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protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 Class Reference

#include <PseudocontactShiftEnergy.hh>

Inheritance diagram for protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2:
Inheritance graph
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Public Types

typedef
core::scoring::methods::WholeStructureEnergy 
parent
 
- Public Types inherited from core::scoring::methods::WholeStructureEnergy
typedef EnergyMethod parent
 
- Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::VirtualBase parent
 

Public Member Functions

 PCS_Energy_Ts2 ()
 c-tor More...
 
 ~PCS_Energy_Ts2 () override
 
PCS_Energy_Ts2operator= (PCS_Energy_Ts2 const &other)
 
 PCS_Energy_Ts2 (PCS_Energy_Ts2 const &other)
 
core::scoring::methods::EnergyMethodOP clone () const override
 clone More...
 
void indicate_required_context_graphs (utility::vector1< bool > &) const override
 Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...
 
void finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::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...
 
core::Real calculate_pcs_score (core::pose::Pose &pose, bool print_to_tracer) const
 
core::Real calculate_scores_and_tensors_from_pose_and_PCS_data (utility::vector1< core::Real > &vec_best_score, utility::vector1< PCS_tensor_Ts2 > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, core::pose::Pose const &pdb, PCS_data_Ts2 &pcs_d) const
 
core::Real minimize_tensors_from_PCS_data (utility::vector1< PCS_tensor_Ts2 > &vec_best_tensor, numeric::xyzVector< core::Real > &best_coo, PCS_data_Ts2 const &pcs_d) const
 
PCS_data_Ts2PCS_data_from_pose (core::pose::Pose &pose) const
 
void dump_PCS_info (utility::vector1< PCS_tensor_Ts2 > const &vec_tensor, numeric::xyzVector< core::Real > const &best_coo, PCS_data_Ts2 const &pcs_d) const
 
void show_additional_info (std::ostream &out, core::pose::Pose &pose, bool verbose=false) const override
 show additional information of the energy method More...
 
core::Size version () const override
 Return the version of the energy method. More...
 
- Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy
 WholeStructureEnergy (EnergyMethodCreatorOP)
 Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More...
 
 ~WholeStructureEnergy () override
 
EnergyMethodType method_type () const override
 Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...
 
virtual Distance atomic_interaction_cutoff () const
 how far apart must two heavy atoms be to have a zero interaction energy? More...
 
- Public Member Functions inherited from core::scoring::methods::EnergyMethod
 EnergyMethod (EnergyMethodCreatorOP creator)
 Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...
 
virtual void setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
 if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...
 
virtual void setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const
 if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More...
 
virtual void prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const
 If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...
 
virtual void update_residue_for_packing (pose::Pose &, Size resid) const
 If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More...
 
virtual void setup_for_scoring (pose::Pose &, ScoreFunction const &) const
 if an energy method needs to cache something in the pose (e.g. in pose.energies()), before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing. More...
 
virtual bool requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const
 Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More...
 
virtual void setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
 Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More...
 
virtual void setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const
 Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More...
 
virtual void finalize_after_minimizing (pose::Pose &pose) const
 Called after minimization, allowing a derived class to do some teardown steps. More...
 
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More...
 
virtual void finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
 called at the end of derivatives evaluation More...
 
virtual bool minimize_in_whole_structure_context (pose::Pose const &) const
 Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...
 
virtual bool defines_high_order_terms (pose::Pose const &) const
 Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...
 
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
 Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...
 
ScoreTypes const & score_types () const
 Returns the score types that this energy method computes. 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...
 

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

Constructor & Destructor Documentation

protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::PCS_Energy_Ts2 ( )

c-tor

protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::~PCS_Energy_Ts2 ( )
overridedefault
protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::PCS_Energy_Ts2 ( PCS_Energy_Ts2 const &  other)
default

Member Function Documentation

core::Real protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_pcs_score ( core::pose::Pose pose,
bool  print_to_tracer 
) const
core::Real protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data ( utility::vector1< core::Real > &  vec_best_score,
utility::vector1< PCS_tensor_Ts2 > &  vec_best_tensor,
numeric::xyzVector< core::Real > &  best_coo,
core::pose::Pose const &  pdb,
PCS_data_Ts2 pcs_d 
) const
core::scoring::methods::EnergyMethodOP protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::clone ( ) const
overridevirtual
void protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::dump_PCS_info ( utility::vector1< PCS_tensor_Ts2 > const &  vec_tensor,
numeric::xyzVector< core::Real > const &  best_coo,
PCS_data_Ts2 const &  pcs_d 
) const
void protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::finalize_total_energy ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  sfxn,
core::scoring::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.

References calculate_pcs_score(), and core::scoring::pcsTs2.

void protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::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.

core::Real protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::minimize_tensors_from_PCS_data ( utility::vector1< PCS_tensor_Ts2 > &  vec_best_tensor,
numeric::xyzVector< core::Real > &  best_coo,
PCS_data_Ts2 const &  pcs_d 
) const
PCS_Energy_Ts2 & protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::operator= ( PCS_Energy_Ts2 const &  other)
PCS_data_Ts2 & protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::PCS_data_from_pose ( core::pose::Pose pose) const
void protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::show_additional_info ( std::ostream &  ,
core::pose::Pose ,
bool  = false 
) const
overridevirtual
core::Size protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::version ( ) const
overridevirtual

Return the version of the energy method.

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


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