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core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy Class Reference

#include <ExactOccludedHbondSolEnergy.hh>

Inheritance diagram for core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy:
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Public Member Functions

 ExactOccludedHbondSolEnergy (etable::Etable const &etable_in, bool const analytic_etable_evaluation, bool const exact_occ_skip_Hbonders=false, bool const exact_occ_pairwise=false, bool const exact_occ_pairwise_by_res=false, bool const exact_occ_split_between_res=false, bool const exact_occ_self_res_occ=true, core::Real const occ_radius_scaling=1., bool const verbose=false)
 
 ExactOccludedHbondSolEnergy (ExactOccludedHbondSolEnergy const &src)
 
 ~ExactOccludedHbondSolEnergy () override
 
methods::EnergyMethodOP clone () const override
 
void init_hbond_data (pose::Pose const &pose) const
 
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 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_derivatives (pose::Pose &pose, ScoreFunction const &) const override
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...
 
void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &, kinematics::MinimizerMapBase const &) const override
 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...
 
void residue_energy (conformation::Residue const &polar_rsd, pose::Pose const &pose, EnergyMap &emap) const override
 Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them). 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...
 
virtual bool defines_intrares_energy (EnergyMap const &) const
 
core::Real compute_donor_atom_energy (conformation::Residue const &polar_rsd, core::Size polar_resnum, core::Size const polar_atom, pose::Pose const &pose) const
 computes the desolvation energy (i.e., either SHO or median LK) of a donor atom More...
 
core::Real compute_acceptor_atom_energy (conformation::Residue const &polar_rsd, core::Size polar_resnum, core::Size const polar_atom, pose::Pose const &pose) const
 computes the desolvation energy (i.e., either SHO or median LK) of an acceptor atom More...
 
core::Real compute_sho_donor_atom_energy (conformation::Residue const &polar_rsd, core::Size polar_resnum, core::Size const polar_atom, pose::Pose const &pose) const
 computes the SHO energy of a donor atom More...
 
core::Real compute_sho_acceptor_atom_energy (conformation::Residue const &polar_rsd, core::Size polar_resnum, core::Size const polar_atom, pose::Pose const &pose) const
 computes the SHO energy of an acceptor atom More...
 
core::Real compute_polar_group_sol_energy (pose::Pose const &pose, conformation::Residue const &polar_rsd, Size const polar_atom, bool const restrict_to_single_occluding_residue=false, Size const single_occluding_resinx=0, bool const restrict_to_single_occluding_atom=false, Size const single_occluding_atominx=0) const
 computes the SHO energy of a polar group More...
 
core::Real get_atom_lk_energy (core::Size const atom_idx, core::conformation::Residue const &res, core::pose::Pose const &ps) const
 returns the LK energy of a given atom due to all its neighboring residues More...
 
hbonds::HBondSetCOP hbond_set () const
 
core::Size version () const override
 Return the version of the energy method. More...
 
- Public Member Functions inherited from core::scoring::methods::ContextDependentOneBodyEnergy
 ContextDependentOneBodyEnergy (EnergyMethodCreatorOP)
 Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing. More...
 
EnergyMethodType method_type () const override
 Returns the cd_1b element of the EnergyMethodType enumeration; this method should NOT be overridden by derived classes. More...
 
- Public Member Functions inherited from core::scoring::methods::OneBodyEnergy
 OneBodyEnergy (EnergyMethodCreatorOP)
 Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing. More...
 
 ~OneBodyEnergy () override
 
virtual bool defines_score_for_residue (conformation::Residue const &) const
 During minimization, energy methods are allowed to decide that they say nothing about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return "true" for all residues. More...
 
virtual bool use_extended_residue_energy_interface () const
 Rely on the extended version of the residue_energy function during score-function evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return 'true' for the extended version. The default method implemented in this class returns 'false'. More...
 
virtual void residue_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) const
 Evaluate the one-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 one body energies into the input EnergyMap. 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 setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More...
 
virtual void setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, kinematics::MinimizerMapBase const &, basic::datacache::BasicDataCache &, ResSingleMinimizationData &) const
 Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResSingleMinimizationData 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. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. 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. More...
 
virtual bool requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation 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_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &res_data_cache) const
 Do any setup work necessary before evaluating the derivatives for this residue. More...
 
virtual void eval_residue_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 an atom in a residue 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 ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. DEPRECATED – too slow. More...
 
virtual bool defines_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_residue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const
 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...
 
- 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 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 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 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 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__:ContextDependentOneBodyEnergy parent
 

Private Member Functions

void allocate_grid_of_occluded_sites ()
 
core::Real compute_fully_buried_ene () const
 computes energy of fully buried polar group More...
 
core::Real compute_grid_constant (core::scoring::hbonds::HBEvalTuple const &hbond_eval_type, core::Real fully_buried_ene) const
 computes the grid constant for a given polar group (i.e., the denominator in the solvation energy equation) More...
 
core::Real compute_polar_group_sol_energy (pose::Pose const &pose, conformation::Residue const &polar_rsd, core::Size const polar_atomno, GridInfo const &grid_info, core::Real const &grid_constant, std::vector< std::vector< std::vector< core::Real > > > const &water_weights, bool const restrict_to_single_occluding_residue=false, core::Size const single_occluding_resinx=0, bool const restrict_to_single_occluding_atom=false, core::Size const single_occluding_atominx=0) const
 computes the SHO energy of a polar group More...
 
core::Real get_atom_lk_energy (core::Size atom_idx, conformation::Residue const &res, conformation::Residue const &occ_res) const
 returns the LK energy of a given atom due to a given residue More...
 

Private Attributes

bool const exact_occ_skip_Hbonders_
 
bool const exact_occ_pairwise_
 
bool const exact_occ_pairwise_by_res_
 
bool const exact_occ_split_between_res_
 
bool const exact_occ_self_res_occ_
 
core::Real const occ_radius_scaling_
 
hbonds::HBondOptionsOP hbondoptions_
 
hbonds::HBondDatabaseCOP hb_database_
 
chemical::AtomTypeSetCAP atom_type_set_ptr_
 
WaterWeightGridSet::Grid occluded_sites_
 
core::scoring::hbonds::HBondSetOP hbond_set_
 stores H-bond info for the entire pose. More...
 
etable::EtableEvaluatorOP etable_evaluator_
 computes LK energies for H-bonded atoms More...
 
core::Real lk_safe_max_dis2_
 interatomic squared distance below which LK energies are computed More...
 
bool const verbose_
 

Additional Inherited Members

- Public Types inherited from core::scoring::methods::ContextDependentOneBodyEnergy
typedef OneBodyEnergy parent
 
- Public Types inherited from core::scoring::methods::OneBodyEnergy
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::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy ( etable::Etable const &  etable_in,
bool const  analytic_etable_evaluation,
bool const  exact_occ_skip_Hbonders = false,
bool const  exact_occ_pairwise = false,
bool const  exact_occ_pairwise_by_res = false,
bool const  exact_occ_split_between_res = false,
bool const  exact_occ_self_res_occ = true,
core::Real const  occ_radius_scaling = 1.,
bool const  verbose = false 
)
core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy ( ExactOccludedHbondSolEnergy const &  src)
core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::~ExactOccludedHbondSolEnergy ( )
overridedefault

Member Function Documentation

void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::allocate_grid_of_occluded_sites ( )
private
methods::EnergyMethodOP core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::clone ( ) const
overridevirtual
core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy ( conformation::Residue const &  polar_rsd,
core::Size  polar_resnum,
core::Size const  polar_atom,
pose::Pose const &  pose 
) const

computes the desolvation energy (i.e., either SHO or median LK) of an acceptor atom

computes the desolvation energy (i.e., either SHO or LK) of an acceptor atom

Parameters
[in]polar_rsdresidue to which the atom belongs
[in]polar_resnumindex of the residue in its pose
[in]polar_atomindex of the atom in the residue
[in]posethe pose

References core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), compute_sho_acceptor_atom_energy(), get_atom_lk_energy(), core::conformation::Residue::has_variant_type(), hbond_set_, core::conformation::Residue::heavyatom_has_polar_hydrogens(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::scoring::geometric_solvation::LK_MATCHING_INTERCEPT, core::scoring::geometric_solvation::LK_MATCHING_SLOPE, core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by residue_energy().

core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy ( conformation::Residue const &  polar_rsd,
core::Size  polar_resnum,
core::Size const  polar_atom,
pose::Pose const &  pose 
) const

computes the desolvation energy (i.e., either SHO or median LK) of a donor atom

computes the desolvation energy (i.e., either SHO or LK) of a donor atom

Parameters
[in]polar_rsdresidue to which the atom belongs
[in]polar_resnumindex of the residue in its pose
[in]polar_atomindex of the atom in the residue
[in]posethe pose

References core::conformation::Residue::atom_base(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), compute_sho_donor_atom_energy(), get_atom_lk_energy(), core::conformation::Residue::has_variant_type(), hbond_set_, core::conformation::Residue::heavyatom_is_an_acceptor(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::scoring::geometric_solvation::LK_MATCHING_INTERCEPT, core::scoring::geometric_solvation::LK_MATCHING_SLOPE, core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by residue_energy().

core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_fully_buried_ene ( ) const
private

computes energy of fully buried polar group

The energy is +5 kcal/mole in any case

Referenced by compute_polar_group_sol_energy(), compute_sho_acceptor_atom_energy(), and compute_sho_donor_atom_energy().

core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_grid_constant ( core::scoring::hbonds::HBEvalTuple const &  hbond_eval_type,
core::Real  fully_buried_ene 
) const
private

computes the grid constant for a given polar group (i.e., the denominator in the solvation energy equation)

Parameters
[in]hbond_eval_typeHBEvalTuple describing the hydrogen bond of the polar group to water
[in]fully_buried_eneenergy of the polar group when fully buried

References core::scoring::hbonds::HBEvalTuple::eval_type(), and core::scoring::geometric_solvation::geosol_kT.

Referenced by compute_polar_group_sol_energy(), compute_sho_acceptor_atom_energy(), and compute_sho_donor_atom_energy().

Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy ( pose::Pose const &  pose,
conformation::Residue const &  polar_rsd,
Size const  polar_atom,
bool const  restrict_to_single_occluding_residue = false,
Size const  single_occluding_resinx = 0,
bool const  restrict_to_single_occluding_atom = false,
Size const  single_occluding_atominx = 0 
) const
core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy ( pose::Pose const &  pose,
conformation::Residue const &  polar_rsd,
core::Size const  polar_atomno,
GridInfo const &  grid_info,
core::Real const &  grid_constant,
std::vector< std::vector< std::vector< core::Real > > > const &  water_weights,
bool const  restrict_to_single_occluding_residue = false,
core::Size const  single_occluding_resinx = 0,
bool const  restrict_to_single_occluding_atom = false,
core::Size const  single_occluding_atominx = 0 
) const
private

computes the SHO energy of a polar group

core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy ( conformation::Residue const &  polar_rsd,
core::Size  polar_resnum,
core::Size const  polar_atom,
pose::Pose const &  pose 
) const
core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy ( conformation::Residue const &  polar_rsd,
core::Size  polar_resnum,
core::Size const  polar_atom,
pose::Pose const &  pose 
) const
virtual bool core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::defines_intrares_energy ( EnergyMap const &  ) const
inlinevirtual
core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy ( core::Size const  atom_idx,
core::conformation::Residue const &  res,
core::pose::Pose const &  ps 
) const
core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy ( core::Size  atom_idx,
conformation::Residue const &  res,
conformation::Residue const &  occ_res 
) const
private
hbonds::HBondSetCOP core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::hbond_set ( ) const
inline

References hbond_set_.

void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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::geometric_solvation::ExactOccludedHbondSolEnergy::init_hbond_data ( pose::Pose const &  pose) const
void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap emap 
) const
overridevirtual
void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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::scoring::TR().

void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::setup_for_minimizing ( pose::Pose ,
ScoreFunction const &  ,
kinematics::MinimizerMapBase const &   
) const
overridevirtual

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.

default implementation noop

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

References core::scoring::TR().

void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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::pose::Pose::update_residue_neighbors().

void core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::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 init_hbond_data(), and core::pose::Pose::update_residue_neighbors().

core::Size core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::version ( ) const
overridevirtual

Return the version of the energy method.

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

Member Data Documentation

core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::__pad0__
chemical::AtomTypeSetCAP core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::atom_type_set_ptr_
private
etable::EtableEvaluatorOP core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::etable_evaluator_
private

computes LK energies for H-bonded atoms

Referenced by ExactOccludedHbondSolEnergy(), and get_atom_lk_energy().

bool const core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::exact_occ_pairwise_
private
bool const core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::exact_occ_pairwise_by_res_
private
bool const core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::exact_occ_self_res_occ_
private
bool const core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::exact_occ_skip_Hbonders_
private
bool const core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::exact_occ_split_between_res_
private
hbonds::HBondDatabaseCOP core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::hb_database_
private
core::scoring::hbonds::HBondSetOP core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::hbond_set_
private

stores H-bond info for the entire pose.

Referenced by compute_acceptor_atom_energy(), compute_donor_atom_energy(), hbond_set(), and init_hbond_data().

hbonds::HBondOptionsOP core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::hbondoptions_
private
core::Real core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::lk_safe_max_dis2_
private

interatomic squared distance below which LK energies are computed

Referenced by get_atom_lk_energy().

core::Real const core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::occ_radius_scaling_
private
WaterWeightGridSet::Grid core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::occluded_sites_
mutableprivate
bool const core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::verbose_
private

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