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

#include <EnergyMethodOptions.hh>

Inheritance diagram for core::scoring::methods::EnergyMethodOptions:
Inheritance graph
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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
 
EnergyMethodOptionsoperator= (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::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 etable options object. More...
 
etable::EtableOptionsetable_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_EnergyMethodOptionsrna_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_Optionsfree_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 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
 
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...
 
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::Realfastdens_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_
 
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
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.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_assume_const_backbone_.

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

Get the assume const backbone for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_assume_const_backbone_.

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

Set the atomic depth above which an atom is considered buried.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_burial_atomic_depth_.

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

Get the atomic depth above which an atom is considered buried.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_burial_atomic_depth_.

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

Set the probe radius for the atomic depth calculation.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_burial_probe_radius_.

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

Get the probe radius for the atomic depth calculation.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_burial_probe_radius_.

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

Set the resolution for the atomic depth calculation.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_burial_resolution_.

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

Get the resolution for the atomic depth calculation.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_burial_resolution_.

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

Set the hbond_bonus_cross_chain for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_hbond_bonus_cross_chain_.

Referenced by core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::ApproximateBuriedUnsatPenalty().

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

Get the hbond_bonus_cross_chain for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_hbond_bonus_cross_chain_.

void core::scoring::methods::EnergyMethodOptions::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.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_.

Referenced by core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::ApproximateBuriedUnsatPenalty().

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

Get the hbond_bonus_ser_to_helix_bb for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_.

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

Set the energy threshold above which a hydrogen bond is not counted.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_hbond_energy_threshold_.

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

Get the energy threshold above which a hydrogen bond is not counted.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_hbond_energy_threshold_.

void core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_natural_corrections1 ( bool const  setting)

Set the natural corrections 1 for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_natural_corrections1_.

Referenced by core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::ApproximateBuriedUnsatPenalty().

bool core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_natural_corrections1 ( ) const

Get the natural corrections 1 for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_natural_corrections1_.

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

Set the oversat penalty for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_oversat_penalty_.

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

Get the oversat penalty for approximate_buried_unsat_penalty.

Used by the ApproximateBuriedUnsatPenalty energy.

References approximate_buried_unsat_penalty_oversat_penalty_.

bool core::scoring::methods::EnergyMethodOptions::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?

References arg_cation_pi_his_can_be_pi_.

void core::scoring::methods::EnergyMethodOptions::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?

References arg_cation_pi_his_can_be_pi_.

core::Real const& core::scoring::methods::EnergyMethodOptions::aspartimide_penalty_value ( ) const
inline

Get the penalty for each aspartimide-forming two-residue sequence.

Used by the aspartimide_penalty score term.

References aspartimide_penalty_value_.

Referenced by core::scoring::methods::AspartimidePenaltyEnergyCreator::create_energy_method(), and show().

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

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_burial_threshold_.

core::Real core::scoring::methods::EnergyMethodOptions::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.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_burial_threshold_.

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

Set the angle exponent for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_cone_angle_exponent_.

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

Get the angle exponent for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_cone_angle_exponent_.

void core::scoring::methods::EnergyMethodOptions::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.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_cone_angle_shift_factor_.

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

Get the angle shift factor for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_cone_angle_shift_factor_.

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

Set the distance exponent for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_cone_dist_exponent_.

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

Get the distance exponent for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_cone_dist_exponent_.

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

Set the distance midpoint for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_cone_dist_midpoint_.

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

Get the distance midpoint for calculating burial by the method of sidechain neighbor cones.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_cone_dist_midpoint_.

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

Set the energy threshold above which a hydrogen bond is not counted.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_hbond_energy_threshold_.

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

Get the energy threshold above which a hydrogen bond is not counted.

Used by the BuriedUnsatPenalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References buried_unsatisfied_penalty_hbond_energy_threshold_.

EnergyMethodOptionsOP core::scoring::methods::EnergyMethodOptions::clone ( ) const
inline

clone

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

Take full-1-5 countpairs for any residue type.

References count_pair_full_.

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

References count_pair_full_.

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

Take full-1-5 countpairs for LIGAND/non-(POLYMER_or_PROTEIN) type.

References count_pair_hybrid_.

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

References count_pair_hybrid_.

std::string core::scoring::methods::EnergyMethodOptions::covalent_labeling_fa_input ( ) const
void core::scoring::methods::EnergyMethodOptions::covalent_labeling_fa_input ( std::string const &  setting)
std::string core::scoring::methods::EnergyMethodOptions::covalent_labeling_input ( ) const
void core::scoring::methods::EnergyMethodOptions::covalent_labeling_input ( std::string const &  setting)
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_.

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

Set whether the dump_trajectory energy produces g-zipped output.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References dump_trajectory_gz_.

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

Get whether the dump_trajectory energy produces g-zipped output.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References dump_trajectory_gz_.

Referenced by initialize_from_options().

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

Set the prefix for the dump_trajectory energy's output.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References dump_trajectory_prefix_.

std::string const& core::scoring::methods::EnergyMethodOptions::dump_trajectory_prefix ( ) const
inline

Get the prefix for the dump_trajectory energy's output.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References dump_trajectory_prefix_.

Referenced by initialize_from_options().

void core::scoring::methods::EnergyMethodOptions::dump_trajectory_stride ( signed long int  setting)

Set the number of function evaluations that elapse before the dump_trajectory mover produces output.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).
Note
The input must be greater than zero. There's a check for this. (The function signature takes a signed long because the options system parses signed integers, so we need to check that the user hasn't provided a negative number.)

References dump_trajectory_stride_.

core::Size core::scoring::methods::EnergyMethodOptions::dump_trajectory_stride ( ) const
inline

Get the number of function evaluations that elapse before the dump_trajectory mover produces output.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References dump_trajectory_stride_.

Referenced by initialize_from_options().

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_.

std::string core::scoring::methods::EnergyMethodOptions::elec_group_file ( ) const

References elec_group_file_.

void core::scoring::methods::EnergyMethodOptions::elec_group_file ( std::string  setting)

References elec_group_file_.

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_.

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

Should fa_elec/gpelec use a sigmoidal dielectric?

References elec_sigmoidal_die_.

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

References elec_sigmoidal_die_.

void core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_die_params ( Real D,
Real D0,
Real S 
) const
bool core::scoring::methods::EnergyMethodOptions::envsmooth_zero_negatives ( ) const
void core::scoring::methods::EnergyMethodOptions::envsmooth_zero_negatives ( bool const  setting)
etable::EtableOptions const & core::scoring::methods::EnergyMethodOptions::etable_options ( ) const
etable::EtableOptions & core::scoring::methods::EnergyMethodOptions::etable_options ( )

non-const access to the etable 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_options_.

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

References exclude_DNA_DNA_, and hbond_options_.

bool core::scoring::methods::EnergyMethodOptions::exclude_intra_res_protein ( ) const
void core::scoring::methods::EnergyMethodOptions::exclude_intra_res_protein ( 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::exclude_RNA_protein_fa_elec ( ) const
void core::scoring::methods::EnergyMethodOptions::exclude_RNA_protein_fa_elec ( bool const  setting)
bool core::scoring::methods::EnergyMethodOptions::exclude_RNA_RNA_fa_elec ( ) const
void core::scoring::methods::EnergyMethodOptions::exclude_RNA_RNA_fa_elec ( bool const  setting)
bool core::scoring::methods::EnergyMethodOptions::fa_stack_base_all ( ) const

References fa_stack_base_all_.

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

References fa_stack_base_all_.

methods::FreeDOF_Options const & core::scoring::methods::EnergyMethodOptions::free_dof_options ( ) const

Read access to the FreeDOF options object.

References free_dof_options_.

methods::FreeDOF_Options & core::scoring::methods::EnergyMethodOptions::free_dof_options ( )

non-const access to the FreeDOF options object

References free_dof_options_.

void core::scoring::methods::EnergyMethodOptions::free_dof_options ( methods::FreeDOF_Options const &  opts)

Set the FreeDOF options object – makes a deep copy.

References free_dof_options_.

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

allow scoring all (i.e. canonical aas) with gen_bonded

References genbonded_score_full_.

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

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

allow scoring all (i.e. canonical aas) with gen_bonded

References genbonded_score_full_.

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

allow scoring torsions lack of any preference term with gen_bonded

References genbonded_score_hybrid_.

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

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

allow scoring torsions lack of any preference term with gen_bonded

References genbonded_score_hybrid_.

core::Size core::scoring::methods::EnergyMethodOptions::geom_sol_interres_path_distance_cutoff ( ) const
void core::scoring::methods::EnergyMethodOptions::geom_sol_interres_path_distance_cutoff ( core::Size const  setting)
core::Size core::scoring::methods::EnergyMethodOptions::geom_sol_intrares_path_distance_cutoff ( ) const
void core::scoring::methods::EnergyMethodOptions::geom_sol_intrares_path_distance_cutoff ( core::Size 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::get_cartesian_bonded_skip_cutpoints ( ) const
inline

get the harmonic bond angle and bond-length spring constants

References cartbonded_skip_cutpoints_.

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

utility::vector1< core::Real > const & core::scoring::methods::EnergyMethodOptions::get_density_sc_scale_byres ( ) const
bool core::scoring::methods::EnergyMethodOptions::grp_cpfxn ( ) const

References grp_cpfxn_.

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

References grp_cpfxn_.

bool core::scoring::methods::EnergyMethodOptions::grpelec_context_dependent ( ) const
void core::scoring::methods::EnergyMethodOptions::grpelec_context_dependent ( bool  setting)
bool core::scoring::methods::EnergyMethodOptions::grpelec_fade_hbond ( ) const

References grpelec_fade_hbond_.

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

References grpelec_fade_hbond_.

core::Real core::scoring::methods::EnergyMethodOptions::grpelec_fade_param1 ( ) const

References grpelec_fade_param1_.

void core::scoring::methods::EnergyMethodOptions::grpelec_fade_param1 ( core::Real  setting)

References grpelec_fade_param1_.

core::Real core::scoring::methods::EnergyMethodOptions::grpelec_fade_param2 ( ) const

References grpelec_fade_param2_.

void core::scoring::methods::EnergyMethodOptions::grpelec_fade_param2 ( core::Real  setting)

References grpelec_fade_param2_.

std::string core::scoring::methods::EnergyMethodOptions::grpelec_fade_type ( ) const

References grpelec_fade_type_.

void core::scoring::methods::EnergyMethodOptions::grpelec_fade_type ( std::string  setting)

References grpelec_fade_type_.

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

Get the bonus function shape for the hbnet energy term.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References hbnet_bonus_ramping_function_.

Referenced by core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::HBNetEnergy().

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

Set the bonus function shape for the hbnet energy term.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References hbnet_bonus_ramping_function_.

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

Get the maximum hydrogen bond network size, beyond which the hbnet score term yields no futher bonus.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References hbnet_max_network_size_.

void core::scoring::methods::EnergyMethodOptions::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.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References hbnet_max_network_size_.

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

Read access to the hbond options object.

References hbond_options_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::residue_selectors::HBondSelector::apply(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::ApproximateBuriedUnsatPenalty(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), protocols::antibody::cdr_energy(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), protocols::coupled_moves::CoupledMovesProtocol::configure_score_fxn(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::ContextIndependentGeometricSolEnergy(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::count_hbonds(), core::scoring::hbonds::NPDHBondEnergyCreator::create_energy_method(), core::scoring::hbonds::HBondEnergyCreator::create_energy_method(), protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), protocols::backrub::BackrubProtocol::finalize_setup(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_scorefxn(), protocols::ligand_docking::ga_ligand_dock::GridScorer::GridScorer(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), protocols::pmut_scan::PointMutScanDriver::PointMutScanDriver(), protocols::task_operations::PruneBuriedUnsatsOperation::PruneBuriedUnsatsOperation(), core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy::setup_for_packing(), and core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy::setup_for_scoring().

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_.

std::string core::scoring::methods::EnergyMethodOptions::hrf_dynamics_input ( ) const

References hrf_dynamics_input_.

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

References hrf_dynamics_input_.

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

Initialize a new EnergyMethodOptions with defaults from the global option collection.

Referenced by EnergyMethodOptions().

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

Initialize a new EnergyMethodOptions with defaults from a (possibly local) option collection.

If you add an option to the EnergyMethodOptions that is initialized from the input option collection, make sure you add that option key to the list_options_read function below.

References aa_composition_setup_files_, approximate_buried_unsat_penalty_assume_const_backbone_, approximate_buried_unsat_penalty_burial_atomic_depth_, approximate_buried_unsat_penalty_burial_probe_radius_, approximate_buried_unsat_penalty_burial_resolution_, approximate_buried_unsat_penalty_hbond_bonus_cross_chain_, approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_, approximate_buried_unsat_penalty_hbond_energy_threshold_, approximate_buried_unsat_penalty_natural_corrections1_, approximate_buried_unsat_penalty_oversat_penalty_, arg_cation_pi_his_can_be_pi_, aspartimide_penalty_value_, buried_unsatisfied_penalty_burial_threshold_, buried_unsatisfied_penalty_cone_angle_exponent_, buried_unsatisfied_penalty_cone_angle_shift_factor_, buried_unsatisfied_penalty_cone_dist_exponent_, buried_unsatisfied_penalty_cone_dist_midpoint_, buried_unsatisfied_penalty_hbond_energy_threshold_, cartbonded_skip_cutpoints_, count_pair_full_, count_pair_hybrid_, covalent_labeling_fa_input_, covalent_labeling_input_, dump_trajectory_gz(), dump_trajectory_prefix(), dump_trajectory_stride(), elec_die_, elec_group_file_, elec_max_dis_, elec_min_dis_, elec_no_dis_dep_die_, elec_sigmoidal_D0_, elec_sigmoidal_D_, elec_sigmoidal_die_, elec_sigmoidal_S_, envsmooth_zero_negatives_, etable_options_, eval_intrares_elec_ST_only_, exclude_DNA_DNA_, exclude_intra_res_protein_, fa_stack_base_all_, fastdens_perres_weights_, genbonded_score_full_, genbonded_score_hybrid_, geom_sol_interres_path_distance_cutoff_, geom_sol_intrares_path_distance_cutoff_, grp_cpfxn_, grpelec_context_dependent_, grpelec_fade_hbond_, grpelec_fade_param1_, grpelec_fade_param2_, grpelec_fade_type_, hbnet_bonus_ramping_function_, hbnet_max_network_size_, hbond_options_, hrf_dynamics_input_, loop_close_use_6D_potential_, mhc_epitope_setup_files_, netcharge_setup_files_, nmer_ref_seq_length_, core::scoring::nmer_svm, nmer_svm_, nmer_svm_aa_matrix_, nmer_svm_aa_matrix_defined_, nmer_svm_avg_rank_as_energy_, nmer_svm_defined_, nmer_svm_list_, nmer_svm_list_defined_, nmer_svm_pssm_feat_, nmer_svm_rank_, nmer_svm_rank_defined_, nmer_svm_rank_list_, nmer_svm_rank_list_defined_, nmer_svm_scorecut_, nmer_svm_scorecut_defined_, nmer_svm_term_length_, core::chemical::num_canonical_aas, ordered_pt_wat_penalty_, ordered_wat_penalty_, protein_dielectric_, put_intra_into_total(), smooth_fa_elec_, split_unfolded_label_type_, core::scoring::SPLIT_UNFOLDED_USER_DEFINED, split_unfolded_value_type_, symmetric_gly_tables_, target_clash_pdb_, unfolded_energies_type_, core::scoring::UNFOLDED_SPLIT_USER_DEFINED, use_gen_kirkwood_, use_polarization_, voids_penalty_energy_cone_distance_cutoff_, voids_penalty_energy_cone_dotproduct_cutoff_, voids_penalty_energy_containing_cones_cutoff_, voids_penalty_energy_disabled_except_during_packing_, voids_penalty_energy_voxel_grid_padding_, voids_penalty_energy_voxel_size_, and water_dielectric_.

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
void core::scoring::methods::EnergyMethodOptions::list_options_read ( utility::options::OptionKeyList &  read_options)
static

Append the option keys read by the initialize_from_options method to the input option-key list.

If you add a read to an option in initialize_from_options above, you must update this function.

References core::scoring::hbonds::HBondOptions::list_options_read(), core::scoring::etable::EtableOptions::list_options_read(), and core::scoring::nmer_svm.

Referenced by core::scoring::ScoreFunction::list_options_read().

bool core::scoring::methods::EnergyMethodOptions::loop_close_use_6D_potential ( ) const
void core::scoring::methods::EnergyMethodOptions::loop_close_use_6D_potential ( bool const  setting)
vector1< Real > const & core::scoring::methods::EnergyMethodOptions::method_weights ( ScoreType const &  type) const
std::string const& core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_file ( core::Size const  index) const
inline

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

References mhc_epitope_setup_files_.

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

core::Size core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_file_count ( ) const
inline

Get the number of mhc_epitope setup files.

References mhc_epitope_setup_files_.

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

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

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

References netcharge_setup_files_.

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

core::Size core::scoring::methods::EnergyMethodOptions::netcharge_setup_file_count ( ) const
inline

Get the number of netcharge setup files.

References netcharge_setup_files_.

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

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

Set reference sequence length.

Used by NMerSVMEnergy.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References nmer_ref_seq_length_.

std::string const & core::scoring::methods::EnergyMethodOptions::nmer_svm ( ) const
void core::scoring::methods::EnergyMethodOptions::nmer_svm ( std::string const &  filename)
std::string const & core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix ( ) const
void core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix ( std::string const &  filename)
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix_defined ( ) const
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_avg_rank_as_energy ( ) const

Get whether the SVM average rank should be treated as an energy.

Used by NMerSVMEnergy.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References nmer_svm_avg_rank_as_energy_.

Referenced by core::scoring::methods::NMerSVMEnergy::initialize_from_options().

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

Set whether the SVM average rank should be treated as an energy.

Used by NMerSVMEnergy.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References nmer_svm_avg_rank_as_energy_.

bool core::scoring::methods::EnergyMethodOptions::nmer_svm_defined ( ) const
std::string const & core::scoring::methods::EnergyMethodOptions::nmer_svm_list ( ) const
void core::scoring::methods::EnergyMethodOptions::nmer_svm_list ( std::string const &  filename)
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_list_defined ( ) const
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_pssm_feat ( ) const
void core::scoring::methods::EnergyMethodOptions::nmer_svm_pssm_feat ( bool const  setting)

Set nmer_svm_pssm_feat_.

Used by NMerSVMEnergy.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References nmer_svm_pssm_feat_.

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

Get SVM rank file that was provided by the user.

Used by NMerSVMEnergy.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References nmer_svm_rank_.

Referenced by core::scoring::methods::NMerSVMEnergy::read_nmer_svms_from_options().

void core::scoring::methods::EnergyMethodOptions::nmer_svm_rank ( std::string const &  filename)
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_defined ( ) const

Get whether an SVM rank file is provided by the user.

Used by NMerSVMEnergy.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References nmer_svm_rank_defined_.

Referenced by core::scoring::methods::NMerSVMEnergy::read_nmer_svms_from_options().

std::string const & core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list ( ) const
void core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list ( std::string const &  filename)
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list_defined ( ) const
core::Real const & core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut ( ) const
void core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut ( core::Real const &  setting)
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut_defined ( ) const
core::Size core::scoring::methods::EnergyMethodOptions::nmer_svm_term_length ( ) const
void core::scoring::methods::EnergyMethodOptions::nmer_svm_term_length ( core::Size const  setting)
EnergyMethodOptions & core::scoring::methods::EnergyMethodOptions::operator= ( EnergyMethodOptions const &  src)

copy operator

References aa_composition_setup_files_, approximate_buried_unsat_penalty_assume_const_backbone_, approximate_buried_unsat_penalty_burial_atomic_depth_, approximate_buried_unsat_penalty_burial_probe_radius_, approximate_buried_unsat_penalty_burial_resolution_, approximate_buried_unsat_penalty_hbond_bonus_cross_chain_, approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_, approximate_buried_unsat_penalty_hbond_energy_threshold_, approximate_buried_unsat_penalty_natural_corrections1_, approximate_buried_unsat_penalty_oversat_penalty_, arg_cation_pi_his_can_be_pi_, aspartimide_penalty_value_, atom_vdw_atom_type_set_name_, bond_angle_central_atoms_to_score_, bond_angle_residue_type_param_set_, buried_unsatisfied_penalty_burial_threshold_, buried_unsatisfied_penalty_cone_angle_exponent_, buried_unsatisfied_penalty_cone_angle_shift_factor_, buried_unsatisfied_penalty_cone_dist_exponent_, buried_unsatisfied_penalty_cone_dist_midpoint_, buried_unsatisfied_penalty_hbond_energy_threshold_, cartbonded_ang_, cartbonded_improper_, cartbonded_len_, cartbonded_linear_, cartbonded_proton_, cartbonded_skip_cutpoints_, cartbonded_tors_, count_pair_full_, count_pair_hybrid_, covalent_labeling_fa_input_, covalent_labeling_input_, cst_max_seq_sep_, dump_trajectory_gz_, dump_trajectory_prefix_, dump_trajectory_stride_, elec_die_, elec_group_file_, elec_max_dis_, elec_min_dis_, elec_no_dis_dep_die_, elec_sigmoidal_D0_, elec_sigmoidal_D_, elec_sigmoidal_die_, elec_sigmoidal_S_, envsmooth_zero_negatives_, etable_options_, eval_intrares_elec_ST_only_, exclude_DNA_DNA_, exclude_intra_res_protein_, exclude_monomer_fa_elec_, exclude_protein_protein_fa_elec_, exclude_RNA_protein_fa_elec_, exclude_RNA_RNA_fa_elec_, fa_stack_base_all_, fastdens_perres_weights_, free_dof_options_, genbonded_score_full_, genbonded_score_hybrid_, geom_sol_interres_path_distance_cutoff_, geom_sol_intrares_path_distance_cutoff_, grp_cpfxn_, grpelec_context_dependent_, grpelec_fade_hbond_, grpelec_fade_param1_, grpelec_fade_param2_, grpelec_fade_type_, hbnet_bonus_ramping_function_, hbnet_max_network_size_, hbond_options_, hrf_dynamics_input_, loop_close_use_6D_potential_, method_weights_, mhc_epitope_setup_files_, netcharge_setup_files_, nmer_ref_seq_length_, nmer_svm_, nmer_svm_aa_matrix_, nmer_svm_aa_matrix_defined_, nmer_svm_avg_rank_as_energy_, nmer_svm_defined_, nmer_svm_list_, nmer_svm_list_defined_, nmer_svm_pssm_feat_, nmer_svm_rank_, nmer_svm_rank_defined_, nmer_svm_rank_list_, nmer_svm_rank_list_defined_, nmer_svm_scorecut_, nmer_svm_scorecut_defined_, nmer_svm_term_length_, ordered_pt_wat_penalty_, ordered_wat_penalty_, pb_bound_tag_, pb_unbound_tag_, protein_dielectric_, put_intra_into_total_, rna_options_, smooth_fa_elec_, split_unfolded_label_type_, split_unfolded_value_type_, ss_weights_, symmetric_gly_tables_, target_clash_pdb_, unfolded_energies_type_, use_gen_kirkwood_, use_polarization_, voids_penalty_energy_cone_distance_cutoff_, voids_penalty_energy_cone_dotproduct_cutoff_, voids_penalty_energy_containing_cones_cutoff_, voids_penalty_energy_disabled_except_during_packing_, voids_penalty_energy_voxel_grid_padding_, voids_penalty_energy_voxel_size_, and water_dielectric_.

core::Real core::scoring::methods::EnergyMethodOptions::ordered_pt_wat_penalty ( ) const
core::Real core::scoring::methods::EnergyMethodOptions::ordered_wat_penalty ( ) const
std::string const & core::scoring::methods::EnergyMethodOptions::pb_bound_tag ( ) const
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_.

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

References protein_dielectric_.

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

References protein_dielectric_.

bool core::scoring::methods::EnergyMethodOptions::put_intra_into_total ( ) const
void core::scoring::methods::EnergyMethodOptions::put_intra_into_total ( bool const  setting)
rna::RNA_EnergyMethodOptions const & core::scoring::methods::EnergyMethodOptions::rna_options ( ) const
rna::RNA_EnergyMethodOptions & core::scoring::methods::EnergyMethodOptions::rna_options ( )

non-const access to the RNA options object

References rna_options_.

void core::scoring::methods::EnergyMethodOptions::rna_options ( rna::RNA_EnergyMethodOptions const &  opts)

Set the FreeDOF options object – makes a deep copy.

References rna_options_.

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_aa_composition_setup_files ( utility::vector1< std::string > const &  input_filenames)
inline

Set the aa_composition setup file names.

Overrides existing.

References aa_composition_setup_files_.

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_.

Referenced by protocols::hybridization::HybridizeProtocol::apply().

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_cartesian_bonded_skip_cutpoints ( bool  setting)
inline

set the harmonic bond angle and bond-length spring constants

References cartbonded_skip_cutpoints_.

void core::scoring::methods::EnergyMethodOptions::set_density_sc_scale_byres ( core::Real  newscscale)
void core::scoring::methods::EnergyMethodOptions::set_density_sc_scale_byres ( core::chemical::AA  aa,
core::Real  newscscale 
)
void core::scoring::methods::EnergyMethodOptions::set_elec_sigmoidal_die_params ( Real  D,
Real  D0,
Real  S 
)
void core::scoring::methods::EnergyMethodOptions::set_method_weights ( ScoreType const &  type,
utility::vector1< Real > const &  wts 
)
void core::scoring::methods::EnergyMethodOptions::set_mhc_epitope_setup_files ( utility::vector1< std::string > const &  input_filenames)
inline

Set the mhc_epitope setup file names.

Overrides existing.

References mhc_epitope_setup_files_.

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

Set the netcharge setup file names.

Overrides existing.

References netcharge_setup_files_.

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

References aa_composition_setup_file(), aa_composition_setup_file_count(), approximate_buried_unsat_penalty_assume_const_backbone_, approximate_buried_unsat_penalty_burial_atomic_depth_, approximate_buried_unsat_penalty_burial_probe_radius_, approximate_buried_unsat_penalty_burial_resolution_, approximate_buried_unsat_penalty_hbond_bonus_cross_chain_, approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_, approximate_buried_unsat_penalty_hbond_energy_threshold_, approximate_buried_unsat_penalty_natural_corrections1_, approximate_buried_unsat_penalty_oversat_penalty_, arg_cation_pi_his_can_be_pi_, aspartimide_penalty_value(), atom_vdw_atom_type_set_name_, bond_angle_central_atoms_to_score_, bond_angle_residue_type_param_set_, count_pair_full_, count_pair_hybrid_, covalent_labeling_fa_input_, covalent_labeling_input_, cst_max_seq_sep_, dump_trajectory_gz_, dump_trajectory_prefix_, dump_trajectory_stride_, elec_die_, elec_group_file_, elec_max_dis_, elec_min_dis_, elec_no_dis_dep_die_, elec_sigmoidal_D0_, elec_sigmoidal_D_, elec_sigmoidal_die_, elec_sigmoidal_S_, envsmooth_zero_negatives_, etable_options_, eval_intrares_elec_ST_only_, exclude_DNA_DNA_, exclude_intra_res_protein_, exclude_monomer_fa_elec_, exclude_protein_protein_fa_elec_, exclude_RNA_protein_fa_elec_, exclude_RNA_RNA_fa_elec_, free_dof_options_, geom_sol_interres_path_distance_cutoff_, geom_sol_intrares_path_distance_cutoff_, grp_cpfxn_, grpelec_context_dependent_, grpelec_fade_hbond_, grpelec_fade_param1_, grpelec_fade_param2_, grpelec_fade_type_, hbnet_bonus_ramping_function_, hbnet_max_network_size_, hbond_options_, hrf_dynamics_input_, method_weights_, mhc_epitope_setup_file(), mhc_epitope_setup_file_count(), netcharge_setup_file(), netcharge_setup_file_count(), nmer_ref_seq_length_, nmer_svm_, nmer_svm_aa_matrix_, nmer_svm_aa_matrix_defined_, nmer_svm_avg_rank_as_energy_, nmer_svm_defined_, nmer_svm_list_, nmer_svm_list_defined_, nmer_svm_pssm_feat_, nmer_svm_rank_, nmer_svm_rank_defined_, nmer_svm_rank_list_, nmer_svm_rank_list_defined_, nmer_svm_scorecut_, nmer_svm_scorecut_defined_, nmer_svm_term_length_, ordered_pt_wat_penalty_, ordered_wat_penalty_, pb_bound_tag_, pb_unbound_tag_, protein_dielectric_, put_intra_into_total_, rna_options_, smooth_fa_elec_, split_unfolded_label_type_, split_unfolded_value_type_, target_clash_pdb_, unfolded_energies_type_, use_gen_kirkwood_, use_polarization_, voids_penalty_energy_cone_distance_cutoff_, voids_penalty_energy_cone_dotproduct_cutoff_, voids_penalty_energy_containing_cones_cutoff_, voids_penalty_energy_disabled_except_during_packing_, voids_penalty_energy_voxel_grid_padding_, voids_penalty_energy_voxel_size_, and water_dielectric_.

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

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::split_unfolded_label_type ( ) const
void core::scoring::methods::EnergyMethodOptions::split_unfolded_label_type ( std::string const &  label_type)
string const & core::scoring::methods::EnergyMethodOptions::split_unfolded_value_type ( ) const
void core::scoring::methods::EnergyMethodOptions::split_unfolded_value_type ( std::string const &  value_type)
bool core::scoring::methods::EnergyMethodOptions::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)?

Default false.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References symmetric_gly_tables_.

void core::scoring::methods::EnergyMethodOptions::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).

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References symmetric_gly_tables_.

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

geter and setter for target clash energy

References target_clash_pdb_.

std::string core::scoring::methods::EnergyMethodOptions::target_clash_pdb ( ) const

References target_clash_pdb_.

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

References use_gen_kirkwood_.

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

References use_gen_kirkwood_.

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

References use_polarization_.

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

References use_polarization_.

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

Get the cone distance cutoff for the voids penalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_cone_distance_cutoff_.

void core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_distance_cutoff ( core::Real const &  setting)

Set the cone distance cutoff for the voids penalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_cone_distance_cutoff_.

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

Get the cone dot product cutoff for the voids penalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_cone_dotproduct_cutoff_.

void core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_dotproduct_cutoff ( core::Real const &  setting)

Set the cone dot product cutoff for the voids penalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_cone_dotproduct_cutoff_.

core::Size core::scoring::methods::EnergyMethodOptions::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".

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References voids_penalty_energy_containing_cones_cutoff_.

void core::scoring::methods::EnergyMethodOptions::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".

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References voids_penalty_energy_containing_cones_cutoff_.

bool core::scoring::methods::EnergyMethodOptions::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.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_disabled_except_during_packing_.

void core::scoring::methods::EnergyMethodOptions::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.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_disabled_except_during_packing_.

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

Get the voxel grid padding for the voids penalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_voxel_grid_padding_.

void core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_grid_padding ( core::Real const &  setting)

Set the voxel grid padding for the voids penalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_voxel_grid_padding_.

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

Get the voxel size for the voids penalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_voxel_size_.

void core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_size ( core::Real const &  setting)

Set the voxel size for the voids penalty energy.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References voids_penalty_energy_voxel_size_.

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

References water_dielectric_.

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

References water_dielectric_.

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

utility::vector1< std::string > core::scoring::methods::EnergyMethodOptions::aa_composition_setup_files_
private
bool core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_assume_const_backbone_
private
core::Real core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_atomic_depth_
private
core::Real core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_probe_radius_
private
core::Real core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_resolution_
private
core::Real core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_cross_chain_
private
core::Real core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_
private
core::Real core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_energy_threshold_
private
bool core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_natural_corrections1_
private
core::Real core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_oversat_penalty_
private
bool core::scoring::methods::EnergyMethodOptions::arg_cation_pi_his_can_be_pi_
private
core::Real core::scoring::methods::EnergyMethodOptions::aspartimide_penalty_value_
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::buried_unsatisfied_penalty_burial_threshold_
private
core::Real core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_angle_exponent_
private
core::Real core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_angle_shift_factor_
private
core::Real core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_dist_exponent_
private
core::Real core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_cone_dist_midpoint_
private
core::Real core::scoring::methods::EnergyMethodOptions::buried_unsatisfied_penalty_hbond_energy_threshold_
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
bool core::scoring::methods::EnergyMethodOptions::cartbonded_skip_cutpoints_
private
core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_tors_
private
bool core::scoring::methods::EnergyMethodOptions::count_pair_full_
private
bool core::scoring::methods::EnergyMethodOptions::count_pair_hybrid_
private
std::string core::scoring::methods::EnergyMethodOptions::covalent_labeling_fa_input_
private
std::string core::scoring::methods::EnergyMethodOptions::covalent_labeling_input_
private
core::Size core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep_
private
bool core::scoring::methods::EnergyMethodOptions::dump_trajectory_gz_
private
std::string core::scoring::methods::EnergyMethodOptions::dump_trajectory_prefix_
private
core::Size core::scoring::methods::EnergyMethodOptions::dump_trajectory_stride_
private
core::Real core::scoring::methods::EnergyMethodOptions::elec_die_
private
std::string core::scoring::methods::EnergyMethodOptions::elec_group_file_
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
Real core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_D0_
private
Real core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_D_
private
bool core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_die_
private
Real core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_S_
private
bool core::scoring::methods::EnergyMethodOptions::envsmooth_zero_negatives_
private
core::scoring::etable::EtableOptionsOP core::scoring::methods::EnergyMethodOptions::etable_options_
private
bool core::scoring::methods::EnergyMethodOptions::eval_intrares_elec_ST_only_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_intra_res_protein_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_RNA_protein_fa_elec_
private
bool core::scoring::methods::EnergyMethodOptions::exclude_RNA_RNA_fa_elec_
private
bool core::scoring::methods::EnergyMethodOptions::fa_stack_base_all_
private
utility::vector1< core::Real > core::scoring::methods::EnergyMethodOptions::fastdens_perres_weights_
private
methods::FreeDOF_OptionsOP core::scoring::methods::EnergyMethodOptions::free_dof_options_
private
bool core::scoring::methods::EnergyMethodOptions::genbonded_score_full_
private
bool core::scoring::methods::EnergyMethodOptions::genbonded_score_hybrid_
private
core::Size core::scoring::methods::EnergyMethodOptions::geom_sol_interres_path_distance_cutoff_
private
core::Size core::scoring::methods::EnergyMethodOptions::geom_sol_intrares_path_distance_cutoff_
private
bool core::scoring::methods::EnergyMethodOptions::grp_cpfxn_
private
bool core::scoring::methods::EnergyMethodOptions::grpelec_context_dependent_
private
bool core::scoring::methods::EnergyMethodOptions::grpelec_fade_hbond_
private
core::Real core::scoring::methods::EnergyMethodOptions::grpelec_fade_param1_
private
core::Real core::scoring::methods::EnergyMethodOptions::grpelec_fade_param2_
private
std::string core::scoring::methods::EnergyMethodOptions::grpelec_fade_type_
private
std::string core::scoring::methods::EnergyMethodOptions::hbnet_bonus_ramping_function_
private
core::Size core::scoring::methods::EnergyMethodOptions::hbnet_max_network_size_
private
hbonds::HBondOptionsOP core::scoring::methods::EnergyMethodOptions::hbond_options_
private
std::string core::scoring::methods::EnergyMethodOptions::hrf_dynamics_input_
private
bool core::scoring::methods::EnergyMethodOptions::loop_close_use_6D_potential_
private
MethodWeights core::scoring::methods::EnergyMethodOptions::method_weights_
private
utility::vector1< std::string > core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_files_
private
utility::vector1< std::string > core::scoring::methods::EnergyMethodOptions::netcharge_setup_files_
private
core::Size core::scoring::methods::EnergyMethodOptions::nmer_ref_seq_length_ = 9
private
std::string core::scoring::methods::EnergyMethodOptions::nmer_svm_
private
std::string core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix_
private
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix_defined_ = false
private
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_avg_rank_as_energy_ = false
private
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_defined_ = false
private
std::string core::scoring::methods::EnergyMethodOptions::nmer_svm_list_
private
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_list_defined_ = false
private
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_pssm_feat_ = true
private
std::string core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_
private
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_defined_ = false
private
std::string core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list_
private
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list_defined_ = false
private
core::Real core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut_ = 0.0
private
bool core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut_defined_ = false
private
core::Size core::scoring::methods::EnergyMethodOptions::nmer_svm_term_length_ = 3
private
core::Real core::scoring::methods::EnergyMethodOptions::ordered_pt_wat_penalty_
private
core::Real core::scoring::methods::EnergyMethodOptions::ordered_wat_penalty_
private
std::string core::scoring::methods::EnergyMethodOptions::pb_bound_tag_
private
std::string core::scoring::methods::EnergyMethodOptions::pb_unbound_tag_
private
core::Real core::scoring::methods::EnergyMethodOptions::protein_dielectric_
private
bool core::scoring::methods::EnergyMethodOptions::put_intra_into_total_
private
rna::RNA_EnergyMethodOptionsOP core::scoring::methods::EnergyMethodOptions::rna_options_
private
bool core::scoring::methods::EnergyMethodOptions::smooth_fa_elec_
private
std::string core::scoring::methods::EnergyMethodOptions::split_unfolded_label_type_
private
std::string core::scoring::methods::EnergyMethodOptions::split_unfolded_value_type_
private
SecondaryStructureWeights core::scoring::methods::EnergyMethodOptions::ss_weights_
private
bool core::scoring::methods::EnergyMethodOptions::symmetric_gly_tables_
private
std::string core::scoring::methods::EnergyMethodOptions::target_clash_pdb_
private
std::string core::scoring::methods::EnergyMethodOptions::unfolded_energies_type_
private
bool core::scoring::methods::EnergyMethodOptions::use_gen_kirkwood_
private
bool core::scoring::methods::EnergyMethodOptions::use_polarization_
private
core::Real core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_distance_cutoff_
private
core::Real core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_dotproduct_cutoff_
private
core::Size core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_containing_cones_cutoff_
private
bool core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_disabled_except_during_packing_
private
core::Real core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_grid_padding_
private
core::Real core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_size_
private
core::Real core::scoring::methods::EnergyMethodOptions::water_dielectric_
private

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