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core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty Member List

This is the complete list of members for core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty, including all inherited members.

::BuriedUnsatPenaltySymmetricTests classcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyfriend
::BuriedUnsatPenaltyTests classcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyfriend
add_to_list_of_partners_of_changed_nodes(graph::BuriedUnsatPenaltyGraphCOP curstate_graph, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > &changed_node_partners) constcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
atomic_interaction_cutoff() constcore::scoring::methods::WholeStructureEnergyinlinevirtual
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
BuriedUnsatPenalty(core::scoring::methods::EnergyMethodOptions const &options)core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
calculate_energy(utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::Size > const &rotamer_ids, core::Size const substitution_position=0) const overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
calculate_penalty_once_almost_from_scratch_using_reference_graph(utility::vector1< core::conformation::ResidueCOP > const &resvect, graph::BuriedUnsatPenaltyGraph const &reference_graph, core::Size const symm_multiplier) constcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
calculate_penalty_once_from_scratch(core::pose::Pose const &pose) constcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
clean_up_residuearrayannealableenergy_after_packing(core::pose::Pose &pose) overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
clone() const overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
commit_considered_substitution() overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
compute_penalty(core::Size const unsat_acceptor_count, core::Size const unsat_donor_count, core::Size const unsat_acceptor_and_donor_count, core::Size const oversat_acceptor_count, core::Size const oversat_donor_count, core::Size const oversat_acceptor_and_donor_count) constcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
curstate_graph_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltymutableprivate
decrement_counts(core::Size &unsat_acceptor_count_lastconsidered, core::Size &unsat_donor_count_lastconsidered, core::Size &unsat_acceptor_and_donor_count_lastconsidered, core::Size &oversat_acceptor_count_lastconsidered, core::Size &oversat_donor_count_lastconsidered, core::Size &oversat_acceptor_and_donor_count_lastconsidered, utility::vector1< graph::BuriedUnsatPenaltyNodeDataCOP > const &old_data, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > const &changed_node_partners) constcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
defines_high_order_terms(pose::Pose const &) constcore::scoring::methods::EnergyMethodvirtual
disabled_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltymutableprivate
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
finalize_after_derivatives(pose::Pose &, ScoreFunction const &) constcore::scoring::methods::EnergyMethodvirtual
finalize_after_minimizing(core::pose::Pose &pose) const overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
finalize_total_energy(core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap &totals) const overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
graph_options_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
has_atomistic_energies() constcore::scoring::methods::EnergyMethodvirtual
has_atomistic_pairwise_energies() constcore::scoring::methods::EnergyMethodvirtual
hbond_options_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
increment_counts(core::Size &unsat_acceptor_count_lastconsidered, core::Size &unsat_donor_count_lastconsidered, core::Size &unsat_acceptor_and_donor_count_lastconsidered, core::Size &oversat_acceptor_count_lastconsidered, core::Size &oversat_donor_count_lastconsidered, core::Size &oversat_acceptor_and_donor_count_lastconsidered, utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > const &changed_node_partners) constcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
indicate_required_context_graphs(utility::vector1< bool > &context_graphs_required) const overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
initialize_curstate_graph(core::pose::Pose const &pose)core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
initialize_curstate_graph(utility::vector1< core::conformation::ResidueCOP > const &resvect)core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
method_type() const overridecore::scoring::methods::WholeStructureEnergyvirtual
minimize_in_whole_structure_context(pose::Pose const &) constcore::scoring::methods::EnergyMethodvirtual
nres_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
num_symmetric_copies_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
oversat_acceptor_and_donor_count_lastaccepted_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltymutableprivate
oversat_acceptor_count_lastaccepted_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltymutableprivate
oversat_donor_count_lastaccepted_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltymutableprivate
parent typedefcore::scoring::methods::WholeStructureEnergy
parent1 typedefcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
parent2 typedefcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
prepare_rotamers_for_packing(pose::Pose const &, conformation::RotamerSetBase &) constcore::scoring::methods::EnergyMethodvirtual
prevent_pruning_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
provide_citation_info(basic::citation_manager::CitationCollectionList &) const overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
provide_pymol_commands_to_show_groups(std::ostream &out, core::pose::Pose const &pose) constcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
report() constcore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(pose::Pose const &pose) constcore::scoring::methods::EnergyMethodvirtual
ResidueArrayAnnealableEnergy()core::scoring::annealing::ResidueArrayAnnealableEnergy
ResidueArrayAnnealableEnergy(ResidueArrayAnnealableEnergy const &src)core::scoring::annealing::ResidueArrayAnnealableEnergy
score_types() constcore::scoring::methods::EnergyMethodinline
score_types_core::scoring::methods::EnergyMethodprivate
set_prevent_pruning(bool const setting)core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyinline
set_score_types(EnergyMethodCreatorOP creator)core::scoring::methods::EnergyMethodprotected
set_up_residuearrayannealableenergy_for_packing(core::pose::Pose &pose, core::pack::rotamer_set::RotamerSets const &rotamersets, core::scoring::ScoreFunction const &sfxn) overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
setup_for_derivatives(pose::Pose &pose, ScoreFunction const &sfxn) constcore::scoring::methods::EnergyMethodvirtual
setup_for_minimizing(core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MinimizerMapBase const &minmap) const overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
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, basic::datacache::BasicDataCache &residue_data_cache) constcore::scoring::methods::EnergyMethodvirtual
show_additional_info(std::ostream &, pose::Pose &, bool) constcore::scoring::methods::EnergyMethodvirtual
symmetric_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
unsat_acceptor_and_donor_count_lastaccepted_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltymutableprivate
unsat_acceptor_count_lastaccepted_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltymutableprivate
unsat_donor_count_lastaccepted_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltymutableprivate
unsat_graph_core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyprivate
update_residue_for_packing(pose::Pose &, Size resid) constcore::scoring::methods::EnergyMethodvirtual
version() const overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyvirtual
WholeStructureEnergy(EnergyMethodCreatorOP)core::scoring::methods::WholeStructureEnergy
~BuriedUnsatPenalty() overridecore::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
~ResidueArrayAnnealableEnergy()core::scoring::annealing::ResidueArrayAnnealableEnergyvirtual
~WholeStructureEnergy() overridecore::scoring::methods::WholeStructureEnergyinline