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core::scoring::hbonds::HBondOptions Class Reference

#include <HBondOptions.hh>

Inheritance diagram for core::scoring::hbonds::HBondOptions:
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Collaboration diagram for core::scoring::hbonds::HBondOptions:
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Public Member Functions

 HBondOptions ()
 
 HBondOptions (std::string params_db_tag)
 
virtual ~HBondOptions ()
 
 HBondOptions (HBondOptions const &src)
 copy constructor More...
 
HBondOptions const & operator= (HBondOptions const &src)
 copy operator More...
 
bool exclude_self_hbonds () const
 Double counted hbonds include: More...
 
void exclude_self_hbonds (bool const setting)
 
bool exclude_DNA_DNA () const
 
void exclude_DNA_DNA (bool const setting)
 
bool include_intra_res_RNA () const
 
void include_intra_res_RNA (bool const setting)
 
bool use_hb_env_dep_DNA () const
 
void use_hb_env_dep_DNA (bool const setting)
 
bool use_hb_env_dep () const
 
void use_hb_env_dep (bool const setting)
 
bool smooth_hb_env_dep () const
 
void smooth_hb_env_dep (bool const setting)
 
bool bb_donor_acceptor_check () const
 
void bb_donor_acceptor_check (bool const setting)
 
bool decompose_bb_hb_into_pair_energies () const
 
void decompose_bb_hb_into_pair_energies (bool const setting)
 
void params_database_tag (std::string const &setting)
 
std::string const & params_database_tag () const
 
bool Mbhbond () const
 pba More...
 
void Mbhbond (bool const setting)
 pba More...
 
bool use_incorrect_deriv () const
 
void use_incorrect_deriv (bool const setting)
 
bool use_sp2_chi_penalty () const
 
void use_sp2_chi_penalty (bool setting)
 
Real sp2_BAH180_rise () const
 Parameter for the sp2 potential that dictates how much worse a head-on hydrogen bond is relative to one at a BAH angle of 120 degrees. Controlled by the command-line flag -corrections:score:hb_sp2_BAH180_rise. Default of 0.75. More...
 
void sp2_BAH180_rise (Real setting)
 
bool measure_sp3acc_BAH_from_hvy () const
 
void measure_sp3acc_BAH_from_hvy (bool setting)
 
void show (std::ostream &out) const
 

Private Attributes

bool exclude_DNA_DNA_
 
bool include_intra_res_RNA_
 
bool exclude_self_hbonds_
 
bool use_hb_env_dep_
 
bool use_hb_env_dep_DNA_
 
bool smooth_hb_env_dep_
 
bool bb_donor_acceptor_check_
 
bool decompose_bb_hb_into_pair_energies_
 
std::string params_database_tag_
 
bool use_incorrect_deriv_
 
bool use_sp2_chi_penalty_
 
Real sp2_BAH180_rise_
 
bool measure_sp3acc_BAH_from_hvy_
 
bool Mbhbond_
 

Friends

bool operator== (HBondOptions const &a, HBondOptions const &b)
 
bool operator!= (HBondOptions const &a, HBondOptions const &b)
 
std::ostream & operator<< (std::ostream &out, const HBondOptions &options)
 

Detailed Description

Definition at line 43 of file HBondOptions.hh.

Constructor & Destructor Documentation

core::scoring::hbonds::HBondOptions::HBondOptions ( )

Definition at line 78 of file HBondOptions.cc.

References bb_donor_acceptor_check_, exclude_DNA_DNA_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, params_database_tag_, sp2_BAH180_rise_, use_incorrect_deriv_, and use_sp2_chi_penalty_.

core::scoring::hbonds::HBondOptions::HBondOptions ( std::string  params_db_tag)

Definition at line 47 of file HBondOptions.cc.

References bb_donor_acceptor_check_, exclude_DNA_DNA_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, sp2_BAH180_rise_, use_incorrect_deriv_, and use_sp2_chi_penalty_.

core::scoring::hbonds::HBondOptions::~HBondOptions ( )
virtual

Definition at line 118 of file HBondOptions.cc.

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

copy constructor

Definition at line 112 of file HBondOptions.cc.

Member Function Documentation

bool core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check ( ) const

Definition at line 244 of file HBondOptions.cc.

References bb_donor_acceptor_check_.

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

void core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check ( bool const  setting)

Definition at line 251 of file HBondOptions.cc.

References bb_donor_acceptor_check_.

bool core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies ( ) const

Definition at line 230 of file HBondOptions.cc.

References decompose_bb_hb_into_pair_energies_.

Referenced by protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), and protocols::pmut_scan::PointMutScanDriver::PointMutScanDriver().

void core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies ( bool const  setting)

Definition at line 237 of file HBondOptions.cc.

References decompose_bb_hb_into_pair_energies_.

bool core::scoring::hbonds::HBondOptions::exclude_DNA_DNA ( ) const

Definition at line 143 of file HBondOptions.cc.

References exclude_DNA_DNA_.

Referenced by core::scoring::hbonds::fill_hbond_set(), and core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold().

void core::scoring::hbonds::HBondOptions::exclude_DNA_DNA ( bool const  setting)

Definition at line 150 of file HBondOptions.cc.

References exclude_DNA_DNA_.

bool core::scoring::hbonds::HBondOptions::exclude_self_hbonds ( ) const

Double counted hbonds include:

  • Hydrogen bonds to self
  • Backbone - sidechain hydrogen bonds where the backbone partner is forming a backbone - backbone hydrogen bond. Turning off this exclusion rule is useful for collecting statistics on hydrogen bond site satisfaction

Definition at line 171 of file HBondOptions.cc.

References exclude_self_hbonds_.

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

void core::scoring::hbonds::HBondOptions::exclude_self_hbonds ( bool const  setting)

Definition at line 178 of file HBondOptions.cc.

References exclude_self_hbonds_.

bool core::scoring::hbonds::HBondOptions::include_intra_res_RNA ( ) const

Definition at line 157 of file HBondOptions.cc.

References include_intra_res_RNA_.

Referenced by core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), and core::scoring::hbonds::identify_intra_res_hbonds().

void core::scoring::hbonds::HBondOptions::include_intra_res_RNA ( bool const  setting)

Definition at line 164 of file HBondOptions.cc.

References include_intra_res_RNA_.

bool core::scoring::hbonds::HBondOptions::Mbhbond ( ) const

pba

Definition at line 272 of file HBondOptions.cc.

References Mbhbond_.

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

void core::scoring::hbonds::HBondOptions::Mbhbond ( bool const  setting)

pba

Definition at line 279 of file HBondOptions.cc.

References Mbhbond_.

bool core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy ( ) const

When calculating the BAH angle for sp3 hybridized acceptors: true: the angle should be measured from the heavy-atom base (CB for S/T); false: from the base-2 atom (HG for S/T).

Definition at line 311 of file HBondOptions.cc.

References measure_sp3acc_BAH_from_hvy_.

Referenced by core::scoring::hbonds::assign_abase_derivs(), core::scoring::hbonds::hb_energy_deriv_u2(), core::scoring::hbonds::hbond_compute_energy(), and core::scoring::hbonds::make_hbBasetoAcc_unitvector().

void core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy ( bool  setting)

Definition at line 312 of file HBondOptions.cc.

References measure_sp3acc_BAH_from_hvy_.

HBondOptions const & core::scoring::hbonds::HBondOptions::operator= ( HBondOptions const &  src)

copy operator

Definition at line 122 of file HBondOptions.cc.

References bb_donor_acceptor_check_, decompose_bb_hb_into_pair_energies_, exclude_DNA_DNA_, exclude_self_hbonds_, include_intra_res_RNA_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, params_database_tag_, smooth_hb_env_dep_, sp2_BAH180_rise_, use_hb_env_dep_, use_hb_env_dep_DNA_, use_incorrect_deriv_, and use_sp2_chi_penalty_.

void core::scoring::hbonds::HBondOptions::params_database_tag ( std::string const &  setting)

Definition at line 265 of file HBondOptions.cc.

References params_database_tag_.

Referenced by core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::hbonds::fill_intra_res_hbond_set(), core::scoring::hbonds::HBondDatabase::get_database(), and core::scoring::hbonds::HBondDatabase::HBondDatabase().

std::string const & core::scoring::hbonds::HBondOptions::params_database_tag ( ) const

Definition at line 258 of file HBondOptions.cc.

References params_database_tag_.

void core::scoring::hbonds::HBondOptions::show ( std::ostream &  out) const

Definition at line 348 of file HBondOptions.cc.

References bb_donor_acceptor_check_, decompose_bb_hb_into_pair_energies_, exclude_DNA_DNA_, exclude_self_hbonds_, include_intra_res_RNA_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, params_database_tag_, smooth_hb_env_dep_, sp2_BAH180_rise_, use_hb_env_dep_, use_hb_env_dep_DNA_, use_incorrect_deriv_, and use_sp2_chi_penalty_.

Referenced by core::scoring::hbonds::operator<<().

bool core::scoring::hbonds::HBondOptions::smooth_hb_env_dep ( ) const

Definition at line 216 of file HBondOptions.cc.

References smooth_hb_env_dep_.

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

void core::scoring::hbonds::HBondOptions::smooth_hb_env_dep ( bool const  setting)

Definition at line 223 of file HBondOptions.cc.

References smooth_hb_env_dep_.

Real core::scoring::hbonds::HBondOptions::sp2_BAH180_rise ( ) const

Parameter for the sp2 potential that dictates how much worse a head-on hydrogen bond is relative to one at a BAH angle of 120 degrees. Controlled by the command-line flag -corrections:score:hb_sp2_BAH180_rise. Default of 0.75.

Definition at line 308 of file HBondOptions.cc.

References sp2_BAH180_rise_.

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

void core::scoring::hbonds::HBondOptions::sp2_BAH180_rise ( Real  setting)

Definition at line 309 of file HBondOptions.cc.

References sp2_BAH180_rise_.

bool core::scoring::hbonds::HBondOptions::use_hb_env_dep ( ) const

Definition at line 202 of file HBondOptions.cc.

References use_hb_env_dep_.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), and core::scoring::hbonds::identify_hbonds_1way().

void core::scoring::hbonds::HBondOptions::use_hb_env_dep ( bool const  setting)

Definition at line 209 of file HBondOptions.cc.

References use_hb_env_dep_.

bool core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA ( ) const

Definition at line 188 of file HBondOptions.cc.

References use_hb_env_dep_DNA_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction().

void core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA ( bool const  setting)

Definition at line 195 of file HBondOptions.cc.

References use_hb_env_dep_DNA_.

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

Definition at line 286 of file HBondOptions.cc.

References use_incorrect_deriv_.

Referenced by core::scoring::hbonds::hb_energy_deriv_u2().

void core::scoring::hbonds::HBondOptions::use_incorrect_deriv ( bool const  setting)

Definition at line 293 of file HBondOptions.cc.

References use_incorrect_deriv_.

bool core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty ( ) const

Definition at line 298 of file HBondOptions.cc.

References use_sp2_chi_penalty_.

Referenced by core::scoring::hbonds::hb_energy_deriv_u2(), and core::scoring::hbonds::hbond_compute_energy().

void core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty ( bool  setting)

Definition at line 303 of file HBondOptions.cc.

References use_sp2_chi_penalty_.

Friends And Related Function Documentation

bool operator!= ( HBondOptions const &  a,
HBondOptions const &  b 
)
friend

Definition at line 335 of file HBondOptions.cc.

std::ostream& operator<< ( std::ostream &  out,
const HBondOptions &  options 
)
friend

Definition at line 341 of file HBondOptions.cc.

bool operator== ( HBondOptions const &  a,
HBondOptions const &  b 
)
friend

Definition at line 316 of file HBondOptions.cc.

Member Data Documentation

bool core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check_
private

Definition at line 192 of file HBondOptions.hh.

Referenced by bb_donor_acceptor_check(), HBondOptions(), operator=(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies_
private

Definition at line 193 of file HBondOptions.hh.

Referenced by decompose_bb_hb_into_pair_energies(), operator=(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBondOptions::exclude_DNA_DNA_
private

Definition at line 186 of file HBondOptions.hh.

Referenced by exclude_DNA_DNA(), HBondOptions(), operator=(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBondOptions::exclude_self_hbonds_
private

Definition at line 188 of file HBondOptions.hh.

Referenced by exclude_self_hbonds(), operator=(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBondOptions::include_intra_res_RNA_
private

Definition at line 187 of file HBondOptions.hh.

Referenced by include_intra_res_RNA(), operator=(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBondOptions::Mbhbond_
private

Definition at line 199 of file HBondOptions.hh.

Referenced by HBondOptions(), Mbhbond(), operator=(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy_
private

Definition at line 198 of file HBondOptions.hh.

Referenced by HBondOptions(), measure_sp3acc_BAH_from_hvy(), operator=(), core::scoring::hbonds::operator==(), and show().

std::string core::scoring::hbonds::HBondOptions::params_database_tag_
private

Definition at line 194 of file HBondOptions.hh.

Referenced by HBondOptions(), operator=(), core::scoring::hbonds::operator==(), params_database_tag(), and show().

bool core::scoring::hbonds::HBondOptions::smooth_hb_env_dep_
private

Definition at line 191 of file HBondOptions.hh.

Referenced by operator=(), core::scoring::hbonds::operator==(), show(), and smooth_hb_env_dep().

Real core::scoring::hbonds::HBondOptions::sp2_BAH180_rise_
private

Definition at line 197 of file HBondOptions.hh.

Referenced by HBondOptions(), operator=(), core::scoring::hbonds::operator==(), show(), and sp2_BAH180_rise().

bool core::scoring::hbonds::HBondOptions::use_hb_env_dep_
private

Definition at line 189 of file HBondOptions.hh.

Referenced by operator=(), core::scoring::hbonds::operator==(), show(), and use_hb_env_dep().

bool core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA_
private

Definition at line 190 of file HBondOptions.hh.

Referenced by operator=(), core::scoring::hbonds::operator==(), show(), and use_hb_env_dep_DNA().

bool core::scoring::hbonds::HBondOptions::use_incorrect_deriv_
private

Definition at line 195 of file HBondOptions.hh.

Referenced by HBondOptions(), operator=(), core::scoring::hbonds::operator==(), show(), and use_incorrect_deriv().

bool core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty_
private

Definition at line 196 of file HBondOptions.hh.

Referenced by HBondOptions(), operator=(), core::scoring::hbonds::operator==(), show(), and use_sp2_chi_penalty().

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