#include <EnergyMethodOptions.hh>

Inheritance diagram for core::scoring::methods::EnergyMethodOptions:

Public Member Functions
	EnergyMethodOptions ()
	Default constructor, reads from the global options system. More...

	EnergyMethodOptions (utility::options::OptionCollection const &options)
	Initialize an EnergyMethodOptions object from a (possibly local) option collection. More...

	EnergyMethodOptions (EnergyMethodOptions const &src)
	copy constructor More...

	~EnergyMethodOptions () override

EnergyMethodOptions &	operator= (EnergyMethodOptions const &src)
	copy operator More...

EnergyMethodOptionsOP	clone () const
	clone More...

void	initialize_from_options ()
	Initialize a new EnergyMethodOptions with defaults from the global option collection. More...

void	initialize_from_options (utility::options::OptionCollection const &options)
	Initialize a new EnergyMethodOptions with defaults from a (possibly local) option collection. More...

std::string const &	aa_composition_setup_file (core::Size const index) const
	Get the nth aa_composition setup file name from the list of setup files. More...

core::Size	aa_composition_setup_file_count () const
	Get the number of aa_composition setup files. More...

void	set_aa_composition_setup_files (utility::vector1< std::string > const &input_filenames)
	Set the aa_composition setup file names. More...

void	append_aa_composition_setup_files (utility::vector1< std::string > const &input_filenames)
	Appends additional files to the aa_composition setup file names. More...

std::string const &	mhc_epitope_setup_file (core::Size const index) const
	Get the nth mhc_epitope setup file name from the list of setup files. More...

core::Size	mhc_epitope_setup_file_count () const
	Get the number of mhc_epitope setup files. More...

void	set_mhc_epitope_setup_files (utility::vector1< std::string > const &input_filenames)
	Set the mhc_epitope setup file names. More...

void	append_mhc_epitope_setup_files (utility::vector1< std::string > const &input_filenames)
	Appends additional files to the mhc_epitope setup file names. More...

std::string const &	netcharge_setup_file (core::Size const index) const
	Get the nth netcharge setup file name from the list of setup files. More...

core::Size	netcharge_setup_file_count () const
	Get the number of netcharge setup files. More...

void	set_netcharge_setup_files (utility::vector1< std::string > const &input_filenames)
	Set the netcharge setup file names. More...

void	append_netcharge_setup_files (utility::vector1< std::string > const &input_filenames)
	Appends additional files to the netcharge setup file names. More...

core::Real const &	aspartimide_penalty_value () const
	Get the penalty for each aspartimide-forming two-residue sequence. 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)

std::string const &	split_unfolded_label_type () const

void	split_unfolded_label_type (std::string const &label_type)

std::string const &	split_unfolded_value_type () const

void	split_unfolded_value_type (std::string const &value_type)

bool	exclude_protein_protein_fa_elec () const

void	exclude_protein_protein_fa_elec (bool const setting)

bool	exclude_RNA_RNA_fa_elec () const

void	exclude_RNA_RNA_fa_elec (bool const setting)

bool	exclude_RNA_protein_fa_elec () const

void	exclude_RNA_protein_fa_elec (bool const setting)

bool	exclude_monomer_fa_elec () const

void	exclude_monomer_fa_elec (bool const setting)

std::string	covalent_labeling_input () const

void	covalent_labeling_input (std::string const &setting)

std::string	covalent_labeling_fa_input () const

void	covalent_labeling_fa_input (std::string const &setting)

std::string	hrf_dynamics_input () const

void	hrf_dynamics_input (std::string 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	elec_sigmoidal_die () const
	Should fa_elec/gpelec use a sigmoidal dielectric? More...

void	elec_sigmoidal_die (bool const setting)

void	elec_sigmoidal_die_params (Real &D, Real &D0, Real &S) const

void	set_elec_sigmoidal_die_params (Real D, Real D0, Real S)

bool	smooth_fa_elec () const

void	smooth_fa_elec (bool setting)

std::string	grpelec_fade_type () const

void	grpelec_fade_type (std::string setting)

core::Real	grpelec_fade_param1 () const

void	grpelec_fade_param1 (core::Real setting)

core::Real	grpelec_fade_param2 () const

void	grpelec_fade_param2 (core::Real setting)

bool	grpelec_fade_hbond () const

void	grpelec_fade_hbond (bool setting)

bool	grp_cpfxn () const

void	grp_cpfxn (bool setting)

std::string	elec_group_file () const

void	elec_group_file (std::string setting)

bool	grpelec_context_dependent () const

void	grpelec_context_dependent (bool setting)

bool	use_polarization () const

void	use_polarization (bool setting)

bool	use_gen_kirkwood () const

void	use_gen_kirkwood (bool setting)

Real	protein_dielectric () const

void	protein_dielectric (Real setting)

Real	water_dielectric () const

void	water_dielectric (Real setting)

bool	exclude_DNA_DNA () const

void	exclude_DNA_DNA (bool const setting)

bool	exclude_intra_res_protein () const

void	exclude_intra_res_protein (bool const setting)

bool	count_pair_hybrid () const
	Take full-1-5 countpairs for LIGAND/non-(POLYMER_or_PROTEIN) type. More...

void	count_pair_hybrid (bool const setting)

bool	count_pair_full () const
	Take full-1-5 countpairs for any residue type. More...

void	count_pair_full (bool const setting)

bool	put_intra_into_total () const

void	put_intra_into_total (bool const setting)

core::Size	geom_sol_interres_path_distance_cutoff () const

void	geom_sol_interres_path_distance_cutoff (core::Size const setting)

core::Size	geom_sol_intrares_path_distance_cutoff () const

void	geom_sol_intrares_path_distance_cutoff (core::Size const setting)

bool	eval_intrares_elec_ST_only () const

void	eval_intrsres_elec_ST_only (bool setting)

bool	envsmooth_zero_negatives () const

void	envsmooth_zero_negatives (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...

etable::EtableOptions const &	etable_options () const
	Read access to the etable options object. More...

etable::EtableOptions &	etable_options ()
	non-const access to the etable options object More...

void	etable_options (etable::EtableOptions const &opts)
	Set the etable options object – makes a deep copy. More...

rna::RNA_EnergyMethodOptions const &	rna_options () const
	Read access to the RNA options object. More...

rna::RNA_EnergyMethodOptions &	rna_options ()
	non-const access to the RNA options object More...

void	rna_options (rna::RNA_EnergyMethodOptions const &opts)
	Set the FreeDOF options object – makes a deep copy. More...

methods::FreeDOF_Options const &	free_dof_options () const
	Read access to the FreeDOF options object. More...

methods::FreeDOF_Options &	free_dof_options ()
	non-const access to the FreeDOF options object More...

void	free_dof_options (methods::FreeDOF_Options const &opts)
	Set the FreeDOF 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)

bool	arg_cation_pi_his_can_be_pi () const
	For the arg_cation_pi scoreterm. Can histidine be the pi-side of an Arginine cation-pi interaction? More...

void	arg_cation_pi_his_can_be_pi (bool const setting)
	For the arg_cation_pi scoreterm. Can histidine be the pi-side of an Arginine cation-pi interaction? More...

bool	symmetric_gly_tables () const
	Should glyceine's Ramachandran and P_AA_PP tables be symmetrized (e.g. for scoring in a mixed D/L context)? More...

void	symmetric_gly_tables (bool const setting)
	Set whether glyceine's Ramachandran and P_AA_PP tables should be symmetrized (e.g. for scoring in a mixed D/L context). More...

core::Size	voids_penalty_energy_containing_cones_cutoff () const
	Get the number of cones in which a voxel must lie in order for that voxel to be considered to be "buried". More...

core::Real	voids_penalty_energy_cone_distance_cutoff () const
	Get the cone distance cutoff for the voids penalty energy. More...

core::Real	voids_penalty_energy_cone_dotproduct_cutoff () const
	Get the cone dot product cutoff for the voids penalty energy. More...

core::Real	voids_penalty_energy_voxel_grid_padding () const
	Get the voxel grid padding for the voids penalty energy. More...

core::Real	voids_penalty_energy_voxel_size () const
	Get the voxel size for the voids penalty energy. More...

core::Size	nmer_ref_seq_length () const
	Get reference sequence length. More...

core::Size	nmer_svm_term_length () const
	Get SVM term length. More...

bool	nmer_svm_pssm_feat () const
	Get nmer_svm_pssm_feat_. More...

bool	nmer_svm_scorecut_defined () const
	Get whether the SVM scorecut is defined. More...

core::Real const &	nmer_svm_scorecut () const
	Get the SVM scorecut. More...

bool	nmer_svm_avg_rank_as_energy () const
	Get whether the SVM average rank should be treated as an energy. More...

bool	nmer_svm_aa_matrix_defined () const
	Get whether we have a user-specified AA matrix. More...

std::string const &	nmer_svm_aa_matrix () const
	Get the user-specified AA matrix filename. More...

bool	nmer_svm_list_defined () const
	Get whether SVM list is provided by user. More...

std::string const &	nmer_svm_list () const
	Get SVM filename list file. More...

bool	nmer_svm_defined () const
	Get whether SVM is provided by the user. More...

std::string const &	nmer_svm () const
	Get SVM file provided by the user. More...

bool	nmer_svm_rank_list_defined () const
	Get whether SVM rank list is provided by the user. More...

std::string const &	nmer_svm_rank_list () const
	Get SVM rank list provided by the user. More...

bool	nmer_svm_rank_defined () const
	Get whether an SVM rank file is provided by the user. More...

std::string const &	nmer_svm_rank () const
	Get SVM rank file that was provided by the user. More...

void	nmer_ref_seq_length (core::Size const setting)
	Set reference sequence length. More...

void	nmer_svm_term_length (core::Size const setting)
	Set SVM term length. More...

void	nmer_svm_pssm_feat (bool const setting)
	Set nmer_svm_pssm_feat_. More...

void	nmer_svm_scorecut (core::Real const &setting)
	Set the SVM scorecut. More...

void	nmer_svm_avg_rank_as_energy (bool const setting)
	Set whether the SVM average rank should be treated as an energy. More...

void	nmer_svm_aa_matrix (std::string const &filename)
	Set the user-specified AA matrix filename. More...

void	nmer_svm_list (std::string const &filename)
	Set SVM filename list file. More...

void	nmer_svm (std::string const &filename)
	Set SVM file. More...

void	nmer_svm_rank_list (std::string const &filename)
	Set SVM rank list. More...

void	nmer_svm_rank (std::string const &filename)
	Set SVM rank file. More...

bool	voids_penalty_energy_disabled_except_during_packing () const
	Get whether we're prohibiting evaluation of the voids_penalty score term outside of the context of the packer. More...

void	voids_penalty_energy_containing_cones_cutoff (core::Size const setting)
	Set the number of cones in which a voxel must lie in order for that voxel to be considered to be "buried". More...

void	voids_penalty_energy_cone_distance_cutoff (core::Real const &setting)
	Set the cone distance cutoff for the voids penalty energy. More...

void	voids_penalty_energy_cone_dotproduct_cutoff (core::Real const &setting)
	Set the cone dot product cutoff for the voids penalty energy. More...

void	voids_penalty_energy_voxel_grid_padding (core::Real const &setting)
	Set the voxel grid padding for the voids penalty energy. More...

void	voids_penalty_energy_voxel_size (core::Real const &setting)
	Set the voxel size for the voids penalty energy. More...

void	voids_penalty_energy_disabled_except_during_packing (bool const setting)
	Set whether we're prohibiting evaluation of the voids_penalty score term outside of the context of the packer. More...

std::string const &	hbnet_bonus_function_ramping () const
	Get the bonus function shape for the hbnet energy term. More...

void	hbnet_bonus_function_ramping (std::string const &setting)
	Set the bonus function shape for the hbnet energy term. More...

core::Size	hbnet_max_network_size () const
	Get the maximum hydrogen bond network size, beyond which the hbnet score term yields no futher bonus. More...

void	hbnet_max_network_size (core::Size const setting)
	Set the maximum hydrogen bond network size, beyond which the hbnet score term yields no futher bonus. More...

bool	loop_close_use_6D_potential () const

void	loop_close_use_6D_potential (bool const setting)

bool	fa_stack_base_all () const

void	fa_stack_base_all (bool const setting)

void	hb_cen_soft (bool const setting)
	Set whether the CenHBEnergy will use a softened version of its potential. Default false. More...

bool	hb_cen_soft () const
	Get whether the CenHBEnergy should use a softened version of its potential. Default false. More...

void	buried_unsatisfied_penalty_cone_angle_exponent (core::Real const setting)
	Set the angle exponent for calculating burial by the method of sidechain neighbor cones. More...

void	buried_unsatisfied_penalty_cone_angle_shift_factor (core::Real const setting)
	Set the angle shift factor for calculating burial by the method of sidechain neighbor cones. More...

void	buried_unsatisfied_penalty_cone_dist_exponent (core::Real const setting)
	Set the distance exponent for calculating burial by the method of sidechain neighbor cones. More...

void	buried_unsatisfied_penalty_cone_dist_midpoint (core::Real const setting)
	Set the distance midpoint for calculating burial by the method of sidechain neighbor cones. More...

void	buried_unsatisfied_penalty_burial_threshold (core::Real const setting)
	Set the number of cones in which a point must lie to be considered "buried" by the method of sidechain neighbor cones. More...

void	buried_unsatisfied_penalty_hbond_energy_threshold (core::Real const setting)
	Set the energy threshold above which a hydrogen bond is not counted. More...

core::Real	buried_unsatisfied_penalty_cone_angle_exponent () const
	Get the angle exponent for calculating burial by the method of sidechain neighbor cones. More...

core::Real	buried_unsatisfied_penalty_cone_angle_shift_factor () const
	Get the angle shift factor for calculating burial by the method of sidechain neighbor cones. More...

core::Real	buried_unsatisfied_penalty_cone_dist_exponent () const
	Get the distance exponent for calculating burial by the method of sidechain neighbor cones. More...

core::Real	buried_unsatisfied_penalty_cone_dist_midpoint () const
	Get the distance midpoint for calculating burial by the method of sidechain neighbor cones. More...

core::Real	buried_unsatisfied_penalty_burial_threshold () const
	Get the number of cones in which a point must lie to be considered "buried" by the method of sidechain neighbor cones. More...

core::Real	buried_unsatisfied_penalty_hbond_energy_threshold () const
	Get the energy threshold above which a hydrogen bond is not counted. More...

void	approximate_buried_unsat_penalty_hbond_energy_threshold (core::Real const setting)
	Set the energy threshold above which a hydrogen bond is not counted. More...

void	approximate_buried_unsat_penalty_burial_atomic_depth (core::Real const setting)
	Set the atomic depth above which an atom is considered buried. More...

void	approximate_buried_unsat_penalty_burial_probe_radius (core::Real const setting)
	Set the probe radius for the atomic depth calculation. More...

void	approximate_buried_unsat_penalty_burial_resolution (core::Real const setting)
	Set the resolution for the atomic depth calculation. More...

void	approximate_buried_unsat_penalty_oversat_penalty (core::Real const setting)
	Set the oversat penalty for approximate_buried_unsat_penalty. More...

void	approximate_buried_unsat_penalty_assume_const_backbone (bool const setting)
	Set the assume const backbone for approximate_buried_unsat_penalty. More...

void	approximate_buried_unsat_penalty_natural_corrections1 (bool const setting)
	Set the natural corrections 1 for approximate_buried_unsat_penalty. More...

void	approximate_buried_unsat_penalty_hbond_bonus_cross_chain (core::Real const setting)
	Set the hbond_bonus_cross_chain for approximate_buried_unsat_penalty. More...

void	approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb (core::Real const setting)
	Set the hbond_bonus_ser_to_helix_bb for approximate_buried_unsat_penalty. More...

core::Real	approximate_buried_unsat_penalty_hbond_energy_threshold () const
	Get the energy threshold above which a hydrogen bond is not counted. More...

core::Real	approximate_buried_unsat_penalty_burial_atomic_depth () const
	Get the atomic depth above which an atom is considered buried. More...

core::Real	approximate_buried_unsat_penalty_burial_probe_radius () const
	Get the probe radius for the atomic depth calculation. More...

core::Real	approximate_buried_unsat_penalty_burial_resolution () const
	Get the resolution for the atomic depth calculation. More...

core::Real	approximate_buried_unsat_penalty_oversat_penalty () const
	Get the oversat penalty for approximate_buried_unsat_penalty. More...

bool	approximate_buried_unsat_penalty_assume_const_backbone () const
	Get the assume const backbone for approximate_buried_unsat_penalty. More...

bool	approximate_buried_unsat_penalty_natural_corrections1 () const
	Get the natural corrections 1 for approximate_buried_unsat_penalty. More...

core::Real	approximate_buried_unsat_penalty_hbond_bonus_cross_chain () const
	Get the hbond_bonus_cross_chain for approximate_buried_unsat_penalty. More...

core::Real	approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb () const
	Get the hbond_bonus_ser_to_helix_bb for approximate_buried_unsat_penalty. More...

void	target_clash_pdb (std::string const &setting)
	geter and setter for target clash energy More...

std::string	target_clash_pdb () const

void	dump_trajectory_prefix (std::string const &setting)
	Set the prefix for the dump_trajectory energy's output. More...

void	dump_trajectory_gz (bool const setting)
	Set whether the dump_trajectory energy produces g-zipped output. More...

void	dump_trajectory_stride (signed long int setting)
	Set the number of function evaluations that elapse before the dump_trajectory mover produces output. More...

std::string const &	dump_trajectory_prefix () const
	Get the prefix for the dump_trajectory energy's output. More...

bool	dump_trajectory_gz () const
	Get whether the dump_trajectory energy produces g-zipped output. More...

core::Size	dump_trajectory_stride () const
	Get the number of function evaluations that elapse before the dump_trajectory mover produces output. More...

utility::vector1< core::Real > const &	get_density_sc_scale_byres () const

void	set_density_sc_scale_byres (core::Real newscscale)

void	set_density_sc_scale_byres (core::chemical::AA aa, core::Real newscscale)

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...

bool	get_cartesian_bonded_skip_cutpoints () const
	get the harmonic bond angle and bond-length spring constants More...

void	set_cartesian_bonded_skip_cutpoints (bool setting)
	set the harmonic bond angle and bond-length spring constants More...

bool	genbonded_score_full () const
	allow scoring all (i.e. canonical aas) with gen_bonded More...

void	genbonded_score_full (bool setting)
	allow scoring all (i.e. canonical aas) with gen_bonded More...

bool	genbonded_score_hybrid () const
	allow scoring torsions lack of any preference term with gen_bonded More...

void	genbonded_score_hybrid (bool setting)
	allow scoring torsions lack of any preference term with gen_bonded More...

core::Real	ordered_wat_penalty () const

core::Real	ordered_pt_wat_penalty () const

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	list_options_read (utility::options::OptionKeyList &read_options)
	Append the option keys read by the initialize_from_options method to the input option-key list. More...

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
utility::vector1< std::string >	aa_composition_setup_files_

utility::vector1< std::string >	mhc_epitope_setup_files_

utility::vector1< std::string >	netcharge_setup_files_

core::Real	aspartimide_penalty_value_

std::string	atom_vdw_atom_type_set_name_

std::string	unfolded_energies_type_

std::string	split_unfolded_label_type_

std::string	split_unfolded_value_type_

MethodWeights	method_weights_

SecondaryStructureWeights	ss_weights_

std::string	covalent_labeling_input_

std::string	covalent_labeling_fa_input_

std::string	hrf_dynamics_input_

bool	exclude_protein_protein_fa_elec_

bool	exclude_RNA_RNA_fa_elec_

bool	exclude_RNA_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	elec_sigmoidal_die_

Real	elec_sigmoidal_D_

Real	elec_sigmoidal_D0_

Real	elec_sigmoidal_S_

std::string	grpelec_fade_type_

core::Real	grpelec_fade_param1_

core::Real	grpelec_fade_param2_

bool	grpelec_fade_hbond_

bool	grp_cpfxn_

std::string	elec_group_file_

bool	grpelec_context_dependent_

bool	use_polarization_

bool	use_gen_kirkwood_

core::Real	protein_dielectric_

core::Real	water_dielectric_

bool	exclude_DNA_DNA_

bool	exclude_intra_res_protein_

bool	count_pair_hybrid_

bool	count_pair_full_

bool	put_intra_into_total_

core::Size	geom_sol_interres_path_distance_cutoff_

core::Size	geom_sol_intrares_path_distance_cutoff_

bool	eval_intrares_elec_ST_only_

bool	envsmooth_zero_negatives_

hbonds::HBondOptionsOP	hbond_options_

core::scoring::etable::EtableOptionsOP	etable_options_

rna::RNA_EnergyMethodOptionsOP	rna_options_

methods::FreeDOF_OptionsOP	free_dof_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_

bool	cartbonded_skip_cutpoints_

bool	genbonded_score_full_

bool	genbonded_score_hybrid_

std::string	pb_bound_tag_

std::string	pb_unbound_tag_

bool	arg_cation_pi_his_can_be_pi_

utility::vector1< core::Real >	fastdens_perres_weights_

core::Real	ordered_wat_penalty_

core::Real	ordered_pt_wat_penalty_

bool	symmetric_gly_tables_

bool	loop_close_use_6D_potential_

bool	fa_stack_base_all_

bool	hb_cen_soft_ = false

core::Size	nmer_ref_seq_length_ = 9

core::Size	nmer_svm_term_length_ = 3

bool	nmer_svm_pssm_feat_ = true

bool	nmer_svm_scorecut_defined_ = false

core::Real	nmer_svm_scorecut_ = 0.0

bool	nmer_svm_avg_rank_as_energy_ = false

bool	nmer_svm_aa_matrix_defined_ = false

std::string	nmer_svm_aa_matrix_

bool	nmer_svm_list_defined_ = false

std::string	nmer_svm_list_

bool	nmer_svm_defined_ = false

std::string	nmer_svm_

bool	nmer_svm_rank_list_defined_ = false

std::string	nmer_svm_rank_list_

bool	nmer_svm_rank_defined_ = false

std::string	nmer_svm_rank_

core::Real	buried_unsatisfied_penalty_cone_angle_exponent_

core::Real	buried_unsatisfied_penalty_cone_angle_shift_factor_

core::Real	buried_unsatisfied_penalty_cone_dist_exponent_

core::Real	buried_unsatisfied_penalty_cone_dist_midpoint_

core::Real	buried_unsatisfied_penalty_burial_threshold_

core::Real	buried_unsatisfied_penalty_hbond_energy_threshold_

core::Size	voids_penalty_energy_containing_cones_cutoff_

core::Real	voids_penalty_energy_cone_dotproduct_cutoff_

core::Real	voids_penalty_energy_cone_distance_cutoff_

core::Real	voids_penalty_energy_voxel_size_

core::Real	voids_penalty_energy_voxel_grid_padding_

bool	voids_penalty_energy_disabled_except_during_packing_

std::string	hbnet_bonus_ramping_function_

core::Size	hbnet_max_network_size_

core::Real	approximate_buried_unsat_penalty_hbond_energy_threshold_

core::Real	approximate_buried_unsat_penalty_burial_atomic_depth_

core::Real	approximate_buried_unsat_penalty_burial_probe_radius_

core::Real	approximate_buried_unsat_penalty_burial_resolution_

core::Real	approximate_buried_unsat_penalty_oversat_penalty_

bool	approximate_buried_unsat_penalty_assume_const_backbone_

bool	approximate_buried_unsat_penalty_natural_corrections1_

core::Real	approximate_buried_unsat_penalty_hbond_bonus_cross_chain_

core::Real	approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_

std::string	target_clash_pdb_

std::string	dump_trajectory_prefix_

bool	dump_trajectory_gz_

core::Size	dump_trajectory_stride_

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

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

private

expand this to a class and include ss weights inside

Constructor & Destructor Documentation

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

Default constructor, reads from the global options system.

Delegating constructor using the global option collection

core::scoring::methods::EnergyMethodOptions::EnergyMethodOptions ( utility::options::OptionCollection const & options )

Initialize an EnergyMethodOptions object from a (possibly local) option collection.

References core::scoring::free_res, initialize_from_options(), and method_weights_.

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

copy constructor

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

overridedefault

Member Function Documentation

std::string const& core::scoring::methods::EnergyMethodOptions::aa_composition_setup_file ( core::Size const index ) const

inline

Get the nth aa_composition setup file name from the list of setup files.

References aa_composition_setup_files_.

Referenced by core::scoring::ScoringManager::get_cloned_aa_comp_setup_helpers(), and show().

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

inline

Get the number of aa_composition setup files.

References aa_composition_setup_files_.

Referenced by core::scoring::ScoringManager::get_cloned_aa_comp_setup_helpers(), and show().

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

References etable_options_.

Referenced by core::energy_methods::LK_PolarNonPolarEnergyCreator::create_energy_method(), core::scoring::etable::EtableEnergyCreator::create_energy_method(), core::scoring::etable::EtableClassicIntraEnergyCreator::create_energy_method(), core::energy_methods::create_ExactSHOEnergy_from_cmdline(), and core::energy_methods::RNA_FullAtomVDW_BasePhosphate::RNA_FullAtomVDW_BasePhosphate().

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

References etable_options_.

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

inline

Appends additional files to the aa_composition setup file names.

Does not override existing.

References aa_composition_setup_files_.

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

inline

Appends additional files to the mhc_epitope setup file names.

Does not override existing.

References mhc_epitope_setup_files_.

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

inline

Appends additional files to the netcharge setup file names.

Does not override existing.

References netcharge_setup_files_.

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

Set the assume const backbone for approximate_buried_unsat_penalty.