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protocols::scoring::methods::saxs::PDDFEnergy Class Reference

#include <PDDFEnergy.hh>

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Public Member Functions

 PDDFEnergy ()
 
 PDDFEnergy (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &)
 c-tors More...
 
virtual ~PDDFEnergy ()
 
virtual
core::scoring::methods::EnergyMethodOP 
clone () const
 
virtual void finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &totals) 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...
 
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. More...
 
core::scoring::methods::EnergyMethodOP create_energy_method (core::scoring::methods::EnergyMethodOptions const &) const
 
utility::vector1< core::Real > & get_pddf ()
 
utility::vector1< core::Real > & get_dist_bins ()
 
utility::vector1< core::Real > & compute_pddf (const core::pose::Pose &) const
 
utility::vector1< core::Real > & compute_pddf_without_ff (const core::pose::Pose &) const
 
core::Real compute_chi (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &) const
 
core::Real compute_L1 (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &) const
 
void create_pddf (core::pose::Pose &, core::Real, core::Real, core::Real)
 
core::Real evaluate_pddf_energy (const core::pose::Pose &pose) const
 
- Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy
 WholeStructureEnergy (EnergyMethodCreatorOP)
 Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More...
 
virtual ~WholeStructureEnergy ()
 
EnergyMethodType method_type () const
 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...
 
 EnergyMethod (EnergyMethod const &src)
 Copy constructor copies over the score types of the source. More...
 
virtual ~EnergyMethod ()
 
virtual void setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
 
virtual void prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const
 
virtual void update_residue_for_packing (pose::Pose &, Size resid) const
 ensure this function gets called. The default behavior is to do nothing. More...
 
virtual void setup_for_scoring (pose::Pose &, ScoreFunction const &) const
 
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 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...
 

Private Member Functions

void read_pddf (std::string)
 
virtual core::Size version () const
 Return the version of the energy method. More...
 

Private Attributes

utility::vector1
< utility::vector1< core::Real > > 
factors_
 
utility::vector1< core::Sizer_ids_
 
utility::vector1< core::Sizea_ids_
 
utility::vector1
< utility::vector1< core::Real > > 
dmatrix_
 
utility::vector1< boolis_glob_
 
core::Real norm_
 
bool if_fit_area_
 
utility::vector1< core::Reald_
 
utility::vector1< core::Realpose_pddf_
 
utility::vector1< core::Realreference_pddf_
 
core::scoring::saxs::FormFactorManagerff_manager_
 
core::Real bin_size_
 
core::Size min_bin_
 
core::Size max_bin_
 
bool if_hydrogens_
 

Additional Inherited Members

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

protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy ( )
protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy ( utility::vector1< core::Real > const &  reference_d,
utility::vector1< core::Real > const &  reference_pddf 
)
virtual protocols::scoring::methods::saxs::PDDFEnergy::~PDDFEnergy ( )
inlinevirtual

Member Function Documentation

virtual core::scoring::methods::EnergyMethodOP protocols::scoring::methods::saxs::PDDFEnergy::clone ( ) const
inlinevirtual
core::Real protocols::scoring::methods::saxs::PDDFEnergy::compute_chi ( utility::vector1< core::Real > const &  pddf_scored,
utility::vector1< core::Real > const &  pddf_reference 
) const
core::Real protocols::scoring::methods::saxs::PDDFEnergy::compute_L1 ( utility::vector1< core::Real > const &  pddf_scored,
utility::vector1< core::Real > const &  pddf_reference 
) const
utility::vector1< core::Real > & protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf ( const core::pose::Pose pose) const
utility::vector1< core::Real > & protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff ( const core::pose::Pose pose) const
core::scoring::methods::EnergyMethodOP protocols::scoring::methods::saxs::PDDFEnergy::create_energy_method ( core::scoring::methods::EnergyMethodOptions const &  ) const
inline

References PDDFEnergy().

void protocols::scoring::methods::saxs::PDDFEnergy::create_pddf ( core::pose::Pose ref_pose,
core::Real  d_min,
core::Real  d_step,
core::Real  d_max 
)
core::Real protocols::scoring::methods::saxs::PDDFEnergy::evaluate_pddf_energy ( const core::pose::Pose pose) const
void protocols::scoring::methods::saxs::PDDFEnergy::finalize_total_energy ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  sfxn,
core::scoring::EnergyMap total_energy 
) const
virtual

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 compute_chi(), compute_pddf_without_ff(), core::scoring::pddf_score, pose_pddf_, and reference_pddf_.

utility::vector1<core::Real>& protocols::scoring::methods::saxs::PDDFEnergy::get_dist_bins ( )
inline

References d_.

utility::vector1<core::Real>& protocols::scoring::methods::saxs::PDDFEnergy::get_pddf ( )
inline

References pose_pddf_.

virtual void protocols::scoring::methods::saxs::PDDFEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const
inlinevirtual

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 protocols::scoring::methods::saxs::PDDFEnergy::read_pddf ( std::string  file_name)
private

References bin_size_, d_, pose_pddf_, and reference_pddf_.

Referenced by PDDFEnergy().

core::Size protocols::scoring::methods::saxs::PDDFEnergy::version ( ) const
privatevirtual

Return the version of the energy method.

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

Member Data Documentation

utility::vector1<core::Size> protocols::scoring::methods::saxs::PDDFEnergy::a_ids_
mutableprivate
core::Real protocols::scoring::methods::saxs::PDDFEnergy::bin_size_
private
utility::vector1<core::Real> protocols::scoring::methods::saxs::PDDFEnergy::d_
private
utility::vector1< utility::vector1<core::Real> > protocols::scoring::methods::saxs::PDDFEnergy::dmatrix_
mutableprivate

Referenced by compute_pddf().

utility::vector1< utility::vector1<core::Real> > protocols::scoring::methods::saxs::PDDFEnergy::factors_
mutableprivate

Referenced by compute_pddf().

core::scoring::saxs::FormFactorManager* protocols::scoring::methods::saxs::PDDFEnergy::ff_manager_
private

Referenced by compute_pddf().

bool protocols::scoring::methods::saxs::PDDFEnergy::if_fit_area_
private

Referenced by compute_chi(), and PDDFEnergy().

bool protocols::scoring::methods::saxs::PDDFEnergy::if_hydrogens_
private
utility::vector1<bool> protocols::scoring::methods::saxs::PDDFEnergy::is_glob_
mutableprivate

Referenced by compute_pddf().

core::Size protocols::scoring::methods::saxs::PDDFEnergy::max_bin_
private

Referenced by compute_chi(), and PDDFEnergy().

core::Size protocols::scoring::methods::saxs::PDDFEnergy::min_bin_
private

Referenced by compute_chi(), and PDDFEnergy().

core::Real protocols::scoring::methods::saxs::PDDFEnergy::norm_
private

Referenced by PDDFEnergy().

utility::vector1<core::Real> protocols::scoring::methods::saxs::PDDFEnergy::pose_pddf_
mutableprivate
utility::vector1<core::Size> protocols::scoring::methods::saxs::PDDFEnergy::r_ids_
mutableprivate
utility::vector1<core::Real> protocols::scoring::methods::saxs::PDDFEnergy::reference_pddf_
private

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