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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)
 

Constructor & Destructor Documentation

core::scoring::hbonds::HBondOptions::HBondOptions ( )
core::scoring::hbonds::HBondOptions::HBondOptions ( std::string  params_db_tag)
core::scoring::hbonds::HBondOptions::~HBondOptions ( )
virtual
core::scoring::hbonds::HBondOptions::HBondOptions ( HBondOptions const &  src)

copy constructor

Member Function Documentation

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

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

References exclude_self_hbonds_.

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

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

References exclude_self_hbonds_.

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

pba

References Mbhbond_.

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

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

pba

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).

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

References params_database_tag_.

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

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.

References sp2_BAH180_rise_.

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

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

References sp2_BAH180_rise_.

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

References use_hb_env_dep_.

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

References use_hb_env_dep_DNA_.

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

References use_incorrect_deriv_.

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

References use_sp2_chi_penalty_.

Friends And Related Function Documentation

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

Member Data Documentation

bool core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check_
private
bool core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies_
private
bool core::scoring::hbonds::HBondOptions::exclude_DNA_DNA_
private
bool core::scoring::hbonds::HBondOptions::exclude_self_hbonds_
private
bool core::scoring::hbonds::HBondOptions::include_intra_res_RNA_
private
bool core::scoring::hbonds::HBondOptions::Mbhbond_
private
bool core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy_
private
std::string core::scoring::hbonds::HBondOptions::params_database_tag_
private
bool core::scoring::hbonds::HBondOptions::smooth_hb_env_dep_
private
Real core::scoring::hbonds::HBondOptions::sp2_BAH180_rise_
private
bool core::scoring::hbonds::HBondOptions::use_hb_env_dep_
private
bool core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA_
private
bool core::scoring::hbonds::HBondOptions::use_incorrect_deriv_
private
bool core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty_
private

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