#include <RNA_LowResolutionPotential.hh>
Public Member Functions | |
| RNA_LowResolutionPotential () | |
| RNA_LowResolutionPotential (std::string const &filename) | |
| methods::EnergyMethodOP | clone () const override |
| clone More... | |
| void | indicate_required_context_graphs (utility::vector1< bool > &) const override |
| Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More... | |
| core::Size | version () const override |
| Return the version of the energy method. More... | |
| void | update_rna_centroid_info (pose::Pose &pose) const |
| void | update_rna_base_base_interactions (pose::Pose &pose) const |
| void | update_rna_base_pair_list (pose::Pose &pose) const |
| void | finalize (pose::Pose &pose) const |
| Real | rna_base_backbone_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const ¢roid1, Vector const ¢roid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const |
| Real | get_base_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Size const &m) const |
| Real | rna_backbone_backbone_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const |
| Real | rna_repulsive_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const |
| Real | get_rna_stack_score (Distance const x, Distance const y, Distance const z, Real &deriv_x=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_y=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_z=RNA_LowResolutionPotential::dummy_deriv) const |
| void | eval_atom_derivative_base_base (id::AtomID const &atom_id, pose::Pose const &pose, scoring::EnergyMap const &weights, Vector &F1, Vector &F2) const |
| void | eval_atom_derivative_rna_base_backbone (id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const |
| void | eval_atom_derivative_rna_backbone_backbone (id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const |
| void | eval_atom_derivative_rna_repulsive (id::AtomID const &atom_id, pose::Pose const &pose, Vector &F1, Vector &F2) const |
| bool | check_clear_for_stacking (pose::Pose &pose, Size const &i, int const &sign) const |
| bool | check_forming_base_pair (pose::Pose &pose, Size const &i, Size const &j) const |
| void | eval_rna_base_pair_energy (pose::rna::RNA_RawBaseBaseInfo &rna_raw_base_base_info, conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const ¢roid1, Vector const ¢roid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const |
| void | more_precise_base_pair_classification (bool const &value) |
| Distance | base_backbone_distance_cutoff () const |
| Distance | base_backbone_z_cutoff () const |
| Distance | base_backbone_rho_cutoff () const |
| void | get_zeta_cutoff (conformation::Residue const &res_i, Real &zeta_hoogsteen_cutoff, Real &zeta_sugar_cutoff) const |
| bool | check_for_base_neighbor (conformation::Residue const &rsd1, Vector const &heavy_atom_j, Real &atom_cutoff_weight) const |
 Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy | |
| WholeStructureEnergy (EnergyMethodCreatorOP) | |
| Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More... | |
| ~WholeStructureEnergy () override | |
| EnergyMethodType | method_type () const override |
| Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More... | |
| virtual Distance | atomic_interaction_cutoff () const |
| how far apart must two heavy atoms be to have a zero interaction energy? More... | |
| Public Member Functions inherited from core::scoring::methods::EnergyMethod | |
| EnergyMethod (EnergyMethodCreatorOP creator) | |
| Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More... | |
| virtual void | setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const |
| if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More... | |
| virtual void | setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const |
| if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More... | |
| virtual void | prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const |
| If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More... | |
| virtual void | update_residue_for_packing (pose::Pose &, Size resid) const |
| If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More... | |
| virtual void | setup_for_scoring (pose::Pose &, ScoreFunction const &) const |
| if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing. More... | |
| virtual bool | requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const |
| Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More... | |
| virtual void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const |
| Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More... | |
| virtual void | setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const |
| Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More... | |
| virtual void | finalize_after_minimizing (pose::Pose &pose) const |
| Called after minimization, allowing a derived class to do some teardown steps. More... | |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const |
| Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More... | |
| virtual void | finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const |
| called at the end of derivatives evaluation More... | |
| virtual bool | minimize_in_whole_structure_context (pose::Pose const &) const |
| Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More... | |
| virtual bool | defines_high_order_terms (pose::Pose const &) const |
| Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More... | |
| virtual bool | has_atomistic_energies () const |
| Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method? Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it's not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods. More... | |
| virtual bool | has_atomistic_pairwise_energies () const |
| Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method? NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. More... | |
| virtual void | atomistic_energy (core::Size atmno, conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const |
| Evaluate the (one body) energy associated with a particular atom This may be a "self" energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies() More... | |
| virtual void | 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) const |
| Evaluate the energy for a particular pair of atoms This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies() More... | |
| virtual void | 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 |
| Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More... | |
| virtual void | finalize_total_energy (pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) const |
| called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call. More... | |
| ScoreTypes const & | score_types () const |
| Returns the score types that this energy method computes. More... | |
| virtual void | show_additional_info (std::ostream &, pose::Pose &, bool) const |
| show additional information of the energy method More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Public Attributes | |
| __pad0__:WholeStructureEnergy parent | |
Static Public Attributes | |
| static Real | dummy_deriv = 0.0 |
Additional Inherited Members | |
| Public Types inherited from core::scoring::methods::WholeStructureEnergy | |
| typedef EnergyMethod | parent |
| Public Types inherited from core::scoring::methods::EnergyMethod | |
| typedef utility::VirtualBase | parent |
| Protected Member Functions inherited from core::scoring::methods::EnergyMethod | |
| void | set_score_types (EnergyMethodCreatorOP creator) |
| Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More... | |
Constructor & Destructor Documentation
◆ RNA_LowResolutionPotential() [1/2]
| core::scoring::rna::RNA_LowResolutionPotential::RNA_LowResolutionPotential | ( | ) |
◆ RNA_LowResolutionPotential() [2/2]
| core::scoring::rna::RNA_LowResolutionPotential::RNA_LowResolutionPotential | ( | std::string const & | filename | ) |
References axis_num_bins_, backbone_backbone_num_bins_, base_backbone_bin_width_, base_backbone_num_bins_, base_backbone_table_size_, basepair_xy_bin_width_, basepair_xy_num_bins_, basepair_xy_table_size_, initialize_atom_numbers_for_backbone_score_calculations(), initialize_more_precise_base_pair_cutoffs(), initialize_rna_axis(), initialize_rna_backbone_backbone(), initialize_rna_backbone_backbone_weights(), initialize_RNA_backbone_oxygen_atoms(), initialize_rna_base_backbone_xy(), initialize_rna_basepair_xy(), initialize_rna_repulsive_weights(), initialize_rna_stagger(), num_RNA_backbone_oxygen_atoms_, num_RNA_base_pair_orientations_, num_RNA_res_types_, rna_axis_, rna_backbone_backbone_potential_, rna_base_backbone_xy_, rna_base_pair_xy_filename_, rna_basepair_xy_, rna_repulsive_weight_, rna_stagger_, and stagger_num_bins_.
Member Function Documentation
◆ base_backbone_distance_cutoff()
|
inline |
References base_backbone_distance_cutoff_.
Referenced by core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime().
◆ base_backbone_rho_cutoff()
|
inline |
References base_backbone_rho_cutoff_.
Referenced by core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime().
◆ base_backbone_z_cutoff()
|
inline |
References base_backbone_z_cutoff_.
Referenced by core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime().
◆ check_atom_numbers_for_backbone_oxygens()
|
private |
◆ check_clear_for_stacking()
| bool core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking | ( | pose::Pose & | pose, |
| Size const & | i, | ||
| int const & | sign | ||
| ) | const |
References core::conformation::Residue::atom_name(), core::scoring::rna::RNA_CentroidInfo::base_centroids(), base_stack_max_height_, base_stack_min_height_, base_stack_radius2_, core::scoring::rna::RNA_CentroidInfo::base_stubs(), core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::conformation::Residue::natoms(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::pose::Pose::size(), core::scoring::tr(), core::scoring::rna::RNA_CentroidInfo::update(), and core::conformation::Residue::xyz().
Referenced by core::import_pose::RNA_BasePairHandler::check_base_pairs().
◆ check_for_base_neighbor()
| bool core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor | ( | conformation::Residue const & | rsd1, |
| Vector const & | heavy_atom_j, | ||
| Real & | atom_cutoff_weight | ||
| ) | const |
References base_backbone_atom_dist_cutoff_, base_backbone_check_atom_neighbor_, core::conformation::Residue::first_sidechain_atom(), core::scoring::rna::get_fade_correction(), core::conformation::Residue::nheavyatoms(), core::pose::num_heavy_atoms(), and core::conformation::Residue::xyz().
Referenced by eval_atom_derivative_rna_base_backbone(), get_base_backbone(), and core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime().
◆ check_forming_base_pair()
| bool core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair | ( | pose::Pose & | pose, |
| Size const & | i, | ||
| Size const & | j | ||
| ) | const |
References core::scoring::rna::RNA_CentroidInfo::base_centroids(), core::scoring::rna::RNA_CentroidInfo::base_stubs(), core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), rna_basepair_radius_cutoff2_, rna_basepair_stagger_cutoff_, core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().
Referenced by core::import_pose::RNA_BasePairHandler::check_base_pairs().
◆ clone()
|
inlineoverridevirtual |
◆ eval_atom_derivative_base_base()
| void core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base | ( | id::AtomID const & | atom_id, |
| pose::Pose const & | pose, | ||
| scoring::EnergyMap const & | weights, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const |
References core::id::AtomID::atomno(), core::scoring::rna::RNA_CentroidInfo::base_centroids(), core::scoring::rna::RNA_CentroidInfo::base_stubs(), core::pose::rna::RNA_FilteredBaseBaseInfo::basepair_axis_stagger_scaling(), core::pose::rna::RNA_FilteredBaseBaseInfo::basestack_axis_scaling(), core::chemical::rna::chi1_torsion_atom_index(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_axis_array(), core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array(), core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_array(), core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_axis_array(), core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stagger_array(), get_rna_axis_score(), get_rna_basepair_xy(), get_rna_stack_score(), get_rna_stagger_score(), core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::pose::Pose::residue(), core::scoring::rna_base_axis, core::scoring::rna_base_pair, core::scoring::rna_base_stack, core::scoring::rna_base_stack_axis, core::scoring::rna_base_stagger, core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::rna::rna_scoring_info_from_pose(), core::id::AtomID::rsd(), core::pose::rna::RNA_FilteredBaseBaseInfo::scale_axis_stagger(), and core::conformation::Residue::type().
Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative().
◆ eval_atom_derivative_rna_backbone_backbone()
| void core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone | ( | id::AtomID const & | atom_id, |
| pose::Pose const & | pose, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const |
References atom_numbers_for_backbone_score_calculations_, core::id::AtomID::atomno(), backbone_backbone_distance_cutoff_, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_backbone_oxygen_atom(), get_rna_backbone_backbone_score(), core::conformation::Residue::has_variant_type(), interpolate_, core::conformation::Residue::is_RNA(), num_RNA_backbone_oxygen_atoms_, o2prime_index_within_special_backbone_atoms_, core::chemical::REPL_PHOSPHATE, core::pose::Pose::residue(), rna_backbone_backbone_weight_, core::id::AtomID::rsd(), and core::conformation::Residue::xyz().
Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative().
◆ eval_atom_derivative_rna_base_backbone()
| void core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone | ( | id::AtomID const & | atom_id, |
| pose::Pose const & | pose, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const |
References atom_numbers_for_backbone_score_calculations_, core::id::AtomID::atomno(), base_backbone_distance_cutoff_, base_backbone_rho_cutoff_, base_backbone_z_cutoff_, core::scoring::rna::RNA_CentroidInfo::base_centroids(), core::scoring::rna::RNA_CentroidInfo::base_stubs(), check_for_base_neighbor(), core::chemical::rna::chi1_torsion_atom_index(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_backbone_oxygen_atom(), get_rna_base_backbone_xy(), core::conformation::Residue::has_variant_type(), interpolate_, core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, num_RNA_backbone_oxygen_atoms_, core::chemical::REPL_PHOSPHATE, core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::rna_scoring_info_from_pose(), core::id::AtomID::rsd(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative().
◆ eval_atom_derivative_rna_repulsive()
| void core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive | ( | id::AtomID const & | atom_id, |
| pose::Pose const & | pose, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const |
References atom_numbers_for_backbone_score_calculations_, core::id::AtomID::atomno(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), find_backbone_oxygen_atom(), get_rna_repulsive_score(), core::conformation::Residue::is_RNA(), num_RNA_backbone_oxygen_atoms_, o2p_index_within_special_backbone_atoms_, core::pose::Pose::residue(), rna_repulse_all_, rna_repulsive_distance_cutoff_, rna_repulsive_weight_, core::id::AtomID::rsd(), and core::conformation::Residue::xyz().
Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative().
◆ eval_rna_base_pair_energy()
| void core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy | ( | pose::rna::RNA_RawBaseBaseInfo & | rna_raw_base_base_info, |
| conformation::Residue const & | rsd1, | ||
| conformation::Residue const & | rsd2, | ||
| Vector const & | centroid1, | ||
| Vector const & | centroid2, | ||
| core::kinematics::Stub const & | stub1, | ||
| core::kinematics::Stub const & | stub2 | ||
| ) | const |
References eval_rna_base_pair_energy_one_way().
Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::residue_pair_energy().
◆ eval_rna_base_pair_energy_one_way()
|
private |
References core::pose::rna::RNA_RawBaseBaseInfo::base_axis_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_height_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_pair_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_stack_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_stack_axis_array(), base_stack_max_height_, base_stack_min_height_, base_stack_radius2_, core::pose::rna::RNA_RawBaseBaseInfo::base_stagger_array(), core::chemical::element::F, get_rna_axis_score(), get_rna_basepair_xy(), get_rna_stack_score(), get_rna_stagger_score(), get_zeta_cutoff(), core::chemical::rna::HOOGSTEEN, core::chemical::element::I, core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::conformation::Residue::name3(), core::chemical::rna::NUM_EDGES(), rna_basepair_radius_cutoff2_, rna_basepair_stagger_cutoff_, rna_verbose_, core::conformation::Residue::seqpos(), core::chemical::rna::SUGAR, core::scoring::tr(), and core::chemical::rna::WATSON_CRICK.
Referenced by eval_rna_base_pair_energy().
◆ fill_atom_numbers_for_backbone_oxygens()
|
private |
◆ finalize()
| void core::scoring::rna::RNA_LowResolutionPotential::finalize | ( | pose::Pose & | pose | ) | const |
◆ find_backbone_oxygen_atom() [1/2]
◆ find_backbone_oxygen_atom() [2/2]
◆ get_base_backbone() [1/2]
| Real core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| Size const & | m | ||
| ) | const |
◆ get_base_backbone() [2/2]
|
private |
References core::conformation::Residue::atom_name(), atom_numbers_for_backbone_score_calculations_, base_backbone_distance_cutoff_, base_backbone_rho_cutoff_, base_backbone_z_cutoff_, check_for_base_neighbor(), core::chemical::element::F, get_rna_base_backbone_xy(), core::conformation::Residue::has_variant_type(), core::chemical::element::I, core::kinematics::Stub::M, core::conformation::Residue::name3(), core::chemical::REPL_PHOSPHATE, rna_verbose_, core::conformation::Residue::seqpos(), core::scoring::tr(), and core::conformation::Residue::xyz().
◆ get_rna_axis_score()
|
private |
◆ get_rna_backbone_backbone_score()
|
private |
References backbone_backbone_bin_width_, backbone_backbone_num_bins_, interpolate_, core::scoring::interpolate_value_and_deriv(), rna_backbone_backbone_potential_, and rna_backbone_backbone_weight_.
Referenced by eval_atom_derivative_rna_backbone_backbone(), and rna_backbone_backbone_pair_energy_one_way().
◆ get_rna_backbone_backbone_xy()
|
private |
◆ get_rna_base_backbone_xy()
|
private |
References base_backbone_bin_width_, base_backbone_num_bins_, base_backbone_rho_cutoff_, base_backbone_rho_fade_zone_, base_backbone_table_size_, base_backbone_z_cutoff_, base_backbone_z_fade_zone_, fade_, core::scoring::rna::get_bin(), core::scoring::rna::get_fade_correction(), interpolate_, and rna_base_backbone_xy_.
Referenced by eval_atom_derivative_rna_base_backbone(), and get_base_backbone().
◆ get_rna_basepair_xy()
|
private |
References base_stack_rho_fade_zone_, basepair_xy_bin_width_, basepair_xy_num_bins_, basepair_xy_table_size_, basepair_xy_z_fade_zone_, fade_, core::scoring::rna::get_bin(), core::scoring::rna::get_fade_correction(), interpolate_, core::conformation::Residue::is_RNA(), rna_basepair_radius_cutoff_, rna_basepair_stagger_cutoff_, and rna_basepair_xy_.
Referenced by eval_atom_derivative_base_base(), eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().
◆ get_rna_repulsive_score()
|
private |
References rna_repulsive_weight_.
Referenced by eval_atom_derivative_rna_repulsive(), and rna_repulsive_pair_energy_one_way().
◆ get_rna_stack_score()
| Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_stack_score | ( | Distance const | x, |
| Distance const | y, | ||
| Distance const | z, | ||
| Real & | deriv_x = RNA_LowResolutionPotential::dummy_deriv, |
||
| Real & | deriv_y = RNA_LowResolutionPotential::dummy_deriv, |
||
| Real & | deriv_z = RNA_LowResolutionPotential::dummy_deriv |
||
| ) | const |
References base_stack_max_height_, base_stack_min_height_, base_stack_radius_, base_stack_rho_fade_zone_, base_stack_z_fade_zone_, fade_, and core::scoring::rna::get_fade_correction().
Referenced by eval_atom_derivative_base_base(), eval_rna_base_pair_energy_one_way(), and update_rna_base_base_interactions().
◆ get_rna_stagger_score()
|
private |
◆ get_zeta_cutoff()
| void core::scoring::rna::RNA_LowResolutionPotential::get_zeta_cutoff | ( | conformation::Residue const & | res_i, |
| Real & | zeta_hoogsteen_cutoff, | ||
| Real & | zeta_sugar_cutoff | ||
| ) | const |
References core::scoring::rna::get_bin(), more_precise_base_pair_classification_, zeta_hoogsteen_cutoff_precise_, and zeta_sugar_cutoff_precise_.
Referenced by eval_rna_base_pair_energy_one_way(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), and update_rna_base_base_interactions().
◆ indicate_required_context_graphs()
|
inlineoverridevirtual |
Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
◆ initialize_atom_numbers_for_backbone_score_calculations()
|
private |
◆ initialize_more_precise_base_pair_cutoffs()
|
private |
◆ initialize_rna_axis()
|
private |
References rna_axis_.
Referenced by RNA_LowResolutionPotential().
◆ initialize_rna_backbone_backbone()
|
private |
◆ initialize_rna_backbone_backbone_weights()
|
private |
References rna_backbone_backbone_weight_.
Referenced by RNA_LowResolutionPotential().
◆ initialize_RNA_backbone_oxygen_atoms()
|
private |
References o2p_index_within_special_backbone_atoms_, o2prime_index_within_special_backbone_atoms_, and RNA_backbone_oxygen_atoms_.
Referenced by RNA_LowResolutionPotential().
◆ initialize_rna_base_backbone_xy()
|
private |
References protocols::abinitio::filename(), rna_base_backbone_xy_, and core::scoring::tr().
Referenced by RNA_LowResolutionPotential().
◆ initialize_rna_basepair_xy()
|
private |
References rna_base_pair_xy_filename_, rna_basepair_xy_, and core::scoring::tr().
Referenced by RNA_LowResolutionPotential().
◆ initialize_rna_repulsive_weights()
|
private |
References rna_repulsive_weight_.
Referenced by RNA_LowResolutionPotential().
◆ initialize_rna_stagger()
|
private |
References rna_stagger_.
Referenced by RNA_LowResolutionPotential().
◆ more_precise_base_pair_classification()
|
inline |
References more_precise_base_pair_classification_.
◆ rna_backbone_backbone_pair_energy()
| Real core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2 | ||
| ) | const |
◆ rna_backbone_backbone_pair_energy_one_way()
|
private |
References core::conformation::Residue::atom_name(), atom_numbers_for_backbone_score_calculations_, backbone_backbone_distance_cutoff_, core::chemical::element::F, get_rna_backbone_backbone_score(), core::conformation::Residue::has_variant_type(), core::chemical::element::I, core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), num_RNA_backbone_oxygen_atoms_, o2prime_index_within_special_backbone_atoms_, core::chemical::REPL_PHOSPHATE, rna_backbone_backbone_weight_, rna_verbose_, core::conformation::Residue::seqpos(), core::scoring::tr(), and core::conformation::Residue::xyz().
Referenced by rna_backbone_backbone_pair_energy().
◆ rna_base_backbone_pair_energy()
| Real core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| Vector const & | centroid1, | ||
| Vector const & | centroid2, | ||
| core::kinematics::Stub const & | stub1, | ||
| core::kinematics::Stub const & | stub2 | ||
| ) | const |
◆ rna_base_backbone_pair_energy_one_way()
|
private |
◆ rna_repulsive_pair_energy()
| Real core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2 | ||
| ) | const |
References rna_repulsive_pair_energy_one_way().
Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::residue_pair_energy().
◆ rna_repulsive_pair_energy_one_way()
|
private |
References core::conformation::Residue::atom_name(), atom_numbers_for_backbone_score_calculations_, core::chemical::element::F, get_rna_repulsive_score(), core::chemical::element::I, core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name3(), num_RNA_backbone_oxygen_atoms_, o2p_index_within_special_backbone_atoms_, rna_repulse_all_, rna_repulsive_distance_cutoff_, rna_repulsive_weight_, rna_verbose_, core::conformation::Residue::seqpos(), core::scoring::tr(), and core::conformation::Residue::xyz().
Referenced by rna_repulsive_pair_energy().
◆ setup_precise_zeta_cutoffs()
|
private |
References core::chemical::FA_STANDARD, core::scoring::rna::RNA_CentroidInfo::get_base_centroid(), core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(), core::scoring::rna::get_bin(), core::kinematics::Stub::M, core::chemical::na_rad, zeta_hoogsteen_cutoff_precise_, and zeta_sugar_cutoff_precise_.
Referenced by initialize_more_precise_base_pair_cutoffs().
◆ update_rna_base_base_interactions()
| void core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions | ( | pose::Pose & | pose | ) | const |
References core::pose::rna::RNA_RawBaseBaseInfo::base_axis_array(), core::scoring::rna::RNA_CentroidInfo::base_centroids(), core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_height_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_pair_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_stack_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_stack_axis_array(), base_stack_max_height_, base_stack_min_height_, base_stack_radius2_, core::pose::rna::RNA_RawBaseBaseInfo::base_stagger_array(), core::scoring::rna::RNA_CentroidInfo::base_stubs(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::chemical::element::F, get_rna_axis_score(), get_rna_basepair_xy(), get_rna_stack_score(), get_rna_stagger_score(), get_zeta_cutoff(), core::chemical::rna::HOOGSTEEN, core::chemical::element::I, core::conformation::Residue::is_RNA(), core::kinematics::Stub::M, core::conformation::Residue::name3(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), rna_basepair_radius_cutoff2_, rna_basepair_stagger_cutoff_, core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info(), rna_verbose_, core::pose::Pose::size(), core::chemical::rna::SUGAR, core::scoring::tr(), core::scoring::rna::RNA_CentroidInfo::update(), and core::chemical::rna::WATSON_CRICK.
Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), and update_rna_base_pair_list().
◆ update_rna_base_pair_list()
| void core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list | ( | pose::Pose & | pose | ) | const |
References core::pose::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info(), core::pose::Pose::update_residue_neighbors(), and update_rna_base_base_interactions().
◆ update_rna_centroid_info()
| void core::scoring::rna::RNA_LowResolutionPotential::update_rna_centroid_info | ( | pose::Pose & | pose | ) | const |
References core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().
Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::setup_for_packing(), and core::energy_methods::RNA_PairwiseLowResolutionEnergy::setup_for_scoring().
◆ version()
|
inlineoverridevirtual |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
Member Data Documentation
◆ __pad0__
| core::scoring::rna::RNA_LowResolutionPotential::__pad0__ |
◆ atom_numbers_for_backbone_score_calculations_
|
private |
Referenced by check_atom_numbers_for_backbone_oxygens(), eval_atom_derivative_rna_backbone_backbone(), eval_atom_derivative_rna_base_backbone(), eval_atom_derivative_rna_repulsive(), fill_atom_numbers_for_backbone_oxygens(), find_backbone_oxygen_atom(), get_base_backbone(), rna_backbone_backbone_pair_energy_one_way(), and rna_repulsive_pair_energy_one_way().
◆ axis_bin_width_
|
private |
Referenced by get_rna_axis_score().
◆ axis_num_bins_
|
private |
Referenced by get_rna_axis_score(), and RNA_LowResolutionPotential().
◆ backbone_backbone_bin_width_
|
private |
Referenced by get_rna_backbone_backbone_score().
◆ backbone_backbone_distance_cutoff_
|
private |
◆ backbone_backbone_num_bins_
|
private |
Referenced by get_rna_backbone_backbone_score(), and RNA_LowResolutionPotential().
◆ base_backbone_atom_dist_cutoff_
|
private |
Referenced by check_for_base_neighbor().
◆ base_backbone_bin_width_
|
private |
Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().
◆ base_backbone_check_atom_neighbor_
|
private |
Referenced by check_for_base_neighbor().
◆ base_backbone_distance_cutoff_
|
private |
Referenced by base_backbone_distance_cutoff(), eval_atom_derivative_rna_base_backbone(), and get_base_backbone().
◆ base_backbone_num_bins_
|
private |
Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().
◆ base_backbone_rho_cutoff_
|
private |
◆ base_backbone_rho_fade_zone_
|
private |
Referenced by get_rna_base_backbone_xy().
◆ base_backbone_table_size_
|
private |
Referenced by get_rna_base_backbone_xy(), and RNA_LowResolutionPotential().
◆ base_backbone_z_cutoff_
|
private |
◆ base_backbone_z_fade_zone_
|
private |
Referenced by get_rna_base_backbone_xy().
◆ base_stack_max_height_
|
private |
◆ base_stack_min_height_
|
private |
◆ base_stack_radius2_
|
private |
◆ base_stack_radius_
|
private |
Referenced by get_rna_stack_score().
◆ base_stack_rho_fade_zone_
|
private |
Referenced by get_rna_basepair_xy(), and get_rna_stack_score().
◆ base_stack_z_fade_zone_
|
private |
Referenced by get_rna_stack_score().
◆ basepair_xy_bin_width_
|
private |
Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().
◆ basepair_xy_num_bins_
|
private |
Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().
◆ basepair_xy_table_size_
|
private |
Referenced by get_rna_basepair_xy(), and RNA_LowResolutionPotential().
◆ basepair_xy_z_fade_zone_
|
private |
Referenced by get_rna_basepair_xy().
◆ dummy_deriv
|
static |
◆ fade_
|
private |
Referenced by get_rna_base_backbone_xy(), get_rna_basepair_xy(), and get_rna_stack_score().
◆ interpolate_
|
private |
◆ more_precise_base_pair_classification_
|
private |
Referenced by get_zeta_cutoff(), and more_precise_base_pair_classification().
◆ num_RNA_backbone_oxygen_atoms_
|
private |
Referenced by check_atom_numbers_for_backbone_oxygens(), eval_atom_derivative_rna_backbone_backbone(), eval_atom_derivative_rna_base_backbone(), eval_atom_derivative_rna_repulsive(), fill_atom_numbers_for_backbone_oxygens(), find_backbone_oxygen_atom(), rna_backbone_backbone_pair_energy_one_way(), rna_base_backbone_pair_energy_one_way(), RNA_LowResolutionPotential(), and rna_repulsive_pair_energy_one_way().
◆ num_RNA_base_pair_orientations_
|
private |
Referenced by RNA_LowResolutionPotential().
◆ num_RNA_res_types_
|
private |
Referenced by RNA_LowResolutionPotential().
◆ o2p_index_within_special_backbone_atoms_
|
private |
◆ o2prime_index_within_special_backbone_atoms_
|
private |
◆ rna_axis_
|
private |
Referenced by get_rna_axis_score(), initialize_rna_axis(), and RNA_LowResolutionPotential().
◆ rna_backbone_backbone_potential_
|
private |
◆ rna_backbone_backbone_weight_
|
private |
◆ RNA_backbone_oxygen_atoms_
|
private |
◆ rna_base_backbone_xy_
|
private |
Referenced by get_rna_base_backbone_xy(), initialize_rna_base_backbone_xy(), and RNA_LowResolutionPotential().
◆ rna_base_pair_xy_filename_
|
private |
Referenced by clone(), initialize_rna_basepair_xy(), and RNA_LowResolutionPotential().
◆ rna_basepair_radius_cutoff2_
|
private |
◆ rna_basepair_radius_cutoff_
|
private |
Referenced by get_rna_basepair_xy().
◆ rna_basepair_stagger_cutoff_
|
private |
◆ rna_basepair_xy_
|
private |
Referenced by get_rna_basepair_xy(), initialize_rna_basepair_xy(), and RNA_LowResolutionPotential().
◆ rna_repulse_all_
|
private |
Referenced by eval_atom_derivative_rna_repulsive(), and rna_repulsive_pair_energy_one_way().
◆ rna_repulsive_distance_cutoff_
|
private |
Referenced by eval_atom_derivative_rna_repulsive(), and rna_repulsive_pair_energy_one_way().
◆ rna_repulsive_max_penalty_
|
private |
◆ rna_repulsive_screen_scale_
|
private |
◆ rna_repulsive_weight_
|
private |
◆ rna_stagger_
|
private |
Referenced by get_rna_stagger_score(), initialize_rna_stagger(), and RNA_LowResolutionPotential().
◆ rna_verbose_
|
private |
◆ stagger_bin_width_
|
private |
Referenced by get_rna_stagger_score().
◆ stagger_distance_cutoff_
|
private |
Referenced by get_rna_stagger_score().
◆ stagger_num_bins_
|
private |
Referenced by get_rna_stagger_score(), and RNA_LowResolutionPotential().
◆ zeta_hoogsteen_cutoff_precise_
|
private |
Referenced by get_zeta_cutoff(), initialize_more_precise_base_pair_cutoffs(), and setup_precise_zeta_cutoffs().
◆ zeta_sugar_cutoff_precise_
|
private |
Referenced by get_zeta_cutoff(), initialize_more_precise_base_pair_cutoffs(), and setup_precise_zeta_cutoffs().
The documentation for this class was generated from the following files:
- src/core/scoring/rna/RNA_LowResolutionPotential.hh
- src/core/scoring/rna/RNA_LowResolutionPotential.cc
