Rosetta Core  2014.35
Public Member Functions | Static Public Member Functions | Private Types | Private Attributes | Friends | List of all members
core::scoring::methods::EnergyMethodOptions Class Reference

#include <EnergyMethodOptions.hh>

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_fa_elec () const
 
void exclude_protein_protein_fa_elec (bool const setting)
 
bool exclude_monomer_fa_elec () const
 
void exclude_monomer_fa_elec (bool const setting)
 
core::Real elec_max_dis () const
 The maximum (all atom) distance at which fa_elec is non-zero. More...
 
void elec_max_dis (core::Real setting)
 
core::Real elec_min_dis () const
 The minimium (all atom) distance for which fa_elec changes with distances. More...
 
void elec_min_dis (core::Real setting)
 
core::Real elec_die () const
 The dielectric used for the fa_elec term. More...
 
void elec_die (core::Real setting)
 
bool elec_no_dis_dep_die () const
 Should fa_elec use a constant (non-distance dependant) dielectric? More...
 
void elec_no_dis_dep_die (bool setting)
 
bool smooth_fa_elec () const
 
void smooth_fa_elec (bool setting)
 
bool exclude_DNA_DNA () const
 
void exclude_DNA_DNA (bool const setting)
 
core::Real intrares_elec_correction_scale () const
 
void intrares_elec_correction_scale (core::Real setting)
 
hbonds::HBondOptions const & hbond_options () const
 Read access to the hbond options object. More...
 
hbonds::HBondOptionshbond_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...
 
etable::EtableOptions const & etable_options () const
 Read access to the hbond options object. More...
 
etable::EtableOptionsetable_options ()
 non-const access to the hbond options object More...
 
void etable_options (etable::EtableOptions const &opts)
 Set the etable 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
 
SecondaryStructureWeightssecondary_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_fa_elec_
 
bool exclude_monomer_fa_elec_
 
core::Real elec_max_dis_
 
core::Real elec_min_dis_
 
core::Real elec_die_
 
bool elec_no_dis_dep_die_
 
bool smooth_fa_elec_
 
bool exclude_DNA_DNA_
 
core::Real intrares_elec_correction_scale_
 
hbonds::HBondOptionsOP hbond_options_
 
core::scoring::etable::EtableOptionsOP etable_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

Member Typedef Documentation

expand this to a class and include ss weights inside

Constructor & Destructor Documentation

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

copy constructor

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

Member Function Documentation

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

References atom_vdw_atom_type_set_name_.

void core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name ( std::string const &  setting)
vector1< string > const & core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score ( ) const
void core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score ( utility::vector1< std::string > const &  atom_names)
core::scoring::mm::MMBondAngleResidueTypeParamSetOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set ( )
core::scoring::mm::MMBondAngleResidueTypeParamSetCOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set ( ) const
void core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set ( scoring::mm::MMBondAngleResidueTypeParamSetOP  param_set)
core::Size core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep ( ) const
void core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep ( Size const  setting)

References cst_max_seq_sep_.

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

The dielectric used for the fa_elec term.

References elec_die_.

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

References elec_die_.

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

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

References elec_max_dis_.

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

References elec_max_dis_.

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

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

References elec_min_dis_.

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

References elec_min_dis_.

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

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

References elec_no_dis_dep_die_.

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

References elec_no_dis_dep_die_.

etable::EtableOptions const & core::scoring::methods::EnergyMethodOptions::etable_options ( ) const

Read access to the hbond options object.

References etable_options_.

Referenced by core::scoring::ScoringManager::etable().

etable::EtableOptions & core::scoring::methods::EnergyMethodOptions::etable_options ( )

non-const access to the hbond options object

References etable_options_.

void core::scoring::methods::EnergyMethodOptions::etable_options ( etable::EtableOptions const &  opts)

Set the etable options object – makes a deep copy.

References etable_options_.

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

References etable_type_.

bool core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA ( ) const
void core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA ( bool const  setting)
bool core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec ( ) const
void core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec ( bool const  setting)
bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec ( ) const
void core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec ( bool const  setting)
bool core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_linear ( ) const
inline

get the harmonic bond angle and bond-length spring constants

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

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

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

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

non-const access to the hbond options object

References hbond_options_.

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

Set the hbond options object – makes a deep copy.

References hbond_options_.

void core::scoring::methods::EnergyMethodOptions::initialize_from_options ( )
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
core::Real core::scoring::methods::EnergyMethodOptions::intrares_elec_correction_scale ( ) const
void core::scoring::methods::EnergyMethodOptions::intrares_elec_correction_scale ( core::Real  setting)
vector1< Real > const & core::scoring::methods::EnergyMethodOptions::method_weights ( ScoreType const &  type) const
EnergyMethodOptions const & core::scoring::methods::EnergyMethodOptions::operator= ( EnergyMethodOptions const &  src)
std::string const & core::scoring::methods::EnergyMethodOptions::pb_bound_tag ( ) const

References pb_bound_tag_.

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

References pb_bound_tag_.

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

References pb_bound_tag_.

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

References pb_unbound_tag_.

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

References pb_unbound_tag_.

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

References pb_unbound_tag_.

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

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

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

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 
)

References method_weights_.

void core::scoring::methods::EnergyMethodOptions::set_strand_strand_weights ( int  ss_lowstrand,
int  ss_cutoff 
)
void core::scoring::methods::EnergyMethodOptions::show ( std::ostream &  out) const
bool core::scoring::methods::EnergyMethodOptions::smooth_fa_elec ( ) const

References smooth_fa_elec_.

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

References smooth_fa_elec_.

string const & core::scoring::methods::EnergyMethodOptions::unfolded_energies_type ( ) const
void core::scoring::methods::EnergyMethodOptions::unfolded_energies_type ( std::string const &  type)
void core::scoring::methods::EnergyMethodOptions::write_score_function_method_options_table_schema ( utility::sql_database::sessionOP  db_session)
static

Friends And Related Function Documentation

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

Member Data Documentation

bool core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation_
private
std::string core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name_
private
utility::vector1<std::string> core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score_
private
core::scoring::mm::MMBondAngleResidueTypeParamSetOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set_
private
core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_ang_
private
core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_improper_
private
core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_len_
private
bool core::scoring::methods::EnergyMethodOptions::cartbonded_linear_
private
core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_proton_
private
core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_tors_
private
core::Size core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep_
private
core::Real core::scoring::methods::EnergyMethodOptions::elec_die_
private
core::Real core::scoring::methods::EnergyMethodOptions::elec_max_dis_
private
core::Real core::scoring::methods::EnergyMethodOptions::elec_min_dis_
private
bool core::scoring::methods::EnergyMethodOptions::elec_no_dis_dep_die_
private
core::scoring::etable::EtableOptionsOP core::scoring::methods::EnergyMethodOptions::etable_options_
private
std::string core::scoring::methods::EnergyMethodOptions::etable_type_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec_
private
hbonds::HBondOptionsOP core::scoring::methods::EnergyMethodOptions::hbond_options_
private
core::Real core::scoring::methods::EnergyMethodOptions::intrares_elec_correction_scale_
private
MethodWeights core::scoring::methods::EnergyMethodOptions::method_weights_
private
std::string core::scoring::methods::EnergyMethodOptions::pb_bound_tag_
private
std::string core::scoring::methods::EnergyMethodOptions::pb_unbound_tag_
private
bool core::scoring::methods::EnergyMethodOptions::smooth_fa_elec_
private
SecondaryStructureWeights core::scoring::methods::EnergyMethodOptions::ss_weights_
private
std::string core::scoring::methods::EnergyMethodOptions::unfolded_energies_type_
private

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