Rosetta 3.4
Public Member Functions | Friends
core::scoring::methods::EnergyMethodOptions Class Reference

#include <EnergyMethodOptions.hh>

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List of all members.

Public Member Functions

 EnergyMethodOptions ()
void initialize_from_options ()
 Initialize a new EnergyMethodOptions with defaults from the command line.
 EnergyMethodOptions (EnergyMethodOptions const &src)
 copy constructor
virtual ~EnergyMethodOptions ()
EnergyMethodOptions const & operator= (EnergyMethodOptions const &src)
 copy operator
std::string const & etable_type () const
void etable_type (std::string const &type)
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.
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.
void hackelec_min_dis (core::Real setting)
core::Real hackelec_die () const
 The dielectric used for the hack_elec term.
void hackelec_die (core::Real setting)
bool hackelec_no_dis_dep_die () const
 Should hack_elec use a constant (non-distance dependant) dielectric?
void hackelec_no_dis_dep_die (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.
hbonds::HBondOptionshbond_options ()
 non-const access to the hbond options object
void hbond_options (hbonds::HBondOptions const &opts)
 Set the hbond options object -- makes a deep copy
std::string const & atom_vdw_atom_type_set_name () const
 This is used in the construction of the VDW_Energy's AtomVDW object.
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
void bond_angle_central_atoms_to_score (utility::vector1< std::string > const &atom_names)
 depricated
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) const
 get the harmonic bond angle and bond-length spring constants
void set_cartesian_bonded_parameters (Real len, Real ang, Real tors, Real proton)
 set the harmonic bond angle and bond-length spring constants
bool get_cartesian_bonded_linear () const
 get the harmonic bond angle and bond-length spring constants
void set_cartesian_bonded_linear (bool lin_in)
 set the harmonic bond angle and bond-length spring constants
void show (std::ostream &out) const

Friends

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

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


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

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.

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)

depricated

deprecated

void core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set ( scoring::mm::MMBondAngleResidueTypeParamSetOP  param_set)
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
core::Size core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep ( ) const
void core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep ( Size const  setting)
void core::scoring::methods::EnergyMethodOptions::etable_type ( std::string const &  type)
string const & core::scoring::methods::EnergyMethodOptions::etable_type ( ) const
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_hack_elec ( ) const
void core::scoring::methods::EnergyMethodOptions::exclude_monomer_hack_elec ( bool const  setting)
void core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec ( bool const  setting)
bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec ( ) const
bool core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_linear ( ) const [inline]

get the harmonic bond angle and bond-length spring constants

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

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

get the harmonic bond angle and bond-length spring constants

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

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

The dielectric used for the hack_elec term.

Referenced by initialize_from_options().

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

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

Referenced by initialize_from_options().

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

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

Referenced by initialize_from_options().

void core::scoring::methods::EnergyMethodOptions::hackelec_min_dis ( core::Real  setting)
bool core::scoring::methods::EnergyMethodOptions::hackelec_no_dis_dep_die ( ) const

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

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

Set the hbond options object -- makes a deep copy

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

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

Initialize a new EnergyMethodOptions with defaults from the command line.

References hackelec_die(), hackelec_max_dis(), and hackelec_min_dis().

Referenced by EnergyMethodOptions().

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

copy operator

SecondaryStructureWeights & core::scoring::methods::EnergyMethodOptions::secondary_structure_weights ( )
SecondaryStructureWeights const & core::scoring::methods::EnergyMethodOptions::secondary_structure_weights ( ) const
void core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_linear ( bool  lin_in) [inline]

set the harmonic bond angle and bond-length spring constants

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

set the harmonic bond angle and bond-length spring constants

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

Friends And Related Function Documentation

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

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