Rosetta Core  2014.35
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 > &) const core::scoring::methods::NMerSVMEnergy
add_pssm_features(std::string const, core::Size const, utility::vector1< core::Real > &) const core::scoring::methods::NMerSVMEnergy
all_nmer_svms_core::scoring::methods::NMerSVMEnergyprivate
clone() const core::scoring::methods::NMerSVMEnergyvirtual
ContextIndependentOneBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::ContextIndependentOneBodyEnergy
defines_dof_derivatives(pose::Pose const &p) const core::scoring::methods::OneBodyEnergyvirtual
defines_high_order_terms(pose::Pose const &) const core::scoring::methods::EnergyMethodvirtual
defines_score_for_residue(conformation::Residue const &) const core::scoring::methods::OneBodyEnergyvirtual
encode_aa_string(std::string const ) const core::scoring::methods::NMerSVMEnergy
encode_nmer(std::string const, core::Size const, core::Size const ) const core::scoring::methods::NMerSVMEnergy
encode_wtd_avg_aa_string(std::string const, utility::vector1< core::Real > const ) const core::scoring::methods::NMerSVMEnergy
EnergyMethod(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethod
EnergyMethod(EnergyMethod const &src)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) const core::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) const core::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) const core::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) const core::scoring::methods::OneBodyEnergyvirtual
finalize_after_derivatives(pose::Pose &, ScoreFunction const &) const core::scoring::methods::EnergyMethodvirtual
finalize_total_energy(pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) const core::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 &, utility::vector1< core::Real > &) const core::scoring::methods::NMerSVMEnergy
get_svm_nodes(utility::vector1< core::Real > const ) const core::scoring::methods::NMerSVMEnergy
indicate_required_context_graphs(utility::vector1< bool > &) const core::scoring::methods::NMerSVMEnergyvirtual
initialize_from_options()core::scoring::methods::NMerSVMEnergyprivate
method_type() const core::scoring::methods::ContextIndependentOneBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) const core::scoring::methods::NMerSVMEnergyinlinevirtual
n_svms() const core::scoring::methods::NMerSVMEnergy
nmer_cterm_core::scoring::methods::NMerSVMEnergyprivate
nmer_length(core::Size const )core::scoring::methods::NMerSVMEnergy
nmer_length() const core::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()core::scoring::methods::NMerSVMEnergy
NMerSVMEnergy(utility::vector1< std::string > const &svm_fnames)core::scoring::methods::NMerSVMEnergy
OneBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::OneBodyEnergy
parent typedefcore::scoring::methods::NMerSVMEnergy
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const core::scoring::methods::EnergyMethodvirtual
read_aa_encoding_matrix(std::string const )core::scoring::methods::NMerSVMEnergy
read_nmer_svm(std::string const )core::scoring::methods::NMerSVMEnergy
read_nmer_svm_list(std::string const )core::scoring::methods::NMerSVMEnergy
read_nmer_svms_from_options()core::scoring::methods::NMerSVMEnergyprivate
requires_a_setup_for_derivatives_for_residue_opportunity(pose::Pose const &pose) const core::scoring::methods::OneBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity(pose::Pose const &pose) const core::scoring::methods::OneBodyEnergyvirtual
residue_energy(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const core::scoring::methods::NMerSVMEnergyvirtual
residue_energy_ext(conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) const core::scoring::methods::OneBodyEnergyvirtual
score_types() const core::scoring::methods::EnergyMethodinline
set_score_types(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethodprotected
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) const core::scoring::methods::EnergyMethodvirtual
setup_for_derivatives_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const core::scoring::methods::OneBodyEnergyvirtual
setup_for_minimizing(pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const core::scoring::methods::EnergyMethodvirtual
setup_for_minimizing_for_residue(conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, kinematics::MinimizerMapBase const &, ResSingleMinimizationData &) const core::scoring::methods::OneBodyEnergyvirtual
setup_for_packing(pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const core::scoring::methods::EnergyMethodvirtual
setup_for_scoring(pose::Pose &, ScoreFunction const &) const core::scoring::methods::EnergyMethodvirtual
setup_for_scoring_for_residue(conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const core::scoring::methods::OneBodyEnergyvirtual
term_length(core::Size const )core::scoring::methods::NMerSVMEnergy
term_length() const core::scoring::methods::NMerSVMEnergy
term_length_core::scoring::methods::NMerSVMEnergyprivate
update_residue_for_packing(pose::Pose &, Size resid) const core::scoring::methods::EnergyMethodvirtual
use_extended_residue_energy_interface() const core::scoring::methods::OneBodyEnergyvirtual
use_pssm_features(bool const )core::scoring::methods::NMerSVMEnergy
use_pssm_features_core::scoring::methods::NMerSVMEnergyprivate
version() const core::scoring::methods::NMerSVMEnergyprivatevirtual
~EnergyMethod()core::scoring::methods::EnergyMethodvirtual
~NMerSVMEnergy()core::scoring::methods::NMerSVMEnergyvirtual
~OneBodyEnergy()core::scoring::methods::OneBodyEnergyvirtual