definition at line 206 of file HBondDatabase.hh.
Referenced by HBPoly1D_from_name(), initialize_HBPoly1D(), and report_parameter_features().
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Definition at line 195 of file HBondDatabase.hh.
Referenced by initialize(), and initialized().
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Definition at line 218 of file HBondDatabase.hh.
Referenced by get_database(), and initialize().
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Definition at line 197 of file HBondDatabase.hh.
Referenced by HBondDatabase(), initialize(), initialize_acc_strength(), initialize_don_strength(), initialize_HBEval(), initialize_HBFadeInterval(), initialize_HBPoly1D(), and report_parameter_features().
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Definition at line 216 of file HBondDatabase.hh.
Referenced by initialize_HBEval(), and weight_type_lookup().
1.8.4