Rosetta  2021.07
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core::scoring::methods::NMerPSSMEnergy Member List

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

all_nmer_pssms_core::scoring::methods::NMerPSSMEnergyprivate
atoms_with_dof_derivatives(conformation::Residue const &res, pose::Pose const &pose) const core::scoring::methods::OneBodyEnergyvirtual
clone() const overridecore::scoring::methods::NMerPSSMEnergyvirtual
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
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) 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::NMerPSSMEnergyvirtual
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_after_minimizing(pose::Pose &pose) const core::scoring::methods::EnergyMethodvirtual
finalize_total_energy(pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) const core::scoring::methods::EnergyMethodvirtual
gate_pssm_scores(bool const )core::scoring::methods::NMerPSSMEnergy
gate_pssm_scores_core::scoring::methods::NMerPSSMEnergyprivate
indicate_required_context_graphs(utility::vector1< bool > &) const overridecore::scoring::methods::NMerPSSMEnergyvirtual
initialize_from_options()core::scoring::methods::NMerPSSMEnergyprivate
method_type() const overridecore::scoring::methods::ContextIndependentOneBodyEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) const overridecore::scoring::methods::NMerPSSMEnergyinlinevirtual
n_pssms() const core::scoring::methods::NMerPSSMEnergy
nmer_cterm_core::scoring::methods::NMerPSSMEnergyprivate
nmer_length(core::Size const )core::scoring::methods::NMerPSSMEnergy
nmer_length_core::scoring::methods::NMerPSSMEnergyprivate
nmer_pssm_scorecut(core::Real const )core::scoring::methods::NMerPSSMEnergy
nmer_pssm_scorecut_core::scoring::methods::NMerPSSMEnergyprivate
NMerPSSMEnergy()core::scoring::methods::NMerPSSMEnergy
NMerPSSMEnergy(utility::vector1< std::map< core::chemical::AA, utility::vector1< core::Real > > > const &all_nmer_pssms_in)core::scoring::methods::NMerPSSMEnergy
NMerPSSMEnergy(core::Size const nmer_length, bool const gate_pssm_scores, core::Real const nmer_pssm_scorecut, utility::vector1< std::string > const &pssm_fname_vec)core::scoring::methods::NMerPSSMEnergy
OneBodyEnergy(EnergyMethodCreatorOP)core::scoring::methods::OneBodyEnergy
operator==(NMerPSSMEnergy const &) const core::scoring::methods::NMerPSSMEnergyvirtual
parent typedefcore::scoring::methods::NMerPSSMEnergy
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) const core::scoring::methods::EnergyMethodvirtual
provide_citation_info(basic::citation_manager::CitationCollectionList &) const core::scoring::methods::EnergyMethodvirtual
pssm_energy_at_frame_seqpos(core::Size const, core::chemical::AA const, core::Size const ) const core::scoring::methods::NMerPSSMEnergy
read_nmer_pssm(std::string)core::scoring::methods::NMerPSSMEnergy
read_nmer_pssm_fname_vector(utility::vector1< std::string > const &)core::scoring::methods::NMerPSSMEnergy
read_nmer_pssm_list(std::string)core::scoring::methods::NMerPSSMEnergy
read_nmer_pssms_from_options()core::scoring::methods::NMerPSSMEnergyprivate
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_during_minimization(pose::Pose const &pose) const core::scoring::methods::OneBodyEnergyvirtual
requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) const core::scoring::methods::EnergyMethodvirtual
residue_energy(conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const overridecore::scoring::methods::NMerPSSMEnergyvirtual
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, basic::datacache::BasicDataCache &res_data_cache) 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 &, basic::datacache::BasicDataCache &, 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_packing_with_rotsets(pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) 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
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) const core::scoring::methods::EnergyMethodvirtual
show_additional_info(std::ostream &, pose::Pose &, bool) const core::scoring::methods::EnergyMethodvirtual
update_residue_for_packing(pose::Pose &, Size resid) const core::scoring::methods::EnergyMethodvirtual
use_extended_residue_energy_interface() const core::scoring::methods::OneBodyEnergyvirtual
version() const overridecore::scoring::methods::NMerPSSMEnergyprivatevirtual
~NMerPSSMEnergy() overridecore::scoring::methods::NMerPSSMEnergy
~OneBodyEnergy() overridecore::scoring::methods::OneBodyEnergy