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core::scoring::methods::EnergyMethodOptions Class Reference

#include <EnergyMethodOptions.hh>

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Public Member Functions

 EnergyMethodOptions ()
 
void initialize_from_options ()
 Initialize a new EnergyMethodOptions with defaults from the command line. More...
 
 EnergyMethodOptions (EnergyMethodOptions const &src)
 copy constructor More...
 
virtual ~EnergyMethodOptions ()
 
EnergyMethodOptions const & operator= (EnergyMethodOptions const &src)
 copy operator More...
 
std::string const & etable_type () const
 
void etable_type (std::string const &type)
 
bool analytic_etable_evaluation () const
 
void analytic_etable_evaluation (bool setting)
 
std::string const & unfolded_energies_type () const
 
void unfolded_energies_type (std::string const &type)
 
bool exclude_protein_protein_hack_elec () const
 
void exclude_protein_protein_hack_elec (bool const setting)
 
bool exclude_monomer_hack_elec () const
 
void exclude_monomer_hack_elec (bool const setting)
 
core::Real hackelec_max_dis () const
 The maximum (all atom) distance at which hack_elec is non-zero. More...
 
void hackelec_max_dis (core::Real setting)
 
core::Real hackelec_min_dis () const
 The minimium (all atom) distance for which hack_elec changes with distances. More...
 
void hackelec_min_dis (core::Real setting)
 
core::Real hackelec_die () const
 The dielectric used for the hack_elec term. More...
 
void hackelec_die (core::Real setting)
 
bool hackelec_no_dis_dep_die () const
 Should hack_elec use a constant (non-distance dependant) dielectric? More...
 
void hackelec_no_dis_dep_die (bool setting)
 
bool smooth_hack_elec () const
 
void smooth_hack_elec (bool setting)
 
bool exclude_DNA_DNA () const
 
void exclude_DNA_DNA (bool const setting)
 
hbonds::HBondOptions const & hbond_options () const
 Read access to the hbond options object. More...
 
hbonds::HBondOptions & hbond_options ()
 non-const access to the hbond options object More...
 
void hbond_options (hbonds::HBondOptions const &opts)
 Set the hbond options object – makes a deep copy More...
 
std::string const & pb_bound_tag () const
 
std::string & pb_bound_tag ()
 
void pb_bound_tag (std::string const &tag)
 
std::string const & pb_unbound_tag () const
 
std::string & pb_unbound_tag ()
 
void pb_unbound_tag (std::string const &tag)
 
std::string const & atom_vdw_atom_type_set_name () const
 This is used in the construction of the VDW_Energy's AtomVDW object. More...
 
void atom_vdw_atom_type_set_name (std::string const &setting)
 
core::Size cst_max_seq_sep () const
 
void cst_max_seq_sep (Size const setting)
 
utility::vector1< std::string >
const & 		bond_angle_central_atoms_to_score () const
 deprecated More...
 
void bond_angle_central_atoms_to_score (utility::vector1< std::string > const &atom_names)
 depricated More...
 
scoring::mm::MMBondAngleResidueTypeParamSetOP bond_angle_residue_type_param_set ()
 
scoring::mm::MMBondAngleResidueTypeParamSetCOP bond_angle_residue_type_param_set () const
 
void bond_angle_residue_type_param_set (scoring::mm::MMBondAngleResidueTypeParamSetOP param_set)
 
void set_strand_strand_weights (int ss_lowstrand, int ss_cutoff)
 
SecondaryStructureWeights const & secondary_structure_weights () const
 
SecondaryStructureWeights & secondary_structure_weights ()
 
bool has_method_weights (ScoreType const &type) const
 
utility::vector1< Real > const & method_weights (ScoreType const &type) const
 
void set_method_weights (ScoreType const &type, utility::vector1< Real > const &wts)
 
void get_cartesian_bonded_parameters (Real &len, Real &ang, Real &tors, Real &proton, Real &imp) const
 get the harmonic bond angle and bond-length spring constants More...
 
void set_cartesian_bonded_parameters (Real len, Real ang, Real tors, Real proton, Real imp)
 set the harmonic bond angle and bond-length spring constants More...
 
bool get_cartesian_bonded_linear () const
 get the harmonic bond angle and bond-length spring constants More...
 
void set_cartesian_bonded_linear (bool lin_in)
 set the harmonic bond angle and bond-length spring constants More...
 
void show (std::ostream &out) const
 
void insert_score_function_method_options_rows (Size batch_id, std::string const &score_function_name, utility::sql_database::sessionOP db_session) const
 

Static Public Member Functions

static void write_score_function_method_options_table_schema (utility::sql_database::sessionOP db_session)
 

Private Types

typedef std::map< ScoreType,
utility::vector1< Real > > 		MethodWeights
 expand this to a class and include ss weights inside More...
 

Private Attributes

std::string etable_type_
 
bool analytic_etable_evaluation_
 
std::string atom_vdw_atom_type_set_name_
 
std::string unfolded_energies_type_
 
MethodWeights method_weights_
 
SecondaryStructureWeights ss_weights_
 
bool exclude_protein_protein_hack_elec_
 
bool exclude_monomer_hack_elec_
 
core::Real hackelec_max_dis_
 
core::Real hackelec_min_dis_
 
core::Real hackelec_die_
 
bool hackelec_no_dis_dep_die_
 
bool smooth_hack_elec_
 
bool exclude_DNA_DNA_
 
hbonds::HBondOptionsOP hbond_options_
 
core::Size cst_max_seq_sep_
 
core::Real cartbonded_len_
 
core::Real cartbonded_ang_
 
core::Real cartbonded_tors_
 
core::Real cartbonded_proton_
 
core::Real cartbonded_improper_
 
bool cartbonded_linear_
 
std::string pb_bound_tag_
 
std::string pb_unbound_tag_
 
utility::vector1< std::string > bond_angle_central_atoms_to_score_
 deprecated More...
 
core::scoring::mm::MMBondAngleResidueTypeParamSetOP bond_angle_residue_type_param_set_
 

Friends

bool operator== (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
 used inside ScoreFunctionInfo::operator== More...
 
bool operator!= (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
 used inside ScoreFunctionInfo::operator== More...
 

Detailed Description

add more options here NOTE: If you add an option, make sure you also update the constructor, the assignment operator, the == comparison operator, and the show method in the .cc file! right now this class should be pretty light-weight since a copy is held inside ScoreFunctionInfo

Definition at line 57 of file EnergyMethodOptions.hh.

Member Typedef Documentation

typedef std::map< ScoreType, utility::vector1< Real > > core::scoring::methods::EnergyMethodOptions::MethodWeights
private

expand this to a class and include ss weights inside

Definition at line 292 of file EnergyMethodOptions.hh.

Constructor & Destructor Documentation

core::scoring::methods::EnergyMethodOptions::EnergyMethodOptions ( )

Definition at line 46 of file EnergyMethodOptions.cc.

References initialize_from_options().

core::scoring::methods::EnergyMethodOptions::EnergyMethodOptions ( EnergyMethodOptions const &  src)

copy constructor

Definition at line 86 of file EnergyMethodOptions.cc.

core::scoring::methods::EnergyMethodOptions::~EnergyMethodOptions ( )
virtual

Definition at line 92 of file EnergyMethodOptions.cc.

Member Function Documentation

bool core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation ( ) const
inline

Definition at line 84 of file EnergyMethodOptions.hh.

References analytic_etable_evaluation_.

Referenced by core::scoring::etable::EtableEnergyCreator::create_energy_method().

void core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation ( bool  setting)
inline

Definition at line 85 of file EnergyMethodOptions.hh.

References analytic_etable_evaluation_.

string const & core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name ( ) const

This is used in the construction of the VDW_Energy's AtomVDW object.

Definition at line 273 of file EnergyMethodOptions.cc.

References atom_vdw_atom_type_set_name_.

Referenced by protocols::relax::CentroidRelax::setup_increased_vdw_radii().

void core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name ( std::string const &  setting)

Definition at line 278 of file EnergyMethodOptions.cc.

References atom_vdw_atom_type_set_name_.

vector1< string > const & core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score ( ) const

deprecated

Definition at line 336 of file EnergyMethodOptions.cc.

References bond_angle_central_atoms_to_score_, and bond_angle_residue_type_param_set_.

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::protein_interface_design::movers::BackrubDDMover::BackrubDDMover(), and protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag().

void core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score ( utility::vector1< std::string > const &  atom_names)

depricated

core::scoring::mm::MMBondAngleResidueTypeParamSetOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set ( )

Definition at line 353 of file EnergyMethodOptions.cc.

References bond_angle_residue_type_param_set_.

Referenced by core::scoring::methods::MMBondAngleEnergy::MMBondAngleEnergy().

core::scoring::mm::MMBondAngleResidueTypeParamSetCOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set ( ) const

Definition at line 358 of file EnergyMethodOptions.cc.

References bond_angle_residue_type_param_set_.

void core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set ( scoring::mm::MMBondAngleResidueTypeParamSetOP  param_set)

Definition at line 363 of file EnergyMethodOptions.cc.

References bond_angle_residue_type_param_set_.

core::Size core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep ( ) const

Definition at line 325 of file EnergyMethodOptions.cc.

References cst_max_seq_sep_.

Referenced by core::scoring::methods::CustomAtomPairEnergyCreator::create_energy_method(), core::scoring::methods::LinearChainbreakEnergyCreator::create_energy_method(), protocols::medal::MedalMover::score_function(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().

void core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep ( Size const  setting)

Definition at line 330 of file EnergyMethodOptions.cc.

References cst_max_seq_sep_.

string const & core::scoring::methods::EnergyMethodOptions::etable_type ( ) const

Definition at line 128 of file EnergyMethodOptions.cc.

References etable_type_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator::create_energy_method(), core::scoring::etable::CoarseEtableEnergyCreator::create_energy_method(), core::scoring::methods::Fa_MbenvEnergyCreator::create_energy_method(), core::scoring::methods::LK_hackCreator::create_energy_method(), core::scoring::methods::LK_CosThetaEnergyCreator::create_energy_method(), core::scoring::etable::EtableEnergyCreator::create_energy_method(), core::scoring::rna::RNA_LJ_BaseEnergyCreator::create_energy_method(), and core::scoring::methods::Fa_MbsolvEnergyCreator::create_energy_method().

void core::scoring::methods::EnergyMethodOptions::etable_type ( std::string const &  type)

Definition at line 133 of file EnergyMethodOptions.cc.

References etable_type_.

bool core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA ( ) const

Definition at line 220 of file EnergyMethodOptions.cc.

References exclude_DNA_DNA_, and hbond_options_.

Referenced by protocols::motifs::IRCollection::incorporate_motifs(), protocols::motifs::IRCollection::successful_loop_closure(), and protocols::motifs::IRCollection::try_for_more().

void core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA ( bool const  setting)

Definition at line 226 of file EnergyMethodOptions.cc.

References exclude_DNA_DNA_, and hbond_options_.

bool core::scoring::methods::EnergyMethodOptions::exclude_monomer_hack_elec ( ) const

Definition at line 158 of file EnergyMethodOptions.cc.

References exclude_monomer_hack_elec_.

void core::scoring::methods::EnergyMethodOptions::exclude_monomer_hack_elec ( bool const  setting)

Definition at line 163 of file EnergyMethodOptions.cc.

References exclude_monomer_hack_elec_.

bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec ( ) const

Definition at line 148 of file EnergyMethodOptions.cc.

References exclude_protein_protein_hack_elec_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), protocols::ligand_docking::LigandBaseProtocol::make_tweaked_scorefxn(), and protocols::enzdes::enzutil::scorefxn_update_from_options().

void core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec ( bool const  setting)

Definition at line 153 of file EnergyMethodOptions.cc.

References exclude_protein_protein_hack_elec_.

bool core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_linear ( ) const
inline

get the harmonic bond angle and bond-length spring constants

Definition at line 255 of file EnergyMethodOptions.hh.

References cartbonded_linear_.

Referenced by core::scoring::methods::CartesianBondedEnergy::CartesianBondedEnergy().

void core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_parameters ( Real &  len,
Real &  ang,
Real &  tors,
Real &  proton,
Real &  imp 
) const
inline

get the harmonic bond angle and bond-length spring constants

Definition at line 236 of file EnergyMethodOptions.hh.

References cartbonded_ang_, cartbonded_improper_, cartbonded_len_, cartbonded_proton_, and cartbonded_tors_.

Referenced by core::scoring::methods::CartesianBondedEnergy::CartesianBondedEnergy().

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_die ( ) const

The dielectric used for the hack_elec term.

Definition at line 188 of file EnergyMethodOptions.cc.

References hackelec_die_.

void core::scoring::methods::EnergyMethodOptions::hackelec_die ( core::Real  setting)

Definition at line 193 of file EnergyMethodOptions.cc.

References hackelec_die_.

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_max_dis ( ) const

The maximum (all atom) distance at which hack_elec is non-zero.

Definition at line 168 of file EnergyMethodOptions.cc.

References hackelec_max_dis_.

void core::scoring::methods::EnergyMethodOptions::hackelec_max_dis ( core::Real  setting)

Definition at line 173 of file EnergyMethodOptions.cc.

References hackelec_max_dis_.

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_min_dis ( ) const

The minimium (all atom) distance for which hack_elec changes with distances.

Definition at line 178 of file EnergyMethodOptions.cc.

References hackelec_min_dis_.

void core::scoring::methods::EnergyMethodOptions::hackelec_min_dis ( core::Real  setting)

Definition at line 183 of file EnergyMethodOptions.cc.

References hackelec_min_dis_.

bool core::scoring::methods::EnergyMethodOptions::hackelec_no_dis_dep_die ( ) const

Should hack_elec use a constant (non-distance dependant) dielectric?

Definition at line 198 of file EnergyMethodOptions.cc.

References hackelec_no_dis_dep_die_.

void core::scoring::methods::EnergyMethodOptions::hackelec_no_dis_dep_die ( bool  setting)

Definition at line 203 of file EnergyMethodOptions.cc.

References hackelec_no_dis_dep_die_.

bool core::scoring::methods::EnergyMethodOptions::has_method_weights ( ScoreType const &  type) const

Definition at line 302 of file EnergyMethodOptions.cc.

References method_weights_.

Referenced by core::scoring::methods::ReferenceEnergyCreator::create_energy_method(), core::scoring::methods::UnfoldedStateEnergyCreator::create_energy_method(), and core::scoring::methods::ReferenceEnergyNoncanonicalCreator::create_energy_method().

hbonds::HBondOptions const & core::scoring::methods::EnergyMethodOptions::hbond_options ( ) const

Read access to the hbond options object.

Definition at line 232 of file EnergyMethodOptions.cc.

References hbond_options_.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), core::scoring::hbonds::HBondEnergyCreator::create_energy_method(), and protocols::pmut_scan::PointMutScanDriver::PointMutScanDriver().

hbonds::HBondOptions & core::scoring::methods::EnergyMethodOptions::hbond_options ( )

non-const access to the hbond options object

Definition at line 237 of file EnergyMethodOptions.cc.

References hbond_options_.

void core::scoring::methods::EnergyMethodOptions::hbond_options ( hbonds::HBondOptions const &  opts)

Set the hbond options object – makes a deep copy

Definition at line 242 of file EnergyMethodOptions.cc.

References hbond_options_.

void core::scoring::methods::EnergyMethodOptions::initialize_from_options ( )

Initialize a new EnergyMethodOptions with defaults from the command line.

Definition at line 75 of file EnergyMethodOptions.cc.

References analytic_etable_evaluation_, exclude_DNA_DNA_, hackelec_die_, hackelec_max_dis_, hackelec_min_dis_, hackelec_no_dis_dep_die_, and smooth_hack_elec_.

Referenced by EnergyMethodOptions().

void core::scoring::methods::EnergyMethodOptions::insert_score_function_method_options_rows ( Size  batch_id,
std::string const &  score_function_name,
utility::sql_database::sessionOP  db_session 
) const

Definition at line 495 of file EnergyMethodOptions.cc.

References analytic_etable_evaluation_, atom_vdw_atom_type_set_name_, cartbonded_ang_, cartbonded_len_, cartbonded_linear_, cartbonded_proton_, cartbonded_tors_, cst_max_seq_sep_, etable_type_, exclude_DNA_DNA_, exclude_monomer_hack_elec_, exclude_protein_protein_hack_elec_, hackelec_die_, hackelec_max_dis_, hackelec_min_dis_, hackelec_no_dis_dep_die_, and unfolded_energies_type_.

vector1< Real > const & core::scoring::methods::EnergyMethodOptions::method_weights ( ScoreType const &  type) const

Definition at line 307 of file EnergyMethodOptions.cc.

References method_weights_, and core::scoring::name_from_score_type().

Referenced by core::scoring::methods::ReferenceEnergyCreator::create_energy_method(), core::scoring::methods::UnfoldedStateEnergyCreator::create_energy_method(), and core::scoring::methods::ReferenceEnergyNoncanonicalCreator::create_energy_method().

EnergyMethodOptions const & core::scoring::methods::EnergyMethodOptions::operator= ( EnergyMethodOptions const &  src)

copy operator

Definition at line 96 of file EnergyMethodOptions.cc.

References analytic_etable_evaluation_, atom_vdw_atom_type_set_name_, bond_angle_central_atoms_to_score_, bond_angle_residue_type_param_set_, cartbonded_ang_, cartbonded_len_, cartbonded_linear_, cartbonded_proton_, cartbonded_tors_, cst_max_seq_sep_, etable_type_, exclude_DNA_DNA_, exclude_monomer_hack_elec_, exclude_protein_protein_hack_elec_, hackelec_die_, hackelec_max_dis_, hackelec_min_dis_, hackelec_no_dis_dep_die_, hbond_options_, method_weights_, pb_bound_tag_, pb_unbound_tag_, smooth_hack_elec_, ss_weights_, and unfolded_energies_type_.

std::string const & core::scoring::methods::EnergyMethodOptions::pb_bound_tag ( ) const

Definition at line 247 of file EnergyMethodOptions.cc.

References pb_bound_tag_.

Referenced by protocols::jd2::parser::ScoreFunctionLoader::load_data().

std::string & core::scoring::methods::EnergyMethodOptions::pb_bound_tag ( )

Definition at line 251 of file EnergyMethodOptions.cc.

References pb_bound_tag_.

void core::scoring::methods::EnergyMethodOptions::pb_bound_tag ( std::string const &  tag)

Definition at line 255 of file EnergyMethodOptions.cc.

References pb_bound_tag_.

std::string const & core::scoring::methods::EnergyMethodOptions::pb_unbound_tag ( ) const

Definition at line 259 of file EnergyMethodOptions.cc.

References pb_unbound_tag_.

std::string & core::scoring::methods::EnergyMethodOptions::pb_unbound_tag ( )

Definition at line 263 of file EnergyMethodOptions.cc.

References pb_unbound_tag_.

void core::scoring::methods::EnergyMethodOptions::pb_unbound_tag ( std::string const &  tag)

Definition at line 267 of file EnergyMethodOptions.cc.

References pb_unbound_tag_.

SecondaryStructureWeights const & core::scoring::methods::EnergyMethodOptions::secondary_structure_weights ( ) const

Definition at line 292 of file EnergyMethodOptions.cc.

References ss_weights_.

Referenced by core::scoring::methods::SecondaryStructureEnergy::finalize_total_energy().

SecondaryStructureWeights & core::scoring::methods::EnergyMethodOptions::secondary_structure_weights ( )

Definition at line 297 of file EnergyMethodOptions.cc.

References ss_weights_.

void core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_linear ( bool  lin_in)
inline

set the harmonic bond angle and bond-length spring constants

Definition at line 260 of file EnergyMethodOptions.hh.

References cartbonded_linear_.

void core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_parameters ( Real  len,
Real  ang,
Real  tors,
Real  proton,
Real  imp 
)
inline

set the harmonic bond angle and bond-length spring constants

Definition at line 246 of file EnergyMethodOptions.hh.

References cartbonded_ang_, cartbonded_improper_, cartbonded_len_, cartbonded_proton_, and cartbonded_tors_.

void core::scoring::methods::EnergyMethodOptions::set_method_weights ( ScoreType const &  type,
utility::vector1< Real > const &  wts 
)

Definition at line 317 of file EnergyMethodOptions.cc.

References method_weights_.

void core::scoring::methods::EnergyMethodOptions::set_strand_strand_weights ( int  ss_lowstrand,
int  ss_cutoff 
)

Definition at line 283 of file EnergyMethodOptions.cc.

References core::scoring::SecondaryStructureWeights::set_ss_cutoff(), core::scoring::SecondaryStructureWeights::set_ss_lowstrand(), and ss_weights_.

Referenced by protocols::hybridization::FoldTreeHybridize::setup_scorefunctions().

void core::scoring::methods::EnergyMethodOptions::show ( std::ostream &  out) const

Definition at line 406 of file EnergyMethodOptions.cc.

References analytic_etable_evaluation_, atom_vdw_atom_type_set_name_, bond_angle_central_atoms_to_score_, bond_angle_residue_type_param_set_, cst_max_seq_sep_, etable_type_, exclude_DNA_DNA_, exclude_monomer_hack_elec_, exclude_protein_protein_hack_elec_, hackelec_die_, hackelec_max_dis_, hackelec_min_dis_, hackelec_no_dis_dep_die_, hbond_options_, method_weights_, pb_bound_tag_, pb_unbound_tag_, smooth_hack_elec_, and unfolded_energies_type_.

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

bool core::scoring::methods::EnergyMethodOptions::smooth_hack_elec ( ) const

Definition at line 208 of file EnergyMethodOptions.cc.

References smooth_hack_elec_.

void core::scoring::methods::EnergyMethodOptions::smooth_hack_elec ( bool  setting)

Definition at line 213 of file EnergyMethodOptions.cc.

References smooth_hack_elec_.

string const & core::scoring::methods::EnergyMethodOptions::unfolded_energies_type ( ) const

Definition at line 138 of file EnergyMethodOptions.cc.

References unfolded_energies_type_.

Referenced by protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), and core::scoring::methods::UnfoldedStateEnergyCreator::create_energy_method().

void core::scoring::methods::EnergyMethodOptions::unfolded_energies_type ( std::string const &  type)

Definition at line 143 of file EnergyMethodOptions.cc.

References unfolded_energies_type_.

void core::scoring::methods::EnergyMethodOptions::write_score_function_method_options_table_schema ( utility::sql_database::sessionOP  db_session)
static

Definition at line 463 of file EnergyMethodOptions.cc.

Referenced by protocols::features::ScoreFunctionFeatures::write_schema_to_db().

Friends And Related Function Documentation

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

used inside ScoreFunctionInfo::operator==

Definition at line 401 of file EnergyMethodOptions.cc.

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

used inside ScoreFunctionInfo::operator==

Definition at line 369 of file EnergyMethodOptions.cc.

Member Data Documentation

bool core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation_
private

Definition at line 301 of file EnergyMethodOptions.hh.

Referenced by analytic_etable_evaluation(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

std::string core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name_
private

Definition at line 302 of file EnergyMethodOptions.hh.

Referenced by atom_vdw_atom_type_set_name(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

utility::vector1<std::string> core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score_
private

deprecated

Definition at line 322 of file EnergyMethodOptions.hh.

Referenced by bond_angle_central_atoms_to_score(), operator=(), core::scoring::methods::operator==(), and show().

core::scoring::mm::MMBondAngleResidueTypeParamSetOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set_
private

Definition at line 323 of file EnergyMethodOptions.hh.

Referenced by bond_angle_central_atoms_to_score(), bond_angle_residue_type_param_set(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_ang_
private

Definition at line 316 of file EnergyMethodOptions.hh.

Referenced by get_cartesian_bonded_parameters(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_parameters().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_improper_
private

Definition at line 316 of file EnergyMethodOptions.hh.

Referenced by get_cartesian_bonded_parameters(), and set_cartesian_bonded_parameters().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_len_
private

Definition at line 316 of file EnergyMethodOptions.hh.

Referenced by get_cartesian_bonded_parameters(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_parameters().

bool core::scoring::methods::EnergyMethodOptions::cartbonded_linear_
private

Definition at line 317 of file EnergyMethodOptions.hh.

Referenced by get_cartesian_bonded_linear(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_linear().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_proton_
private

Definition at line 316 of file EnergyMethodOptions.hh.

Referenced by get_cartesian_bonded_parameters(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_parameters().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_tors_
private

Definition at line 316 of file EnergyMethodOptions.hh.

Referenced by get_cartesian_bonded_parameters(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_parameters().

core::Size core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep_
private

Definition at line 315 of file EnergyMethodOptions.hh.

Referenced by cst_max_seq_sep(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

std::string core::scoring::methods::EnergyMethodOptions::etable_type_
private

Definition at line 300 of file EnergyMethodOptions.hh.

Referenced by etable_type(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

bool core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA_
private

Definition at line 313 of file EnergyMethodOptions.hh.

Referenced by exclude_DNA_DNA(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

bool core::scoring::methods::EnergyMethodOptions::exclude_monomer_hack_elec_
private

Definition at line 307 of file EnergyMethodOptions.hh.

Referenced by exclude_monomer_hack_elec(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec_
private

Definition at line 306 of file EnergyMethodOptions.hh.

Referenced by exclude_protein_protein_hack_elec(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_die_
private

Definition at line 310 of file EnergyMethodOptions.hh.

Referenced by hackelec_die(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_max_dis_
private

Definition at line 308 of file EnergyMethodOptions.hh.

Referenced by hackelec_max_dis(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_min_dis_
private

Definition at line 309 of file EnergyMethodOptions.hh.

Referenced by hackelec_min_dis(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

bool core::scoring::methods::EnergyMethodOptions::hackelec_no_dis_dep_die_
private

Definition at line 311 of file EnergyMethodOptions.hh.

Referenced by hackelec_no_dis_dep_die(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

hbonds::HBondOptionsOP core::scoring::methods::EnergyMethodOptions::hbond_options_
private

Definition at line 314 of file EnergyMethodOptions.hh.

Referenced by exclude_DNA_DNA(), hbond_options(), operator=(), core::scoring::methods::operator==(), and show().

MethodWeights core::scoring::methods::EnergyMethodOptions::method_weights_
private

Definition at line 304 of file EnergyMethodOptions.hh.

Referenced by has_method_weights(), method_weights(), operator=(), core::scoring::methods::operator==(), set_method_weights(), and show().

std::string core::scoring::methods::EnergyMethodOptions::pb_bound_tag_
private

Definition at line 318 of file EnergyMethodOptions.hh.

Referenced by operator=(), core::scoring::methods::operator==(), pb_bound_tag(), and show().

std::string core::scoring::methods::EnergyMethodOptions::pb_unbound_tag_
private

Definition at line 319 of file EnergyMethodOptions.hh.

Referenced by operator=(), core::scoring::methods::operator==(), pb_unbound_tag(), and show().

bool core::scoring::methods::EnergyMethodOptions::smooth_hack_elec_
private

Definition at line 312 of file EnergyMethodOptions.hh.

Referenced by initialize_from_options(), operator=(), core::scoring::methods::operator==(), show(), and smooth_hack_elec().

SecondaryStructureWeights core::scoring::methods::EnergyMethodOptions::ss_weights_
private

Definition at line 305 of file EnergyMethodOptions.hh.

Referenced by operator=(), core::scoring::methods::operator==(), secondary_structure_weights(), and set_strand_strand_weights().

std::string core::scoring::methods::EnergyMethodOptions::unfolded_energies_type_
private

Definition at line 303 of file EnergyMethodOptions.hh.

Referenced by insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), show(), and unfolded_energies_type().

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