Rosetta 3.4
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#include <EnergyMethodOptions.hh>
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::HBondOptions & | hbond_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 |
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) 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== |
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
core::scoring::methods::EnergyMethodOptions::EnergyMethodOptions | ( | ) |
References initialize_from_options().
core::scoring::methods::EnergyMethodOptions::EnergyMethodOptions | ( | EnergyMethodOptions const & | src | ) |
copy constructor
core::scoring::methods::EnergyMethodOptions::~EnergyMethodOptions | ( | ) | [virtual] |
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 |
Referenced by core::scoring::rna::RNA_LJ_BaseEnergyCreator::create_energy_method(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator::create_energy_method(), core::scoring::methods::LK_hackCreator::create_energy_method(), core::scoring::methods::LK_CosThetaEnergyCreator::create_energy_method(), core::scoring::methods::Fa_MbsolvEnergyCreator::create_energy_method(), core::scoring::methods::Fa_MbenvEnergyCreator::create_energy_method(), core::scoring::etable::EtableEnergyCreator::create_energy_method(), and core::scoring::etable::CoarseEtableEnergyCreator::create_energy_method().
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 | ) |
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 |
Read access to the hbond options object.
Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::flexpack::FlexPacker::apply(), and core::scoring::hbonds::HBondEnergyCreator::create_energy_method().
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().
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::show | ( | std::ostream & | out | ) | const |
Referenced by core::scoring::methods::operator<<().
string const & core::scoring::methods::EnergyMethodOptions::unfolded_energies_type | ( | ) | const |
void core::scoring::methods::EnergyMethodOptions::unfolded_energies_type | ( | std::string const & | type | ) |
bool operator!= | ( | EnergyMethodOptions const & | a, |
EnergyMethodOptions const & | b | ||
) | [friend] |
used inside ScoreFunctionInfo::operator==
bool operator== | ( | EnergyMethodOptions const & | a, |
EnergyMethodOptions const & | b | ||
) | [friend] |
used inside ScoreFunctionInfo::operator==