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core::scoring::lkball::LK_BallEnergy Class Reference

#include <LK_BallEnergy.hh>

Inheritance diagram for core::scoring::lkball::LK_BallEnergy:
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Public Types

typedef chemical::ResidueType ResidueType
 convenience typedefs More...
 
typedef utility::vector1< SizeSizes
 
typedef utility::vector1< VectorVectors
 
- Public Types inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
typedef ShortRangeTwoBodyEnergy parent
 
- Public Types inherited from core::scoring::methods::ShortRangeTwoBodyEnergy
typedef TwoBodyEnergy parent
 
- Public Types inherited from core::scoring::methods::TwoBodyEnergy
typedef EnergyMethod parent
 
- Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::VirtualBase parent
 

Public Member Functions

 LK_BallEnergy (methods::EnergyMethodOptions const &options)
 
methods::EnergyMethodOP clone () const override
 clone More...
 
 LK_BallEnergy (LK_BallEnergy const &src)
 
void setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const override
 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...
 
void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const override
 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...
 
void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &rotamer_set) const override
 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...
 
void update_residue_for_packing (pose::Pose &, Size resid) const override
 
void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const override
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...
 
Real calculate_lk_desolvation_of_single_atom_by_residue (Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)
 helper function for outside use More...
 
Real calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair (Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)
 
void calculate_lk_ball_atom_energies (Size const atom1, conformation::Residue const &rsd1, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_waters, Size const atom2, conformation::Residue const &rsd2, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const
 get the lk-ball desolvation of atom1 by atom2, and the unoriented lk desolvation of atom1 by atom2 More...
 
void calculate_lk_ball_atom_energies_cp (Size const atom1, conformation::Residue const &rsd1, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, etable::count_pair::CPCrossoverBehavior const &cp_crossover, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const
 
Real get_lk_fractional_contribution_for_single_water (Vector const &atom2_xyz, Size const atom2_type, Vector const &atom1_water) const
 
void eval_desolvation_derivs_no_count_pair (Real const d2, Size const atom1, conformation::Residue const &rsd1, Size const atom2, conformation::Residue const &rsd2, Real &atom1_lk_desolvation_by_atom2_deriv, Real &atom2_lk_desolvation_by_atom1_deriv)
 
void eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const override
 Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%. More...
 
void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
 This guy is used during scoring if we are not minimizing, or inside linmem_ig packing and things like that... More...
 
bool divides_backbone_and_sidechain_energetics () const override
 Let the energy-method consumers (e.g. the packer) use bounding-sphere logic for deciding whether bb/bb, bb/sc, and sc/sc energies should be evaluated. More...
 
void backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
 The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of bb/bb interactions. More...
 
void backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
 The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of bb/sc interactions; that is, the backbone from residue 1 with the sidechain of residue 2. More...
 
void sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const override
 The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of sc/sc interactions. More...
 
void residue_pair_energy (conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, ScoreFunction const &sf, EnergyMap &emap) const
 
void accumulate_single_atom_contributions (Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_waters, AtomWeights const &atom1_wts, conformation::Residue const &rsd1, Size const atom2_type_index, Vector const &atom2_xyz, Real const lk_desolvation_of_atom1_by_atom2, EnergyMap &emap) const
 
void setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, basic::datacache::BasicDataCache &res_data_cache, ResSingleMinimizationData &resdata) const override
 Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More...
 
void setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &, ScoreFunction const &scorefxn, kinematics::MinimizerMapBase const &min_map, ResSingleMinimizationData const &res1data, ResSingleMinimizationData const &res2data, ResPairMinimizationData &pairdata) const override
 Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More...
 
bool minimize_in_whole_structure_context (pose::Pose const &) const override
 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...
 
bool requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const override
 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...
 
void setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const override
 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...
 
bool requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &) const override
 Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
 
void setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &residue_data_cache) const override
 Do any setup work necessary before evaluating the derivatives for this residue. More...
 
bool defines_intrares_energy (EnergyMap const &) const override
 Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not. More...
 
void eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const override
 Evaluate the intra-residue energy for a given residue. More...
 
void finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const override
 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...
 
void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const override
 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...
 
Distance atomic_interaction_cutoff () const override
 how far apart must two heavy atoms be to have a zero interaction energy? More...
 
void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) 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...
 
Real eval_lk_fraction (Real const d2_delta, Real const width) const
 
Real eval_d_lk_fraction_dr_over_r (Real const d2_delta, Real const width) const
 
Real get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Size atom1_n_attached_waters, Size atom1_water_offset, WaterCoords const &rsd1_waters, WaterDerivContributions &d_weighted_d2_d_di, Real &weighted_water_dis2) const
 
Real get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Size const atom1_n_attached_waters, Size const atom1_water_offset, WaterCoords const &rsd1_waters) const
 
Real get_lkbr_fractional_contribution (Vector const &atom1_base, Vector const &atom2_base, Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters) const
 
Real get_lkbr_fractional_contribution_noangle (Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters) const
 
Real get_lkbr_fractional_contribution (Vector const &atom1_base, Vector const &atom2_base, Size atom1_n_attached_waters, Size atom2_n_attached_waters, Size atom1_water_offset, Size atom2_water_offset, WaterCoords const &rsd1_waters, WaterCoords const &rsd2_waters, WaterDerivVectors &d_weighted_d2_d_di1, Real &weighted_d2_water_delta, Real &pointterm_lkbr, Real &angleterm_lkbr, Real &d_angleterm_lkbr_dr, bool compute_derivs=true) const
 
void evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const override
 Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls the derived class's residue_pair_energy method. More...
 
void evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const override
 Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamr. More...
 
void sum_deriv_contributions_for_heavyatom_pair_one_way (Size const heavyatom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const heavyatom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, EnergyMap const &weights, Real const weight_factor, Real const d2, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const
 
void sum_deriv_contributions_for_heavyatom_pair (Real const d2, Size const heavyatom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const heavyatom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, pose::Pose const &, EnergyMap const &weights, Real const cp_weight, utility::vector1< DerivVectorPair > &r1_at_derivs, utility::vector1< DerivVectorPair > &r2_at_derivs) const
 
void setup_d2_bounds ()
 
etable::Etable const & etable () const
 
ObjexxFCL::FArray3D< Real > const & solv1 () const
 
ObjexxFCL::FArray3D< Real > const & solv2 () const
 
Real etable_bins_per_A2 () const
 
Real lkb_max_dis () const
 
Real lkb_max_dis2 () const
 
Real fasol_max_dis2 () const
 
bool slim_etable () const
 
core::Real get_ramp_width_A2 () const
 
core::Real get_overlap_width_A2 () const
 
core::Real get_multi_water_fade () const
 
core::Real get_lkbridge_angle_widthscale () const
 
core::Real get_overlap_target_len2 () const
 
core::Real get_overlap_gap2 () const
 
core::Real get_d2_low (core::Size idx) const
 
core::Size version () const override
 Return the version of the energy method. More...
 
- Public Member Functions inherited from core::scoring::methods::ContextIndependentTwoBodyEnergy
 ContextIndependentTwoBodyEnergy (EnergyMethodCreatorOP)
 Constructor with an EnergyMethodCreator to inform the ancestor EnergyMethod class which ScoreTypes this EnergyMethod is responsible for computing. More...
 
 ~ContextIndependentTwoBodyEnergy () 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...
 
- Public Member Functions inherited from core::scoring::methods::ShortRangeTwoBodyEnergy
 ShortRangeTwoBodyEnergy (EnergyMethodCreatorOP)
 Constructor with EnergyMethodCreator to provide to the EnergyMethod grandparent the list of the ScoreTypes this EnergyMethod is responsible for computing. More...
 
 ~ShortRangeTwoBodyEnergy () override
 
void evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const override
 Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
void evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const override
 Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
void evaluate_rotamer_background_energy_maps (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const override
 Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range. More...
 
- Public Member Functions inherited from core::scoring::methods::TwoBodyEnergy
 TwoBodyEnergy (EnergyMethodCreatorOP)
 Constructor, requiring an EnergyMethodCreator. No default constructor provided to force EnergyMethod writers to provide an energy-method-creator at construction time. More...
 
 ~TwoBodyEnergy () override
 
virtual bool defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const
 During minimization, energy methods are allowed to decide that they say nothing about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns "true" for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning "false" for residue pairs that do no move wrt each other. More...
 
virtual bool use_extended_residue_pair_energy_interface () const
 Rely on the extended version of the residue_pair_energy function during score-function evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return 'true' from this function to use the extended interface. The default method implemented in this class returns 'false'. More...
 
virtual void residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the two-body energies for a particular residue, in the context of a given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit(). More...
 
virtual bool requires_a_setup_for_scoring_for_residue_opportunity_during_minimization (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More...
 
virtual void setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const
 Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup. More...
 
virtual bool requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
 
virtual void setup_for_scoring_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const
 Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More...
 
virtual bool requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More...
 
virtual void setup_for_derivatives_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const
 Do any setup work necessary before evaluating the derivatives for this residue pair. More...
 
virtual bool defines_intrares_energy_for_residue (conformation::Residue const &res) const
 If a score function defines no intra-residue scores for a particular residue, then it may opt-out of being asked during minimization to evaluate the score for this residue. More...
 
virtual bool use_extended_intrares_energy_interface () const
 Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy during minimization routines should return "true" when this function is invoked on them. This class provides a default "return false" implementation so that classes not desiring to take advantage of this alternate interface need to do nothing. More...
 
virtual void eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the intra-residue energy for a given residue using the data held within the ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return "true" in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies. More...
 
virtual void eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const
 Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd. More...
 
virtual bool defines_intrares_dof_derivatives (pose::Pose const &p) const
 Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More...
 
virtual Real eval_intraresidue_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
 Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...
 
virtual void bump_energy_full (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
 
virtual void bump_energy_backbone (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
 
virtual void evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const
 Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More...
 
virtual void evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const
 Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. 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_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 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_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 finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
 called at the end of derivatives evaluation 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...
 
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__:ContextIndependentTwoBodyEnergy parent
 

Private Member Functions

lkbtrie::LKBRotamerTrieOP create_rotamer_trie (conformation::RotamerSetBase const &rotset) const
 
lkbtrie::LKBRotamerTrieOP create_rotamer_trie (conformation::Residue const &res) const
 
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 figure out the trie count pair function to use Need to refactor this so that the decision "what kind of count pair behavior should I use" can be decoupled from class instantiation, and therefore shared between the creation of the trie count pair classes and the regular count pair classes More...
 
trie::TrieCountPairBaseOP get_count_pair_function_trie (conformation::Residue const &res1, conformation::Residue const &res2, trie::RotamerTrieBaseCOP trie1, trie::RotamerTrieBaseCOP trie2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 

Private Attributes

etable::EtableCOP etable_
 
ObjexxFCL::FArray3D< Real > const & solv1_
 these guys are taken from the etable More...
 
ObjexxFCL::FArray3D< Real > const & solv2_
 
ObjexxFCL::FArray3D< Real > const & dsolv1_
 
Real const etable_bins_per_A2_
 
Real lkb_max_dis_
 
Real lkb_max_dis2_
 
Real fasol_max_dis2_
 
bool const slim_etable_
 
Real ramp_width_A2_
 
Real overlap_width_A2_
 
Real multi_water_fade_
 
Real lkbridge_angle_widthscale_
 
Real overlap_target_len2_
 
Real overlap_gap2_
 
utility::vector1< Reald2_low_
 
utility::vector1< boolatom_type_is_charged_
 
utility::vector1< Reallk_ball_prefactor_
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

convenience typedefs

Constructor & Destructor Documentation

core::scoring::lkball::LK_BallEnergy::LK_BallEnergy ( methods::EnergyMethodOptions const &  options)
core::scoring::lkball::LK_BallEnergy::LK_BallEnergy ( LK_BallEnergy const &  src)

References setup_d2_bounds().

Member Function Documentation

void core::scoring::lkball::LK_BallEnergy::accumulate_single_atom_contributions ( Size  atom1_n_attached_waters,
Size  atom1_water_offset,
WaterCoords const &  rsd1_waters,
AtomWeights const &  atom1_wts,
conformation::Residue const &  rsd1,
Size const  atom2_type_index,
Vector const &  atom2_xyz,
Real const  lk_desolvation_of_atom1_by_atom2,
EnergyMap emap 
) const
Distance core::scoring::lkball::LK_BallEnergy::atomic_interaction_cutoff ( ) const
overridevirtual

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

References lkb_max_dis_.

Referenced by create_rotamer_trie(), core::scoring::lkball::lkbtrie::LKBTrieEvaluator::hydrogen_interaction_cutoff2(), and setup_for_minimizing_for_residue_pair().

void core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
overridevirtual
void core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
overridevirtual

The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2). This function evaluates only the energies of bb/sc interactions; that is, the backbone from residue 1 with the sidechain of residue 2.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), core::conformation::Residue::data(), core::conformation::Residue::data_ptr(), core::conformation::Residue::is_polymer_bonded(), and core::conformation::residue_datacache::LK_BALL_INFO.

void core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies ( Size const  atom1,
conformation::Residue const &  rsd1,
Size  atom1_n_attached_waters,
Size  atom1_water_offset,
WaterCoords const &  rsd1_waters,
Size const  atom2,
conformation::Residue const &  rsd2,
Real lk_desolvation_of_atom1_by_atom2,
Real lk_ball_desolvation_of_atom1_by_atom2 
) const
void core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp ( Size const  atom1,
conformation::Residue const &  rsd1,
Size  atom1_n_attached_waters,
Size  atom1_water_offset,
WaterCoords const &  atom1_waters,
Size const  atom2,
conformation::Residue const &  rsd2,
etable::count_pair::CPCrossoverBehavior const &  cp_crossover,
Real lk_desolvation_of_atom1_by_atom2,
Real lk_ball_desolvation_of_atom1_by_atom2 
) const
Real core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue ( Size const  atom1,
conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
)
Real core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair ( Size const  atom1,
conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
)
methods::EnergyMethodOP core::scoring::lkball::LK_BallEnergy::clone ( ) const
overridevirtual
lkbtrie::LKBRotamerTrieOP core::scoring::lkball::LK_BallEnergy::create_rotamer_trie ( conformation::RotamerSetBase const &  rotset) const
private
lkbtrie::LKBRotamerTrieOP core::scoring::lkball::LK_BallEnergy::create_rotamer_trie ( conformation::Residue const &  res) const
private
bool core::scoring::lkball::LK_BallEnergy::defines_intrares_energy ( EnergyMap const &  weights) const
inlineoverridevirtual

Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.

For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

Implements core::scoring::methods::TwoBodyEnergy.

bool core::scoring::lkball::LK_BallEnergy::divides_backbone_and_sidechain_energetics ( ) const
overridevirtual

Let the energy-method consumers (e.g. the packer) use bounding-sphere logic for deciding whether bb/bb, bb/sc, and sc/sc energies should be evaluated.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

etable::Etable const & core::scoring::lkball::LK_BallEnergy::etable ( ) const
Real core::scoring::lkball::LK_BallEnergy::etable_bins_per_A2 ( ) const
inline
void core::scoring::lkball::LK_BallEnergy::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
overridevirtual

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.

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) "Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations" Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

default implementation does not alter either the F1 or F2 vectors.

Reimplemented from core::scoring::methods::EnergyMethod.

Real core::scoring::lkball::LK_BallEnergy::eval_d_lk_fraction_dr_over_r ( Real const  d2_delta,
Real const  width 
) const
void core::scoring::lkball::LK_BallEnergy::eval_desolvation_derivs_no_count_pair ( Real const  d2,
Size const  atom1,
conformation::Residue const &  rsd1,
Size const  atom2,
conformation::Residue const &  rsd2,
Real atom1_lk_desolvation_by_atom2_deriv,
Real atom2_lk_desolvation_by_atom1_deriv 
)
void core::scoring::lkball::LK_BallEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
inlineoverridevirtual

Evaluate the intra-residue energy for a given residue.

Implements core::scoring::methods::TwoBodyEnergy.

Real core::scoring::lkball::LK_BallEnergy::eval_lk_fraction ( Real const  d2_delta,
Real const  width 
) const
void core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
ResSingleMinimizationData const &  ,
ResSingleMinimizationData const &  ,
ResPairMinimizationData const &  min_data,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const
overridevirtual

Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::conformation::Residue::atom_is_hydrogen(), fasol_max_dis2_, core::scoring::ResPairMinimizationData::get_data_ref(), core::scoring::lk_ball_bridge_uncpl, core::scoring::lkball_nblist, core::conformation::Residue::natoms(), core::scoring::lkball::retrieve_lkb_resdata(), sum_deriv_contributions_for_heavyatom_pair(), and core::conformation::Residue::xyz().

void core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_background_energies ( conformation::RotamerSetBase const &  set,
conformation::Residue const &  residue,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap const &  weights,
utility::vector1< core::PackerEnergy > &  energy_vector 
) const
overridevirtual
void core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_pair_energies ( conformation::RotamerSetBase const &  set1,
conformation::RotamerSetBase const &  set2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap const &  weights,
ObjexxFCL::FArray2D< core::PackerEnergy > &  energy_table 
) const
overridevirtual
Real core::scoring::lkball::LK_BallEnergy::fasol_max_dis2 ( ) const
inline
void core::scoring::lkball::LK_BallEnergy::finalize_total_energy ( pose::Pose pose,
ScoreFunction const &  sfxn,
EnergyMap total_energy 
) const
overridevirtual

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.

called at the end of energy evaluation

Reimplemented from core::scoring::methods::EnergyMethod.

trie::TrieCountPairBaseOP core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie ( conformation::RotamerSetBase const &  set1,
conformation::RotamerSetBase const &  set2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
private

figure out the trie count pair function to use Need to refactor this so that the decision "what kind of count pair behavior should I use" can be decoupled from class instantiation, and therefore shared between the creation of the trie count pair classes and the regular count pair classes

References core::conformation::RotamerSetBase::get_trie(), core::scoring::methods::lkball_method, core::conformation::RotamerSetBase::resid(), and core::pose::Pose::residue().

Referenced by evaluate_rotamer_background_energies(), and evaluate_rotamer_pair_energies().

trie::TrieCountPairBaseOP core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
trie::RotamerTrieBaseCOP  trie1,
trie::RotamerTrieBaseCOP  trie2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const
private
core::Real core::scoring::lkball::LK_BallEnergy::get_d2_low ( core::Size  idx) const
inline

References d2_low_.

Real core::scoring::lkball::LK_BallEnergy::get_lk_fractional_contribution ( Vector const &  atom2_xyz,
Size const  atom2_type,
Size  atom1_n_attached_waters,
Size  atom1_water_offset,
WaterCoords const &  rsd1_waters,
WaterDerivContributions d_weighted_d2_d_di,
Real weighted_d2_water_delta 
) const
Real core::scoring::lkball::LK_BallEnergy::get_lk_fractional_contribution ( Vector const &  atom2_xyz,
Size const  atom2_type_index,
Size const  atom1_n_attached_waters,
Size const  atom1_water_offset,
WaterCoords const &  rsd1_waters 
) const
Real core::scoring::lkball::LK_BallEnergy::get_lk_fractional_contribution_for_single_water ( Vector const &  atom2_xyz,
Size const  atom2_type,
Vector const &  atom1_water 
) const
Real core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution ( Vector const &  atom1_base,
Vector const &  atom2_base,
Size  atom1_n_attached_waters,
Size  atom2_n_attached_waters,
Size  atom1_water_offset,
Size  atom2_water_offset,
WaterCoords const &  rsd1_waters,
WaterCoords const &  rsd2_waters 
) const
Real core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution ( Vector const &  atom1_base,
Vector const &  atom2_base,
Size  atom1_n_attached_waters,
Size  atom2_n_attached_waters,
Size  atom1_water_offset,
Size  atom2_water_offset,
WaterCoords const &  rsd1_waters,
WaterCoords const &  rsd2_waters,
WaterDerivVectors d_weighted_d2_d_di1,
Real weighted_d2_water_delta,
Real pointterm_lkbr,
Real angleterm_lkbr,
Real d_angleterm_lkbr_dr,
bool  compute_derivs = true 
) const
Real core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution_noangle ( Size  atom1_n_attached_waters,
Size  atom2_n_attached_waters,
Size  atom1_water_offset,
Size  atom2_water_offset,
WaterCoords const &  rsd1_waters,
WaterCoords const &  rsd2_waters 
) const
core::Real core::scoring::lkball::LK_BallEnergy::get_lkbridge_angle_widthscale ( ) const
inline
core::Real core::scoring::lkball::LK_BallEnergy::get_multi_water_fade ( ) const
inline

References multi_water_fade_.

core::Real core::scoring::lkball::LK_BallEnergy::get_overlap_gap2 ( ) const
inline

References overlap_gap2_.

core::Real core::scoring::lkball::LK_BallEnergy::get_overlap_target_len2 ( ) const
inline

References overlap_target_len2_.

core::Real core::scoring::lkball::LK_BallEnergy::get_overlap_width_A2 ( ) const
inline

References overlap_width_A2_.

core::Real core::scoring::lkball::LK_BallEnergy::get_ramp_width_A2 ( ) const
inline

References ramp_width_A2_.

void core::scoring::lkball::LK_BallEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const
overridevirtual

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.

Real core::scoring::lkball::LK_BallEnergy::lkb_max_dis ( ) const
inline

References lkb_max_dis_.

Real core::scoring::lkball::LK_BallEnergy::lkb_max_dis2 ( ) const
inline
bool core::scoring::lkball::LK_BallEnergy::minimize_in_whole_structure_context ( pose::Pose const &  ) const
overridevirtual

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.

Reimplemented from core::scoring::methods::EnergyMethod.

void core::scoring::lkball::LK_BallEnergy::prepare_rotamers_for_packing ( pose::Pose const &  ,
conformation::RotamerSetBase  
) const
overridevirtual

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.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References create_rotamer_trie(), core::conformation::RotamerSetBase::data(), core::conformation::residue_datacache::LK_BALL_INFO, core::conformation::RotamerSetCacheableDataType::LK_BALL_ROTAMER_SET_INFO, core::scoring::methods::lkball_method, core::conformation::RotamerSetBase::nonconst_rotamer(), core::conformation::RotamerSetBase::num_rotamers(), rot(), and core::conformation::RotamerSetBase::store_trie().

bool core::scoring::lkball::LK_BallEnergy::requires_a_setup_for_derivatives_for_residue_opportunity ( pose::Pose const &  pose) const
overridevirtual

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

bool core::scoring::lkball::LK_BallEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring ( pose::Pose const &  pose) const
overridevirtual

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.

Reimplemented from core::scoring::methods::EnergyMethod.

void core::scoring::lkball::LK_BallEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
overridevirtual

This guy is used during scoring if we are not minimizing, or inside linmem_ig packing and things like that...

Implements core::scoring::methods::TwoBodyEnergy.

References core::conformation::Residue::data(), and core::conformation::residue_datacache::LK_BALL_INFO.

void core::scoring::lkball::LK_BallEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
LKB_ResidueInfo const &  rsd1_info,
conformation::Residue const &  rsd2,
LKB_ResidueInfo const &  rsd2_info,
ScoreFunction const &  sf,
EnergyMap emap 
) const
void core::scoring::lkball::LK_BallEnergy::setup_d2_bounds ( )
void core::scoring::lkball::LK_BallEnergy::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  sfxn 
) const
overridevirtual

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References core::pose::Pose::update_residue_neighbors().

void core::scoring::lkball::LK_BallEnergy::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
overridevirtual

Do any setup work necessary before evaluating the derivatives for this residue.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::lkball::update_cached_lkb_resinfo().

Referenced by setup_for_minimizing_for_residue().

void core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
kinematics::MinimizerMapBase const &  minmap,
basic::datacache::BasicDataCache &  residue_data_cache,
ResSingleMinimizationData res_data_cache 
) const
overridevirtual

Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References setup_for_derivatives_for_residue().

void core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue_pair ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
kinematics::MinimizerMapBase const &  minmap,
ResSingleMinimizationData const &  res1_data_cache,
ResSingleMinimizationData const &  res2_data_cache,
ResPairMinimizationData data_cache 
) const
overridevirtual

Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References atomic_interaction_cutoff(), core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, protocols::ligand_docking::ga_ligand_dock::crossover(), core::scoring::ResPairMinimizationData::get_data(), core::conformation::Residue::is_polymer_bonded(), core::scoring::lkb_respair_data, core::scoring::lkball_nblist, and core::scoring::ResPairMinimizationData::set_data().

void core::scoring::lkball::LK_BallEnergy::setup_for_packing ( pose::Pose ,
utility::vector1< bool > const &  ,
utility::vector1< bool > const &   
) const
overridevirtual

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.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, create_rotamer_trie(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::LKB_TRIE_COLLECTION, core::pose::Pose::residue(), core::pose::Pose::residue_data(), core::pose::Pose::size(), and core::scoring::lkball::update_cached_lkb_resinfo().

void core::scoring::lkball::LK_BallEnergy::setup_for_scoring ( pose::Pose ,
ScoreFunction const &   
) const
overridevirtual

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.

Reimplemented from core::scoring::methods::EnergyMethod.

References core::pose::Pose::update_residue_neighbors().

Referenced by protocols::cryst::ReportGradientsMover::compute().

void core::scoring::lkball::LK_BallEnergy::setup_for_scoring_for_residue ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
basic::datacache::BasicDataCache &  residue_data_cache 
) const
overridevirtual

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.)

Reimplemented from core::scoring::methods::EnergyMethod.

References core::scoring::lkball::update_cached_lkb_resinfo().

void core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
overridevirtual
bool core::scoring::lkball::LK_BallEnergy::slim_etable ( ) const
inline
ObjexxFCL::FArray3D< Real > const& core::scoring::lkball::LK_BallEnergy::solv1 ( ) const
inline
ObjexxFCL::FArray3D< Real > const& core::scoring::lkball::LK_BallEnergy::solv2 ( ) const
inline
void core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair ( Real const  d2,
Size const  heavyatom1,
conformation::Residue const &  rsd1,
LKB_ResidueInfo const &  rsd1_info,
Size const  heavyatom2,
conformation::Residue const &  rsd2,
LKB_ResidueInfo const &  rsd2_info,
pose::Pose const &  ,
EnergyMap const &  weights,
Real const  cp_weight,
utility::vector1< DerivVectorPair > &  r1_at_derivs,
utility::vector1< DerivVectorPair > &  r2_at_derivs 
) const
Note
Assumes that atom1 is the "moving" atom, ie the atom for which eval_atom_derivative was called
Calculates the water positions for atom2 if d2 < safe_max_dis2

References sum_deriv_contributions_for_heavyatom_pair_one_way().

Referenced by eval_residue_pair_derivatives().

void core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way ( Size const  heavyatom1,
conformation::Residue const &  rsd1,
LKB_ResidueInfo const &  rsd1_info,
Size const  heavyatom2,
conformation::Residue const &  rsd2,
LKB_ResidueInfo const &  rsd2_info,
EnergyMap const &  weights,
Real const  weight_factor,
Real const  d2,
utility::vector1< DerivVectorPair > &  r1_at_derivs,
utility::vector1< DerivVectorPair > &  r2_at_derivs 
) const
void core::scoring::lkball::LK_BallEnergy::update_residue_for_packing ( pose::Pose pose,
Size  resid 
) const
override
core::Size core::scoring::lkball::LK_BallEnergy::version ( ) const
overridevirtual

Return the version of the energy method.

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

Member Data Documentation

core::scoring::lkball::LK_BallEnergy::__pad0__
utility::vector1< bool > core::scoring::lkball::LK_BallEnergy::atom_type_is_charged_
private

Referenced by setup_d2_bounds().

utility::vector1< Real > core::scoring::lkball::LK_BallEnergy::d2_low_
private
ObjexxFCL::FArray3D< Real > const& core::scoring::lkball::LK_BallEnergy::dsolv1_
private
etable::EtableCOP core::scoring::lkball::LK_BallEnergy::etable_
private
Real const core::scoring::lkball::LK_BallEnergy::etable_bins_per_A2_
private
Real core::scoring::lkball::LK_BallEnergy::fasol_max_dis2_
private
utility::vector1< Real > core::scoring::lkball::LK_BallEnergy::lk_ball_prefactor_
private

Referenced by setup_d2_bounds().

Real core::scoring::lkball::LK_BallEnergy::lkb_max_dis2_
private

Referenced by LK_BallEnergy(), and lkb_max_dis2().

Real core::scoring::lkball::LK_BallEnergy::lkb_max_dis_
private
Real core::scoring::lkball::LK_BallEnergy::lkbridge_angle_widthscale_
private
Real core::scoring::lkball::LK_BallEnergy::multi_water_fade_
private
Real core::scoring::lkball::LK_BallEnergy::overlap_gap2_
private
Real core::scoring::lkball::LK_BallEnergy::overlap_target_len2_
private
Real core::scoring::lkball::LK_BallEnergy::overlap_width_A2_
private
Real core::scoring::lkball::LK_BallEnergy::ramp_width_A2_
private
bool const core::scoring::lkball::LK_BallEnergy::slim_etable_
private
ObjexxFCL::FArray3D< Real > const& core::scoring::lkball::LK_BallEnergy::solv1_
private
ObjexxFCL::FArray3D< Real > const& core::scoring::lkball::LK_BallEnergy::solv2_
private

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