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protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy Class Reference

NatbiasSecondaryStructureEnergy. More...

#include <NatbiasSecondaryStructureEnergy.hh>

Inheritance diagram for protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy:
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Public Types

typedef
core::scoring::methods::WholeStructureEnergy 
parent
 
typedef std::string String
 
typedef core::Real Real
 
typedef core::Distance Distance
 
typedef core::pose::Pose Pose
 
typedef core::scoring::EnergyMap EnergyMap
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::methods::EnergyMethodOP 
EnergyMethodOP
 
typedef
protocols::fldsgn::topology::StrandPairingSetOP 
StrandPairingSetOP
 
typedef
protocols::fldsgn::topology::HelixPairingSetOP 
HelixPairingSetOP
 
typedef
protocols::fldsgn::topology::HSSTripletSetOP 
HSSTripletSetOP
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP 
NatbiasHelixPairPotentialOP
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP 
NatbiasHelicesSheetPotentialOP
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotentialOP 
NatbiasStrandPairPotentialOP
 
- 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

 NatbiasSecondaryStructureEnergy ()
 default constructor More...
 
 NatbiasSecondaryStructureEnergy (NatbiasSecondaryStructureEnergy const &src)
 copy constructor More...
 
EnergyMethodOP clone () const override
 clone More...
 
void native_secstruct (String const &secstruct)
 set native secondary structure More...
 
void set_natbias_spairpot (StrandPairingSetOP const spairset)
 set NatbiasStrandPairPotential More...
 
void set_natbias_hpairpot (HelixPairingSetOP const hpairset)
 set NatbiasHelixPairPotential More...
 
void set_natbias_helices_sheet_pot (HSSTripletSetOP const hss3set)
 set NatbiasHelicesSheetPotential More...
 
void set_natbias_spairpot (NatbiasStrandPairPotentialOP const sspot)
 set native NatbiasStrandPairPotential More...
 
void set_natbias_hpairpot (NatbiasHelixPairPotentialOP const hhpot)
 set NatbiasHelixPairPotential More...
 
void set_natbias_helices_sheet_pot (NatbiasHelicesSheetPotentialOP const hspot)
 set NatbiasHelicesSheetPotential More...
 
void use_nobias (bool const b)
 use use original secondary structure potential More...
 
void setup_for_scoring (Pose &pose, ScoreFunction const &scorefxn) const override
 scoring More...
 
void finalize_total_energy (Pose &pose, ScoreFunction const &, EnergyMap &totals) const override
 scoring More...
 
Distance atomic_interaction_cutoff () const override
 The NatbiasSecondaryStructureEnergy class requires that the EnergyGraph span 12 Angstroms between centroids. The centroids residues build-in a 3 Angstrom radius each. More...
 
void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const override
 SecondaryStructureEnergy. 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...
 
- 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 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 void show_additional_info (std::ostream &, pose::Pose &, bool) const
 show additional information of the energy method More...
 
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...
 

Private Attributes

String native_secstruct_
 native secondary structure More...
 
bool use_sspot_
 Is NatbiasStrandPairPotential to be used ? More...
 
bool use_hhpot_
 Is NatbiasHelixPairPotential to be used ? More...
 
bool use_hspot_
 Is NatbiasHelicesSheetPotential to be used ? More...
 
bool use_nobias_
 use original secondary structure potential if this is true More...
 
NatbiasStrandPairPotentialOP sspot_
 pointer of NatbiasStrandPairPotential More...
 
NatbiasHelixPairPotentialOP hhpot_
 pointer of NatbiasHelixPairPotential More...
 
NatbiasHelicesSheetPotentialOP hspot_
 pointer of NatbiasHeliceesSheetPotential 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...
 

Detailed Description

NatbiasSecondaryStructureEnergy.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasSecondaryStructureEnergy ( )

default constructor

protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::NatbiasSecondaryStructureEnergy ( NatbiasSecondaryStructureEnergy const &  src)
default

copy constructor

Member Function Documentation

core::Distance protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::atomic_interaction_cutoff ( ) const
overridevirtual

The NatbiasSecondaryStructureEnergy class requires that the EnergyGraph span 12 Angstroms between centroids. The centroids residues build-in a 3 Angstrom radius each.

SecondaryStructureEnergy distance cutoff.

Reimplemented from core::scoring::methods::WholeStructureEnergy.

NatbiasSecondaryStructureEnergy::EnergyMethodOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::clone ( ) const
overridevirtual
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::finalize_total_energy ( Pose pose,
ScoreFunction const &  ,
EnergyMap totals 
) const
overridevirtual
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const
overridevirtual

SecondaryStructureEnergy.

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

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::native_secstruct ( String const &  secstruct)

set native secondary structure

References native_secstruct_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot ( HSSTripletSetOP const  hss3set)

set NatbiasHelicesSheetPotential

set HelicesSheetPotential

References hspot_, and use_hspot_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot ( NatbiasHelicesSheetPotentialOP const  hspot)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot ( HelixPairingSetOP const  hpairset)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot ( NatbiasHelixPairPotentialOP const  hhpot)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot ( StrandPairingSetOP const  spairset)
void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot ( NatbiasStrandPairPotentialOP const  sspot)

set native NatbiasStrandPairPotential

References sspot_, and use_sspot_.

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::setup_for_scoring ( Pose pose,
ScoreFunction const &  scorefxn 
) const
overridevirtual

scoring

set up for scoring

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

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

void protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias ( bool const  b)
inline

use use original secondary structure potential

References protocols::match::upstream::b, and use_nobias_.

core::Size protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::version ( ) const
overridevirtual

Return the version of the energy method.

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

Member Data Documentation

NatbiasHelixPairPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::hhpot_
private
NatbiasHelicesSheetPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::hspot_
private

pointer of NatbiasHeliceesSheetPotential

Referenced by finalize_total_energy(), and set_natbias_helices_sheet_pot().

String protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::native_secstruct_
private

native secondary structure

Referenced by finalize_total_energy(), and native_secstruct().

NatbiasStrandPairPotentialOP protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::sspot_
private
bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_hhpot_
private
bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_hspot_
private
bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias_
private

use original secondary structure potential if this is true

Referenced by use_nobias().

bool protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_sspot_
private

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