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core::scoring::rna::RNA_LowResolutionPotential Class Reference

#include <RNA_LowResolutionPotential.hh>

Inheritance diagram for core::scoring::rna::RNA_LowResolutionPotential:
Inheritance graph
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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 &centroid1, Vector const &centroid2, 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 &centroid1, Vector const &centroid2, 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 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 bool energy_method_provides_citation_info () const
 Does this energy method provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool energy_method_is_unpublished () const
 Does this energy method indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Public Attributes

 __pad0__:WholeStructureEnergy parent
 

Static Public Attributes

static Real dummy_deriv = 0.0
 

Private Member Functions

void eval_rna_base_pair_energy_one_way (pose::rna::RNA_RawBaseBaseInfo &rna_raw_base_base_info, conformation::Residue const &res_i, conformation::Residue const &res_j, Vector const &centroid1, Vector const &centroid2, core::kinematics::Stub const &stub1, core::kinematics::Stub const &stub2) const
 
Real rna_base_backbone_pair_energy_one_way (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &centroid1, core::kinematics::Stub const &stub1) const
 
Real get_base_backbone (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Vector const &centroid_i, kinematics::Stub const &stub_i, core::Size const &m) const
 
Size find_backbone_oxygen_atom (ObjexxFCL::FArray2D< Size > const &atom_number_for_backbone_score_calculations, Size const &i, Size const &atom_num_i) const
 
Size find_backbone_oxygen_atom (Size const &atom_num_i) const
 
void initialize_rna_basepair_xy ()
 
void initialize_rna_axis ()
 
void initialize_rna_stagger ()
 
void initialize_RNA_backbone_oxygen_atoms ()
 
void initialize_atom_numbers_for_backbone_score_calculations ()
 
void initialize_rna_base_backbone_xy ()
 
void initialize_rna_backbone_backbone_weights ()
 
void initialize_rna_backbone_backbone ()
 
void initialize_rna_repulsive_weights ()
 
void initialize_more_precise_base_pair_cutoffs ()
 
void fill_atom_numbers_for_backbone_oxygens (core::chemical::ResidueTypeSetCAP &rsd_set, core::chemical::AA const &aa)
 
bool check_atom_numbers_for_backbone_oxygens (core::chemical::ResidueTypeSetCAP &rsd_set, core::chemical::AA const &aa) const
 
Real get_rna_axis_score (Real const cos_theta, Real &deriv=RNA_LowResolutionPotential::dummy_deriv) const
 
Real get_rna_stagger_score (Distance const height, Real &deriv=RNA_LowResolutionPotential::dummy_deriv) const
 
Real get_rna_basepair_xy (Distance const x, Distance const y, Distance const z, Real const cos_theta, conformation::Residue const &res_i, conformation::Residue const &res_j, bool const deriv_check=true, Real &deriv_x=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_y=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_z=RNA_LowResolutionPotential::dummy_deriv) const
 
Real get_rna_backbone_backbone_score (Distance const &r, Size const &atom_num_j_bin, Real &deriv=RNA_LowResolutionPotential::dummy_deriv) const
 
Real get_rna_repulsive_score (Distance const &r, Size const &atom_num_j_bin, Real &deriv=RNA_LowResolutionPotential::dummy_deriv) const
 
Real rna_backbone_backbone_pair_energy_one_way (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
 
Real rna_repulsive_pair_energy_one_way (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
 
Real get_rna_base_backbone_xy (Distance const x, Distance const y, Distance const z, conformation::Residue const &res_i, Size const &atom_num_j_bin, bool const deriv_check=false, Real &deriv_x=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_y=RNA_LowResolutionPotential::dummy_deriv, Real &deriv_z=RNA_LowResolutionPotential::dummy_deriv) const
 
Real get_rna_backbone_backbone_xy (Distance const x, Distance const y, conformation::Residue const &res_i, Size const &atom_num_j_bin) const
 
void setup_precise_zeta_cutoffs (chemical::AA const &na_rad, std::string const &hoogsteen_cutoff_atom, std::string const &sugar_cutoff_atom)
 

Private Attributes

ObjexxFCL::FArray5D< Realrna_basepair_xy_
 
ObjexxFCL::FArray1D< Realrna_stagger_
 
ObjexxFCL::FArray1D< Realrna_axis_
 
utility::vector1< std::string > RNA_backbone_oxygen_atoms_
 
utility::vector1< Sizeatom_numbers_for_backbone_score_calculations_
 
ObjexxFCL::FArray4D< Realrna_base_backbone_xy_
 
ObjexxFCL::FArray1D< Realrna_backbone_backbone_weight_
 
ObjexxFCL::FArray1D< Realrna_backbone_backbone_potential_
 
ObjexxFCL::FArray1D< Realrna_repulsive_weight_
 
ObjexxFCL::FArray1D< Realzeta_hoogsteen_cutoff_precise_
 
ObjexxFCL::FArray1D< Realzeta_sugar_cutoff_precise_
 
Distance const rna_basepair_radius_cutoff_ = 8.0
 
Distance const rna_basepair_stagger_cutoff_ = 3.0
 
Real const rna_basepair_radius_cutoff2_ = 64.0
 
Distance const basepair_xy_bin_width_ = 2.0
 
Size const basepair_xy_num_bins_ = 10
 
Size const basepair_xy_table_size_ = 10
 
Distance const basepair_xy_z_fade_zone_ = 0.5
 
Distance const base_stack_min_height_ = 2.4
 
Distance const base_stack_max_height_ = 6.0
 
Distance const base_stack_radius_ = 4.0
 
Real const base_stack_radius2_ = 16.0
 
Distance const base_stack_z_fade_zone_ = 0.5
 
Distance const base_stack_rho_fade_zone_ = 0.5
 
Real const axis_bin_width_ = 0.2
 
Size const axis_num_bins_ = 11
 
Size const stagger_num_bins_ = 11
 
Distance const stagger_bin_width_ = 0.4
 
Distance const stagger_distance_cutoff_ = 2.0
 
Distance const base_backbone_bin_width_ = 1.0
 
Size const base_backbone_num_bins_ = 16
 
Size const base_backbone_table_size_ = 8
 
Distance const base_backbone_distance_cutoff_ = 12.0
 
Distance const base_backbone_z_cutoff_ = 2.0
 
Distance const base_backbone_rho_cutoff_ = 8.0
 
Distance const base_backbone_atom_dist_cutoff_ = 4.0
 
Distance const base_backbone_z_fade_zone_ = 0.25
 
Distance const base_backbone_rho_fade_zone_ = 0.5
 
bool const base_backbone_check_atom_neighbor_ = false
 
Real const backbone_backbone_bin_width_ = 0.25
 
Real const backbone_backbone_distance_cutoff_ = 6.0
 
Size const backbone_backbone_num_bins_ = 20
 
Real const rna_repulsive_max_penalty_ = 8.0
 
Real const rna_repulsive_screen_scale_ = 2.5
 
Real const rna_repulsive_distance_cutoff_ = 8.0
 
bool const rna_repulse_all_ = true
 
Size const num_RNA_base_pair_orientations_ = 2
 
Size const num_RNA_backbone_oxygen_atoms_ = 6
 
Size const num_RNA_res_types_ = 4
 
Size o2prime_index_within_special_backbone_atoms_ = 6
 
Size o2p_index_within_special_backbone_atoms_ = 2
 
bool const interpolate_ = true
 
bool const fade_ = true
 
bool const rna_verbose_ = false
 
bool more_precise_base_pair_classification_ = false
 
std::string rna_base_pair_xy_filename_ = "scoring/rna/rna_base_pair_xy.dat"
 

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

core::scoring::rna::RNA_LowResolutionPotential::RNA_LowResolutionPotential ( )
core::scoring::rna::RNA_LowResolutionPotential::RNA_LowResolutionPotential ( std::string const &  filename)

Member Function Documentation

Distance core::scoring::rna::RNA_LowResolutionPotential::base_backbone_distance_cutoff ( ) const
inline
Distance core::scoring::rna::RNA_LowResolutionPotential::base_backbone_rho_cutoff ( ) const
inline
Distance core::scoring::rna::RNA_LowResolutionPotential::base_backbone_z_cutoff ( ) const
inline
bool core::scoring::rna::RNA_LowResolutionPotential::check_atom_numbers_for_backbone_oxygens ( core::chemical::ResidueTypeSetCAP rsd_set,
core::chemical::AA const &  aa 
) const
private
bool core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking ( pose::Pose pose,
Size const &  i,
int const &  sign 
) const
bool core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor ( conformation::Residue const &  rsd1,
Vector const &  heavy_atom_j,
Real atom_cutoff_weight 
) const
bool core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair ( pose::Pose pose,
Size const &  i,
Size const &  j 
) const
methods::EnergyMethodOP core::scoring::rna::RNA_LowResolutionPotential::clone ( ) const
inlineoverridevirtual
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
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
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
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
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
void core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way ( pose::rna::RNA_RawBaseBaseInfo rna_raw_base_base_info,
conformation::Residue const &  res_i,
conformation::Residue const &  res_j,
Vector const &  centroid1,
Vector const &  centroid2,
core::kinematics::Stub const &  stub1,
core::kinematics::Stub const &  stub2 
) const
private
void core::scoring::rna::RNA_LowResolutionPotential::fill_atom_numbers_for_backbone_oxygens ( core::chemical::ResidueTypeSetCAP rsd_set,
core::chemical::AA const &  aa 
)
private
void core::scoring::rna::RNA_LowResolutionPotential::finalize ( pose::Pose pose) const
Size core::scoring::rna::RNA_LowResolutionPotential::find_backbone_oxygen_atom ( ObjexxFCL::FArray2D< Size > const &  atom_number_for_backbone_score_calculations,
Size const &  i,
Size const &  atom_num_i 
) const
private
Size core::scoring::rna::RNA_LowResolutionPotential::find_backbone_oxygen_atom ( Size const &  atom_num_i) const
private
Real core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Size const &  m 
) const
Real core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Vector const &  centroid_i,
kinematics::Stub const &  stub_i,
core::Size const &  m 
) const
private
Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_axis_score ( Real const  cos_theta,
Real deriv = RNA_LowResolutionPotential::dummy_deriv 
) const
private
Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_backbone_backbone_score ( Distance const &  r,
Size const &  atom_num_j_bin,
Real deriv = RNA_LowResolutionPotential::dummy_deriv 
) const
private
Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_backbone_backbone_xy ( Distance const  x,
Distance const  y,
conformation::Residue const &  res_i,
Size const &  atom_num_j_bin 
) const
private
Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_base_backbone_xy ( Distance const  x,
Distance const  y,
Distance const  z,
conformation::Residue const &  res_i,
Size const &  atom_num_j_bin,
bool const  deriv_check = false,
Real deriv_x = RNA_LowResolutionPotential::dummy_deriv,
Real deriv_y = RNA_LowResolutionPotential::dummy_deriv,
Real deriv_z = RNA_LowResolutionPotential::dummy_deriv 
) const
private
Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy ( Distance const  x,
Distance const  y,
Distance const  z,
Real const  cos_theta,
conformation::Residue const &  res_i,
conformation::Residue const &  res_j,
bool const  deriv_check = true,
Real deriv_x = RNA_LowResolutionPotential::dummy_deriv,
Real deriv_y = RNA_LowResolutionPotential::dummy_deriv,
Real deriv_z = RNA_LowResolutionPotential::dummy_deriv 
) const
private
Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_repulsive_score ( Distance const &  r,
Size const &  atom_num_j_bin,
Real deriv = RNA_LowResolutionPotential::dummy_deriv 
) const
private
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
Real core::scoring::rna::RNA_LowResolutionPotential::get_rna_stagger_score ( Distance const  height,
Real deriv = RNA_LowResolutionPotential::dummy_deriv 
) const
private
void core::scoring::rna::RNA_LowResolutionPotential::get_zeta_cutoff ( conformation::Residue const &  res_i,
Real zeta_hoogsteen_cutoff,
Real zeta_sugar_cutoff 
) const
void core::scoring::rna::RNA_LowResolutionPotential::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const
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.

void core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations ( )
private
void core::scoring::rna::RNA_LowResolutionPotential::initialize_more_precise_base_pair_cutoffs ( )
private
void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_axis ( )
private

References rna_axis_.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone ( )
private
void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_backbone_backbone_weights ( )
private
void core::scoring::rna::RNA_LowResolutionPotential::initialize_RNA_backbone_oxygen_atoms ( )
private
void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_base_backbone_xy ( )
private
void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_basepair_xy ( )
private
void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_repulsive_weights ( )
private
void core::scoring::rna::RNA_LowResolutionPotential::initialize_rna_stagger ( )
private

References rna_stagger_.

Referenced by RNA_LowResolutionPotential().

void core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification ( bool const &  value)
inline
Real core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
) const
Real core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
) const
private
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
Real core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Vector const &  centroid1,
core::kinematics::Stub const &  stub1 
) const
private
Real core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
) const
Real core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
) const
private
void core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs ( chemical::AA const &  na_rad,
std::string const &  hoogsteen_cutoff_atom,
std::string const &  sugar_cutoff_atom 
)
private
void core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions ( pose::Pose pose) const
void core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list ( pose::Pose pose) const
void core::scoring::rna::RNA_LowResolutionPotential::update_rna_centroid_info ( pose::Pose pose) const
core::Size core::scoring::rna::RNA_LowResolutionPotential::version ( ) const
inlineoverridevirtual

Return the version of the energy method.

Implements core::scoring::methods::EnergyMethod.

Member Data Documentation

core::scoring::rna::RNA_LowResolutionPotential::__pad0__
utility::vector1< Size > core::scoring::rna::RNA_LowResolutionPotential::atom_numbers_for_backbone_score_calculations_
private
Real const core::scoring::rna::RNA_LowResolutionPotential::axis_bin_width_ = 0.2
private

Referenced by get_rna_axis_score().

Size const core::scoring::rna::RNA_LowResolutionPotential::axis_num_bins_ = 11
private
Real const core::scoring::rna::RNA_LowResolutionPotential::backbone_backbone_bin_width_ = 0.25
private
Real const core::scoring::rna::RNA_LowResolutionPotential::backbone_backbone_distance_cutoff_ = 6.0
private
Size const core::scoring::rna::RNA_LowResolutionPotential::backbone_backbone_num_bins_ = 20
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_atom_dist_cutoff_ = 4.0
private

Referenced by check_for_base_neighbor().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_bin_width_ = 1.0
private
bool const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_check_atom_neighbor_ = false
private

Referenced by check_for_base_neighbor().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_distance_cutoff_ = 12.0
private
Size const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_num_bins_ = 16
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_rho_cutoff_ = 8.0
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_rho_fade_zone_ = 0.5
private
Size const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_table_size_ = 8
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_z_cutoff_ = 2.0
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_backbone_z_fade_zone_ = 0.25
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_max_height_ = 6.0
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_min_height_ = 2.4
private
Real const core::scoring::rna::RNA_LowResolutionPotential::base_stack_radius2_ = 16.0
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_radius_ = 4.0
private

Referenced by get_rna_stack_score().

Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_rho_fade_zone_ = 0.5
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::base_stack_z_fade_zone_ = 0.5
private

Referenced by get_rna_stack_score().

Distance const core::scoring::rna::RNA_LowResolutionPotential::basepair_xy_bin_width_ = 2.0
private
Size const core::scoring::rna::RNA_LowResolutionPotential::basepair_xy_num_bins_ = 10
private
Size const core::scoring::rna::RNA_LowResolutionPotential::basepair_xy_table_size_ = 10
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::basepair_xy_z_fade_zone_ = 0.5
private

Referenced by get_rna_basepair_xy().

core::Real core::scoring::rna::RNA_LowResolutionPotential::dummy_deriv = 0.0
static
bool const core::scoring::rna::RNA_LowResolutionPotential::fade_ = true
private
bool const core::scoring::rna::RNA_LowResolutionPotential::interpolate_ = true
private
bool core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification_ = false
private
Size const core::scoring::rna::RNA_LowResolutionPotential::num_RNA_backbone_oxygen_atoms_ = 6
private
Size const core::scoring::rna::RNA_LowResolutionPotential::num_RNA_base_pair_orientations_ = 2
private
Size const core::scoring::rna::RNA_LowResolutionPotential::num_RNA_res_types_ = 4
private
Size core::scoring::rna::RNA_LowResolutionPotential::o2p_index_within_special_backbone_atoms_ = 2
private
Size core::scoring::rna::RNA_LowResolutionPotential::o2prime_index_within_special_backbone_atoms_ = 6
private
ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_axis_
private
ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_potential_
private
ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_weight_
private
utility::vector1< std::string > core::scoring::rna::RNA_LowResolutionPotential::RNA_backbone_oxygen_atoms_
private
ObjexxFCL::FArray4D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_xy_
private
std::string core::scoring::rna::RNA_LowResolutionPotential::rna_base_pair_xy_filename_ = "scoring/rna/rna_base_pair_xy.dat"
private
Real const core::scoring::rna::RNA_LowResolutionPotential::rna_basepair_radius_cutoff2_ = 64.0
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::rna_basepair_radius_cutoff_ = 8.0
private

Referenced by get_rna_basepair_xy().

Distance const core::scoring::rna::RNA_LowResolutionPotential::rna_basepair_stagger_cutoff_ = 3.0
private
ObjexxFCL::FArray5D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_basepair_xy_
private
bool const core::scoring::rna::RNA_LowResolutionPotential::rna_repulse_all_ = true
private
Real const core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_distance_cutoff_ = 8.0
private
Real const core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_max_penalty_ = 8.0
private
Real const core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_screen_scale_ = 2.5
private
ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_weight_
private
ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::rna_stagger_
private
bool const core::scoring::rna::RNA_LowResolutionPotential::rna_verbose_ = false
private
Distance const core::scoring::rna::RNA_LowResolutionPotential::stagger_bin_width_ = 0.4
private

Referenced by get_rna_stagger_score().

Distance const core::scoring::rna::RNA_LowResolutionPotential::stagger_distance_cutoff_ = 2.0
private

Referenced by get_rna_stagger_score().

Size const core::scoring::rna::RNA_LowResolutionPotential::stagger_num_bins_ = 11
private
ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::zeta_hoogsteen_cutoff_precise_
private
ObjexxFCL::FArray1D< Real > core::scoring::rna::RNA_LowResolutionPotential::zeta_sugar_cutoff_precise_
private

The documentation for this class was generated from the following files: