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core::scoring::ScoreFunction Member List

This is the complete list of members for core::scoring::ScoreFunction, including all inherited members.

_add_weights_from_file(std::string const &filename, bool patch=false)core::scoring::ScoreFunction
_add_weights_from_stream(std::istream &data, bool patch=false, std::string const &filename="")core::scoring::ScoreFunction
add_extra_method(ScoreType const &new_type, Real const new_weight, methods::EnergyMethod const &new_method)core::scoring::ScoreFunction
add_extra_method(std::map< ScoreType, Real > const &new_weights, methods::EnergyMethod const &new_method)core::scoring::ScoreFunction
add_method(methods::EnergyMethodOP method)core::scoring::ScoreFunctionprivate
add_to_weight(ScoreType const &t, Real const &increment)core::scoring::ScoreFunction
add_weights_from_file(std::string const &filename)core::scoring::ScoreFunction
all_energies_begin() const core::scoring::ScoreFunction
all_energies_end() const core::scoring::ScoreFunction
all_methods() const core::scoring::ScoreFunction
all_methods_core::scoring::ScoreFunctionprivate
AllMethods typedefcore::scoring::ScoreFunction
AllMethodsIterator typedefcore::scoring::ScoreFunction
any_intrares_energies() const core::scoring::ScoreFunctioninlineprotected
any_intrares_energies_core::scoring::ScoreFunctionprivate
any_lr_residue_pair_energy(pose::Pose const &pose, Size res1, Size res2) const core::scoring::ScoreFunction
apply_patch_from_file(std::string const &filename)core::scoring::ScoreFunction
are_they_neighbors(pose::Pose const &pose, Size const pos1, Size const pos2) const core::scoring::ScoreFunction
assign(ScoreFunction const &src)core::scoring::ScoreFunctionvirtual
asym_eval_long_range_twobody_energies(pose::Pose &pose) const core::scoring::ScoreFunctionprotectedvirtual
asym_eval_onebody_energies(pose::Pose &pose) const core::scoring::ScoreFunctionprotectedvirtual
asym_eval_twobody_neighbor_energies(pose::Pose &pose) const core::scoring::ScoreFunctionprotectedvirtual
asym_setup_for_derivatives(pose::Pose &pose) const core::scoring::ScoreFunctionprotectedvirtual
asym_setup_for_minimizing(pose::Pose &pose, kinematics::MinimizerMapBase const &min_map) const core::scoring::ScoreFunctionprotectedvirtual
bump_check_backbone(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
bump_check_full(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
CD_1B_Methods typedefcore::scoring::ScoreFunction
cd_1b_methods_core::scoring::ScoreFunctionprivate
cd_1b_types() const core::scoring::ScoreFunctioninline
cd_2b_begin() const core::scoring::ScoreFunction
cd_2b_end() const core::scoring::ScoreFunction
cd_2b_intrares_core::scoring::ScoreFunctionprivate
cd_2b_intrares_begin() const core::scoring::ScoreFunction
cd_2b_intrares_end() const core::scoring::ScoreFunction
CD_2B_Methods typedefcore::scoring::ScoreFunction
cd_2b_methods_core::scoring::ScoreFunctionprivate
cd_2b_types() const core::scoring::ScoreFunctioninline
CD_LR_2B_MethodIterator typedefcore::scoring::ScoreFunction
CD_LR_2B_Methods typedefcore::scoring::ScoreFunction
cd_lr_2b_methods_core::scoring::ScoreFunctionprivate
cd_lr_2b_methods_begin() const core::scoring::ScoreFunction
cd_lr_2b_methods_end() const core::scoring::ScoreFunction
cd_lr_2b_types() const core::scoring::ScoreFunctioninline
check_methods() const core::scoring::ScoreFunctionprivate
check_methods_in_right_order(ScoreType const &score_type_in_first_method, ScoreType const &score_type_in_second_method) const core::scoring::ScoreFunction
CI_1B_Methods typedefcore::scoring::ScoreFunction
ci_1b_methods_core::scoring::ScoreFunctionprivate
ci_1b_types() const core::scoring::ScoreFunctioninline
ci_2b_begin() const core::scoring::ScoreFunction
ci_2b_end() const core::scoring::ScoreFunction
ci_2b_intrares_core::scoring::ScoreFunctionprivate
ci_2b_intrares_begin() const core::scoring::ScoreFunction
ci_2b_intrares_end() const core::scoring::ScoreFunction
CI_2B_Methods typedefcore::scoring::ScoreFunction
ci_2b_methods_core::scoring::ScoreFunctionprivate
ci_2b_types() const core::scoring::ScoreFunctioninline
CI_LR_2B_MethodIterator typedefcore::scoring::ScoreFunction
CI_LR_2B_Methods typedefcore::scoring::ScoreFunction
ci_lr_2b_methods_core::scoring::ScoreFunctionprivate
ci_lr_2b_methods_begin() const core::scoring::ScoreFunction
ci_lr_2b_methods_end() const core::scoring::ScoreFunction
ci_lr_2b_types() const core::scoring::ScoreFunctioninline
clone() const core::scoring::ScoreFunctionvirtual
clone_as_base_class() const core::scoring::ScoreFunction
correct_arrays_for_symmetry(pose::Pose &pose) const core::scoring::ScoreFunctionprivate
correct_finalize_score(pose::Pose &pose) const core::scoring::ScoreFunctionprivate
energy_method_options() const core::scoring::ScoreFunctioninline
energy_method_options_core::scoring::ScoreFunctionprivate
eval_cd_1b(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunctionvirtual
eval_cd_2b(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunctionvirtual
eval_cd_2b_bb_bb(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_cd_2b_bb_sc(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_cd_2b_sc_sc(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_cd_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunctionvirtual
eval_ci_1b(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_ci_2b(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_ci_2b_bb_bb(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_ci_2b_bb_sc(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_ci_2b_sc_sc(conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_ci_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_dof_derivative(id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose) const core::scoring::ScoreFunction
eval_intrares_energy(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const core::scoring::ScoreFunction
eval_long_range_twobody_energies(pose::Pose &pose) const core::scoring::ScoreFunctionvirtual
eval_npd_atom_derivative(id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, Vector &F1, Vector &F2) const core::scoring::ScoreFunctionvirtual
eval_onebody_energies(pose::Pose &pose) const core::scoring::ScoreFunctionvirtual
eval_twobody_neighbor_energies(pose::Pose &pose) const core::scoring::ScoreFunctionvirtual
evaluate_rotamer_background_energies(conformation::RotamerSetBase const &set1, conformation::Residue const &residue2, pose::Pose const &pose, utility::vector1< core::PackerEnergy > &energy_vector) const core::scoring::ScoreFunction
evaluate_rotamer_intrares_energies(conformation::RotamerSetBase const &set, pose::Pose const &pose, utility::vector1< core::PackerEnergy > &energies) const core::scoring::ScoreFunction
evaluate_rotamer_intrares_energy_maps(conformation::RotamerSetBase const &set, pose::Pose const &pose, utility::vector1< EnergyMap > &emaps) const core::scoring::ScoreFunction
evaluate_rotamer_pair_energies(conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const core::scoring::ScoreFunction
extract_weights_from_file(std::string const &filename, bool patch=false)core::scoring::ScoreFunctionstatic
extract_weights_from_stream(std::istream &data, bool patch=false, std::string const &filename="")core::scoring::ScoreFunctionstatic
finalize_after_derivatives(pose::Pose &pose) const core::scoring::ScoreFunctionvirtual
finalize_after_minimizing(pose::Pose &pose) const core::scoring::ScoreFunctionvirtual
get_name() const core::scoring::ScoreFunctioninline
get_nonzero_weighted_scoretypes() const core::scoring::ScoreFunctioninline
get_self_ptr() const core::scoring::ScoreFunctioninline
get_self_ptr()core::scoring::ScoreFunctioninline
get_sub_score(pose::Pose const &pose, utility::vector1< bool > const &residue_mask) const core::scoring::ScoreFunction
get_sub_score(pose::Pose const &pose, utility::vector1< bool > const &residue_mask, EnergyMap &emap) const core::scoring::ScoreFunction
get_sub_score(pose::Pose &pose, utility::vector1< bool > const &residue_mask) const core::scoring::ScoreFunction
get_sub_score(pose::Pose &pose, utility::vector1< bool > const &residue_mask, EnergyMap &emap) const core::scoring::ScoreFunction
get_sub_score_exclude_res(pose::Pose const &pose, utility::vector1< core::Size > const &exclude_list) const core::scoring::ScoreFunction
get_sub_score_exclude_res(pose::Pose const &pose, utility::vector1< core::Size > const &exclude_list, EnergyMap &emap) const core::scoring::ScoreFunction
get_sub_score_exclude_res(pose::Pose &pose, utility::vector1< core::Size > const &exclude_list) const core::scoring::ScoreFunction
get_sub_score_exclude_res(pose::Pose &pose, utility::vector1< core::Size > const &exclude_list, EnergyMap &emap) const core::scoring::ScoreFunction
get_weight(ScoreType const &t) const core::scoring::ScoreFunction
has_nonzero_weight(ScoreType const &t) const core::scoring::ScoreFunctioninline
has_zero_weight(ScoreType const &t) const core::scoring::ScoreFunctioninline
indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const core::scoring::ScoreFunction
info() const core::scoring::ScoreFunction
initialize_from_file(std::string const &filename)core::scoring::ScoreFunction
initialize_methods_arrays()core::scoring::ScoreFunctionprivate
intersubunit_hbond_energy(pose::Pose &pose, EnergyMap &intersubunit_energy) const core::scoring::ScoreFunctionprivate
list_options_read(utility::options::OptionKeyList &option_list)core::scoring::ScoreFunctionstatic
long_range_energies_begin() const core::scoring::ScoreFunction
long_range_energies_end() const core::scoring::ScoreFunction
LR_2B_MethodIterator typedefcore::scoring::ScoreFunction
LR_2B_Methods typedefcore::scoring::ScoreFunction
lr_2b_methods_core::scoring::ScoreFunctionprivate
max_atomic_interaction_cutoff() const core::scoring::ScoreFunction
merge(const ScoreFunction &scorefxn_to_be_merged)core::scoring::ScoreFunction
methods_by_score_type_core::scoring::ScoreFunctionprivate
name(std::string const &weights_tag)core::scoring::ScoreFunctioninline
name_core::scoring::ScoreFunctionprivate
nonzero_weights_core::scoring::ScoreFunctionprivate
operator()(pose::Pose &pose) const core::scoring::ScoreFunctionvirtual
operator=(ScoreFunction const &)core::scoring::ScoreFunctionprivate
operator[](ScoreType const &t) const core::scoring::ScoreFunctioninline
perturb_weights()core::scoring::ScoreFunction
prepare_rotamers_for_packing(pose::Pose const &pose, conformation::RotamerSetBase &set) const core::scoring::ScoreFunction
provide_authorship_info_for_unpublished() const core::scoring::ScoreFunctionvirtual
provide_citation_info() const core::scoring::ScoreFunctionvirtual
ready_for_nonideal_scoring() const core::scoring::ScoreFunction
reinitialize_minnode_for_residue(MinimizationNode &min_node, conformation::Residue const &rsd, basic::datacache::BasicDataCache &res_data_cache, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose) const core::scoring::ScoreFunction
remove_method(methods::EnergyMethodOP method)core::scoring::ScoreFunctionprivate
reset()core::scoring::ScoreFunction
reset(utility::options::OptionCollection const &options)core::scoring::ScoreFunction
reset_energy_methods()core::scoring::ScoreFunction
score(pose::Pose &pose) const core::scoring::ScoreFunctionvirtual
score_by_scoretype(pose::Pose &pose, ScoreType const t, bool const weighted=true) const core::scoring::ScoreFunction
score_function_info_core::scoring::ScoreFunctionmutableprivate
score_function_info_current_core::scoring::ScoreFunctionmutableprivate
score_types_by_method_type(methods::EnergyMethodType const &t) const core::scoring::ScoreFunctioninline
score_types_by_method_type_core::scoring::ScoreFunctionprivate
ScoreFunction()core::scoring::ScoreFunction
ScoreFunction(utility::options::OptionCollection const &options)core::scoring::ScoreFunction
ScoreFunction(ScoreFunction const &)core::scoring::ScoreFunctionprivate
serialize_weights() const core::scoring::ScoreFunction
set_energy_method_options(methods::EnergyMethodOptions const &energy_method_options_in)core::scoring::ScoreFunction
set_etable(std::string const &etable_name)core::scoring::ScoreFunction
set_method_weights(ScoreType const &t, utility::vector1< Real > const &wts)core::scoring::ScoreFunction
set_symmetric_cenlist(pose::Pose &pose) const core::scoring::ScoreFunctionprivate
set_symmetric_residue_neighbors_hbonds(pose::Pose &pose) const core::scoring::ScoreFunctionprivate
set_weight(ScoreType const &t, Real const &setting)core::scoring::ScoreFunction
set_weight_if_zero(ScoreType const &t, Real const &setting)core::scoring::ScoreFunction
setup_for_derivatives(pose::Pose &pose) const core::scoring::ScoreFunctionvirtual
setup_for_lr2benmeth_minimization_for_respair(conformation::Residue const &res1, conformation::Residue const &res2, methods::LongRangeTwoBodyEnergyCOP lr2benergy, MinimizationGraph &g, kinematics::MinimizerMapBase const &min_map, pose::Pose &p, bool const res_moving_wrt_eachother, bool accumulate_fixed_energies, ResidueNeighborConstIteratorOP rni, EnergyMap &fixed_energies, Real const edge_weight=1.0, Real const edge_dweight=1.0) const core::scoring::ScoreFunction
setup_for_minimizing(pose::Pose &pose, kinematics::MinimizerMapBase const &min_map) const core::scoring::ScoreFunctionvirtual
setup_for_minimizing_for_node(MinimizationNode &min_node, conformation::Residue const &rsd, basic::datacache::BasicDataCache &res_data_cache, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose, bool accumulate_fixed_energies, EnergyMap &fixed_energies) const core::scoring::ScoreFunctionvirtual
setup_for_minimizing_sr2b_enmeths_for_minedge(conformation::Residue const &res1, conformation::Residue const &res2, MinimizationEdge &min_edge, kinematics::MinimizerMapBase const &min_map, pose::Pose &pose, bool const res_moving_wrt_eachother, bool accumulate_fixed_energies, EnergyEdge const *energy_edge, EnergyMap &fixed_energies, Real const edge_weight=1.0) const core::scoring::ScoreFunction
setup_for_packing(pose::Pose &pose, utility::vector1< bool > const &residues_repacking, utility::vector1< bool > const &residues_designing) const core::scoring::ScoreFunction
setup_for_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets) const core::scoring::ScoreFunction
setup_for_scoring(pose::Pose &pose) const core::scoring::ScoreFunction
show(std::ostream &out) const core::scoring::ScoreFunction
show(std::ostream &out, pose::Pose &pose) const core::scoring::ScoreFunction
show(pose::Pose &pose) const core::scoring::ScoreFunction
show_additional(std::ostream &out, pose::Pose &pose, bool verbose=false) const core::scoring::ScoreFunction
show_line(std::ostream &out, pose::Pose const &pose) const core::scoring::ScoreFunction
show_line_headers(std::ostream &out) const core::scoring::ScoreFunction
show_pretty(std::ostream &out) const core::scoring::ScoreFunction
sym_eval_long_range_twobody_energies(pose::Pose &pose) const core::scoring::ScoreFunctionprotectedvirtual
sym_eval_onebody_energies(pose::Pose &pose) const core::scoring::ScoreFunctionprotectedvirtual
sym_eval_twobody_neighbor_energies(pose::Pose &pose) const core::scoring::ScoreFunctionprotectedvirtual
sym_setup_for_derivatives(pose::Pose &pose) const core::scoring::ScoreFunctionprotectedvirtual
sym_setup_for_minimizing(pose::Pose &pose, kinematics::MinimizerMapBase const &min_map) const core::scoring::ScoreFunctionprotectedvirtual
symmetrical_allow_hbonds(pose::Pose &pose) const core::scoring::ScoreFunctionprivate
TWO_B_MethodIterator typedefcore::scoring::ScoreFunction
TWO_B_Methods typedefcore::scoring::ScoreFunction
update_intrares_energy_status()core::scoring::ScoreFunctionprivate
update_residue_for_packing(pose::Pose &pose, Size resid) const core::scoring::ScoreFunction
weighted_sum(EnergyMap const &unweighted) const core::scoring::ScoreFunctioninline
weights() const core::scoring::ScoreFunctioninline
weights_core::scoring::ScoreFunctionprivate
whole_structure_types() const core::scoring::ScoreFunctioninline
WS_MethodIterator typedefcore::scoring::ScoreFunction
WS_Methods typedefcore::scoring::ScoreFunction
ws_methods_core::scoring::ScoreFunctionprivate
ws_methods_begin() const core::scoring::ScoreFunction
ws_methods_end() const core::scoring::ScoreFunction
~ScoreFunction() overridecore::scoring::ScoreFunction