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core::scoring::methods::NMerSVMEnergy Member List

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

aa_encoder_core::scoring::methods::NMerSVMEnergyprivate
add_encoded_termini(std::string const &, core::Size const, utility::vector1< core::Real > &) constcore::scoring::methods::NMerSVMEnergy
add_pssm_features(std::string const &, core::Size const, utility::vector1< core::Real > &) constcore::scoring::methods::NMerSVMEnergy
all_nmer_svms_core::scoring::methods::NMerSVMEnergyprivate
all_nmer_svms_ranks_core::scoring::methods::NMerSVMEnergyprivate
atomistic_energy(core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) constcore::scoring::methods::EnergyMethodvirtual
atomistic_pair_energy(core::Size atmno1, conformation::Residue const &rsd1, core::Size atomno2, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) constcore::scoring::methods::EnergyMethodvirtual
atoms_with_dof_derivatives(conformation::Residue const &res, pose::Pose const &pose) constcore::scoring::methods::OneBodyEnergyvirtual
avg_rank_as_energy(bool const)core::scoring::methods::NMerSVMEnergy
avg_rank_as_energy() constcore::scoring::methods::NMerSVMEnergy
avg_rank_as_energy_core::scoring::methods::NMerSVMEnergyprivate
clone() const overridecore::scoring::methods::NMerSVMEnergyvirtual
ContextIndependentOneBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ContextIndependentOneBodyEnergy
defines_dof_derivatives(pose::Pose const &p) constcore::scoring::methods::OneBodyEnergyvirtual
defines_high_order_terms(pose::Pose const &) constcore::scoring::methods::EnergyMethodvirtual
defines_score_for_residue(conformation::Residue const &) constcore::scoring::methods::OneBodyEnergyvirtual
encode_aa_string(std::string const &) constcore::scoring::methods::NMerSVMEnergy
encode_nmer(std::string const &, core::Size const, core::Size const) constcore::scoring::methods::NMerSVMEnergy
encode_wtd_avg_aa_string(std::string const &, utility::vector1< core::Real > const &) constcore::scoring::methods::NMerSVMEnergy
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
eval_atom_derivative(id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) constcore::scoring::methods::EnergyMethodvirtual
eval_dof_derivative(id::DOF_ID const &dof_id, id::TorsionID const &tor_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) constcore::scoring::methods::NMerSVMEnergyvirtual
eval_residue_derivatives(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) constcore::scoring::methods::OneBodyEnergyvirtual
eval_residue_dof_derivative(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) constcore::scoring::methods::OneBodyEnergyvirtual
finalize_after_derivatives(pose::Pose &, ScoreFunction const &) constcore::scoring::methods::EnergyMethodvirtual
finalize_after_minimizing(pose::Pose &pose) constcore::scoring::methods::EnergyMethodvirtual
finalize_total_energy(pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) constcore::scoring::methods::EnergyMethodvirtual
gate_svm_scores(bool const)core::scoring::methods::NMerSVMEnergy
gate_svm_scores_core::scoring::methods::NMerSVMEnergyprivate
get_residue_energy_by_svm(core::pose::Pose const &, core::Size const &, core::Real &, core::Real &, utility::vector1< core::Real > &, utility::vector1< core::Real > &) constcore::scoring::methods::NMerSVMEnergy
get_residue_energy_from_sequence(std::string const &, core::Size const &, core::Real &, core::Real &, utility::vector1< core::Real > &, utility::vector1< core::Real > &) constcore::scoring::methods::NMerSVMEnergy
get_svm_nodes(utility::vector1< core::Real > const &) constcore::scoring::methods::NMerSVMEnergy
has_atomistic_energies() constcore::scoring::methods::EnergyMethodvirtual
has_atomistic_pairwise_energies() constcore::scoring::methods::EnergyMethodvirtual
indicate_required_context_graphs(utility::vector1< bool > &) const overridecore::scoring::methods::NMerSVMEnergyvirtual
initialize_from_options(EnergyMethodOptions const &options)core::scoring::methods::NMerSVMEnergyprivate
method_type() const overridecore::scoring::methods::ContextIndependentOneBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) const overridecore::scoring::methods::NMerSVMEnergyinlinevirtual
n_svms() constcore::scoring::methods::NMerSVMEnergy
nmer_cterm_core::scoring::methods::NMerSVMEnergyprivate
nmer_length(core::Size const)core::scoring::methods::NMerSVMEnergy
nmer_length() constcore::scoring::methods::NMerSVMEnergy
nmer_length_core::scoring::methods::NMerSVMEnergyprivate
nmer_pssm_core::scoring::methods::NMerSVMEnergyprivate
nmer_svm_scorecut(core::Real const)core::scoring::methods::NMerSVMEnergy
nmer_svm_scorecut_core::scoring::methods::NMerSVMEnergyprivate
NMerSVMEnergy()=deletecore::scoring::methods::NMerSVMEnergy
NMerSVMEnergy(EnergyMethodOptions const &options)core::scoring::methods::NMerSVMEnergy
NMerSVMEnergy(EnergyMethodOptions const &options, utility::vector1< std::string > const &svm_fnames, utility::vector1< std::string > const &svm_rank_fnames)core::scoring::methods::NMerSVMEnergy
NMerSVMEnergy(core::Size const nmer_length, bool const gate_svm_scores, core::Size const term_length, bool const use_pssm_features, bool const avg_rank_as_energy, core::Real const nmer_svm_scorecut, utility::vector1< std::string > const &svm_fname_vec, utility::vector1< std::string > const &svm_rank_fname_vec, utility::vector1< std::string > const &pssm_fname_vec)core::scoring::methods::NMerSVMEnergy
NMerSVMEnergy(core::Size const nmer_length, bool const gate_svm_scores, core::Size const term_length, bool const use_pssm_features, bool const avg_rank_as_energy, core::Real const nmer_svm_scorecut, utility::vector1< std::string > const &svm_fname_vec, utility::vector1< std::string > const &svm_rank_fname_vec, utility::vector1< std::string > const &pssm_fname_vec, std::string const &aa_matrix)core::scoring::methods::NMerSVMEnergy
OneBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::OneBodyEnergy
operator==(NMerSVMEnergy const &) constcore::scoring::methods::NMerSVMEnergyvirtual
parent typedefcore::scoring::methods::NMerSVMEnergy
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) constcore::scoring::methods::EnergyMethodvirtual
provide_citation_info(basic::citation_manager::CitationCollectionList &) const overridecore::scoring::methods::NMerSVMEnergyvirtual
read_aa_encoding_matrix(std::string const &)core::scoring::methods::NMerSVMEnergy
read_nmer_svm(std::string const &)core::scoring::methods::NMerSVMEnergy
read_nmer_svm_fname_vector(utility::vector1< std::string > const &)core::scoring::methods::NMerSVMEnergy
read_nmer_svm_list(std::string const &)core::scoring::methods::NMerSVMEnergy
read_nmer_svm_rank(std::string const &)core::scoring::methods::NMerSVMEnergy
read_nmer_svm_rank_fname_vector(utility::vector1< std::string > const &)core::scoring::methods::NMerSVMEnergy
read_nmer_svm_rank_list(std::string const &)core::scoring::methods::NMerSVMEnergy
read_nmer_svms_from_options(EnergyMethodOptions const &options)core::scoring::methods::NMerSVMEnergyprivate
read_pssm_features(std::string const)core::scoring::methods::NMerSVMEnergy
requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &pose) constcore::scoring::methods::OneBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(pose::Pose const &pose) constcore::scoring::methods::OneBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) constcore::scoring::methods::EnergyMethodvirtual
residue_energy(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const overridecore::scoring::methods::NMerSVMEnergyvirtual
residue_energy_ext(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) constcore::scoring::methods::OneBodyEnergyvirtual
score_types() constcore::scoring::methods::EnergyMethodinline
score_types_core::scoring::methods::EnergyMethodprivate
set_score_types(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethodprotected
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) constcore::scoring::methods::EnergyMethodvirtual
setup_for_derivatives_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &res_data_cache) constcore::scoring::methods::OneBodyEnergyvirtual
setup_for_minimizing(pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) constcore::scoring::methods::EnergyMethodvirtual
setup_for_minimizing_for_residue(conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, kinematics::MinimizerMapBase const &, basic::datacache::BasicDataCache &, ResSingleMinimizationData &) constcore::scoring::methods::OneBodyEnergyvirtual
setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) constcore::scoring::methods::EnergyMethodvirtual
setup_for_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) constcore::scoring::methods::EnergyMethodvirtual
setup_for_scoring(pose::Pose &, ScoreFunction const &) constcore::scoring::methods::EnergyMethodvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) constcore::scoring::methods::OneBodyEnergyvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) constcore::scoring::methods::OneBodyEnergy
core::scoring::methods::EnergyMethod::setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) constcore::scoring::methods::EnergyMethodvirtual
show_additional_info(std::ostream &, pose::Pose &, bool) constcore::scoring::methods::EnergyMethodvirtual
term_length(core::Size const)core::scoring::methods::NMerSVMEnergy
term_length() constcore::scoring::methods::NMerSVMEnergy
term_length_core::scoring::methods::NMerSVMEnergyprivate
update_residue_for_packing(pose::Pose &, Size resid) constcore::scoring::methods::EnergyMethodvirtual
use_extended_residue_energy_interface() constcore::scoring::methods::OneBodyEnergyvirtual
use_pssm_features(bool const)core::scoring::methods::NMerSVMEnergy
use_pssm_features_core::scoring::methods::NMerSVMEnergyprivate
version() const overridecore::scoring::methods::NMerSVMEnergyprivatevirtual
~OneBodyEnergy() overridecore::scoring::methods::OneBodyEnergy