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

#include <HBondOptions.hh>

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

 HBondOptions (std::string const &params_db_tag="")
 Constructor that initializes th. More...
 
 HBondOptions (utility::options::OptionCollection const &options, std::string const &params_db_tag="")
 Constructor using options given in a (possibly local) option collection. More...
 
void initialize_from_options ()
 Initialize this object from the global option collection. More...
 
void initialize_from_options (utility::options::OptionCollection const &option_list)
 Initialize this object from a (possibly local) option collection. More...
 
 ~HBondOptions () override
 
 HBondOptions (HBondOptions const &src)
 copy constructor More...
 
HBondOptionsoperator= (HBondOptions const &src)
 copy operator More...
 
void parse_my_tag (utility::tag::TagCOP tag)
 set hbond options from key value options in a Tag structure, e.g. from a block in the SCOREFXNS section of a RosettaScripts file. More...
 
Real max_hb_energy () const
 Max possible hbond energy. More...
 
void max_hb_energy (Real const setting)
 
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 put_intra_into_total () const
 
void put_intra_into_total (bool const setting)
 
bool exclude_intra_res_protein () const
 
void exclude_intra_res_protein (bool const setting)
 
bool exclude_intra_res_RNA () const
 
void exclude_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 water_hybrid_sf () const
 
void water_hybrid_sf (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 mphbond () const
 Membrane framework hbonding correction. More...
 
void mphbond (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)
 
Real sp2_outer_width () const
 Parameter for the sp2 potential that dictates the width between the peak when CHI=0 and BAH=120 to when the BAH is at a maximum (Units: pi * radians. E.g. 1/3 means the turn off hbonding when BAH < 60, larger values mean a wider potential). -corrections:score:hb_sp2_outer_width Default: 0.357. More...
 
void sp2_outer_width (Real setting)
 
bool 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). More...
 
void measure_sp3acc_BAH_from_hvy (bool setting)
 
bool fade_energy () const
 Rather than having a strict cutoff of hbond definition at 0, fade the energy smoothly in the range [-0.1, 0.1]. This is necessary to prevent a discontinuity in the derivative when E=0 that arise because of the additive form of the hbond function. -corrections:score:hb_fade_energy Default: false. More...
 
void fade_energy (bool setting)
 
bool exclude_ether_oxygens () const
 No H-bonds to ether oxygens, like O4' in DNA or DNA. Replaces -chemical::no_hbond_to_ether_oxygens. More...
 
void exclude_ether_oxygens (bool setting)
 
bool length_dependent_srbb () const
 Enable helix-length-dependent sr bb hbonds Default: false. More...
 
void length_dependent_srbb (bool setting)
 
Real length_dependent_srbb_lowscale () const
 
void length_dependent_srbb_lowscale (Real setting)
 
Real length_dependent_srbb_highscale () const
 
void length_dependent_srbb_highscale (Real setting)
 
Size length_dependent_srbb_minlength () const
 
void length_dependent_srbb_minlength (Size setting)
 
Size length_dependent_srbb_maxlength () const
 
void length_dependent_srbb_maxlength (Size setting)
 
Real hbond_energy_shift () const
 
void hbond_energy_shift (Real)
 
void show (std::ostream &out) const
 

Static Public Member Functions

static void list_options_read (utility::options::OptionKeyList &option_list)
 Documentation functon that lists the options that are read in the initialize_from_options function. More...
 
static void append_schema_attributes (utility::tag::AttributeList &attributes)
 

Private Attributes

Real max_hb_energy_
 
bool exclude_DNA_DNA_
 
bool exclude_intra_res_protein_
 
bool exclude_intra_res_RNA_
 
bool put_intra_into_total_
 
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_sp2_chi_penalty_
 
Real sp2_BAH180_rise_
 
Real sp2_outer_width_
 
bool measure_sp3acc_BAH_from_hvy_
 
bool fade_energy_
 
bool exclude_ether_oxygens_
 
bool Mbhbond_
 
bool mphbond_
 
Real hbond_energy_shift_
 
bool length_dependent_srbb_
 
Real ldsrbb_low_scale_
 
Real ldsrbb_high_scale_
 
Size ldsrbb_minlength_
 
Size ldsrbb_maxlength_
 
bool water_hybrid_sf_
 

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 ( std::string const &  params_db_tag = "")

Constructor that initializes th.

delegating constructor passing in the global option collection

core::scoring::hbonds::HBondOptions::HBondOptions ( utility::options::OptionCollection const &  options,
std::string const &  params_db_tag = "" 
)

Constructor using options given in a (possibly local) option collection.

References initialize_from_options().

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

copy constructor

Member Function Documentation

void core::scoring::hbonds::HBondOptions::append_schema_attributes ( utility::tag::AttributeList &  attributes)
static
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_ether_oxygens ( ) const

No H-bonds to ether oxygens, like O4' in DNA or DNA. Replaces -chemical::no_hbond_to_ether_oxygens.

References exclude_ether_oxygens_.

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

void core::scoring::hbonds::HBondOptions::exclude_ether_oxygens ( bool  setting)
bool core::scoring::hbonds::HBondOptions::exclude_intra_res_protein ( ) const
void core::scoring::hbonds::HBondOptions::exclude_intra_res_protein ( bool const  setting)
bool core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA ( ) const
void core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA ( bool const  setting)
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::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), core::scoring::hbonds::fill_hbond_set(), and parse_my_tag().

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

References exclude_self_hbonds_.

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

Rather than having a strict cutoff of hbond definition at 0, fade the energy smoothly in the range [-0.1, 0.1]. This is necessary to prevent a discontinuity in the derivative when E=0 that arise because of the additive form of the hbond function. -corrections:score:hb_fade_energy Default: false.

References fade_energy_.

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

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

References fade_energy_.

Real core::scoring::hbonds::HBondOptions::hbond_energy_shift ( ) const
void core::scoring::hbonds::HBondOptions::hbond_energy_shift ( Real  setting)

References hbond_energy_shift_.

void core::scoring::hbonds::HBondOptions::initialize_from_options ( )

Initialize this object from the global option collection.

Referenced by HBondOptions().

void core::scoring::hbonds::HBondOptions::initialize_from_options ( utility::options::OptionCollection const &  option_list)
bool core::scoring::hbonds::HBondOptions::length_dependent_srbb ( ) const

Enable helix-length-dependent sr bb hbonds Default: false.

References length_dependent_srbb_.

void core::scoring::hbonds::HBondOptions::length_dependent_srbb ( bool  setting)
Real core::scoring::hbonds::HBondOptions::length_dependent_srbb_highscale ( ) const

References ldsrbb_high_scale_.

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

References ldsrbb_high_scale_.

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

References ldsrbb_low_scale_.

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

References ldsrbb_low_scale_.

Size core::scoring::hbonds::HBondOptions::length_dependent_srbb_maxlength ( ) const

References ldsrbb_maxlength_.

void core::scoring::hbonds::HBondOptions::length_dependent_srbb_maxlength ( Size  setting)

References ldsrbb_maxlength_.

Size core::scoring::hbonds::HBondOptions::length_dependent_srbb_minlength ( ) const

References ldsrbb_minlength_.

void core::scoring::hbonds::HBondOptions::length_dependent_srbb_minlength ( Size  setting)

References ldsrbb_minlength_.

void core::scoring::hbonds::HBondOptions::list_options_read ( utility::options::OptionKeyList &  option_list)
static

Documentation functon that lists the options that are read in the initialize_from_options function.

References core::scoring::hbond.

Referenced by core::scoring::methods::EnergyMethodOptions::list_options_read().

Real core::scoring::hbonds::HBondOptions::max_hb_energy ( ) const
void core::scoring::hbonds::HBondOptions::max_hb_energy ( Real const  setting)

References max_hb_energy_.

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(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), and parse_my_tag().

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

Membrane framework hbonding correction.

References mphbond_.

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

References mphbond_.

HBondOptions & 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_.

Referenced by parse_my_tag().

void core::scoring::hbonds::HBondOptions::parse_my_tag ( utility::tag::TagCOP  tag)
bool core::scoring::hbonds::HBondOptions::put_intra_into_total ( ) const
void core::scoring::hbonds::HBondOptions::put_intra_into_total ( bool const  setting)

References put_intra_into_total_.

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(), and parse_my_tag().

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

References sp2_BAH180_rise_.

Real core::scoring::hbonds::HBondOptions::sp2_outer_width ( ) const

Parameter for the sp2 potential that dictates the width between the peak when CHI=0 and BAH=120 to when the BAH is at a maximum (Units: pi * radians. E.g. 1/3 means the turn off hbonding when BAH < 60, larger values mean a wider potential). -corrections:score:hb_sp2_outer_width Default: 0.357.

References sp2_outer_width_.

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

void core::scoring::hbonds::HBondOptions::sp2_outer_width ( Real  setting)

References sp2_outer_width_.

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_sp2_chi_penalty ( ) const
void core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty ( bool  setting)

References use_sp2_chi_penalty_.

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

References water_hybrid_sf_.

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_ether_oxygens_
private
bool core::scoring::hbonds::HBondOptions::exclude_intra_res_protein_
private
bool core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA_
private
bool core::scoring::hbonds::HBondOptions::exclude_self_hbonds_
private
bool core::scoring::hbonds::HBondOptions::fade_energy_
private
Real core::scoring::hbonds::HBondOptions::hbond_energy_shift_
private
Real core::scoring::hbonds::HBondOptions::ldsrbb_high_scale_
private
Real core::scoring::hbonds::HBondOptions::ldsrbb_low_scale_
private
Size core::scoring::hbonds::HBondOptions::ldsrbb_maxlength_
private
Size core::scoring::hbonds::HBondOptions::ldsrbb_minlength_
private
bool core::scoring::hbonds::HBondOptions::length_dependent_srbb_
private
Real core::scoring::hbonds::HBondOptions::max_hb_energy_
private
bool core::scoring::hbonds::HBondOptions::Mbhbond_
private
bool core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy_
private
bool core::scoring::hbonds::HBondOptions::mphbond_
private
std::string core::scoring::hbonds::HBondOptions::params_database_tag_
private
bool core::scoring::hbonds::HBondOptions::put_intra_into_total_
private
bool core::scoring::hbonds::HBondOptions::smooth_hb_env_dep_
private
Real core::scoring::hbonds::HBondOptions::sp2_BAH180_rise_
private
Real core::scoring::hbonds::HBondOptions::sp2_outer_width_
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_sp2_chi_penalty_
private
bool core::scoring::hbonds::HBondOptions::water_hybrid_sf_
private

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