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

NatbiasSecondaryStructureEnergy. More...

#include <NatbiasSecondaryStructureEnergy.hh>

Inheritance diagram for protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy:
Inheritance graph
Collaboration diagram for protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy:
Collaboration graph

Public Types

typedef std::string String
typedef core::Real Real
typedef core::Distance Distance
typedef core::pose::Pose Pose
typedef core::scoring::EnergyMap EnergyMap
- Public Types inherited from core::scoring::methods::WholeStructureEnergy
typedef EnergyMethod parent
- Public Types inherited from core::scoring::methods::EnergyMethod

Public Member Functions

 NatbiasSecondaryStructureEnergy ()
 default constructor More...
 NatbiasSecondaryStructureEnergy (NatbiasSecondaryStructureEnergy const &src)
 copy constructor More...
virtual EnergyMethodOP clone () const
 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...
virtual void setup_for_scoring (Pose &pose, ScoreFunction const &scorefxn) const
 scoring More...
virtual void finalize_total_energy (Pose &pose, ScoreFunction const &, EnergyMap &totals) const
 scoring More...
virtual Distance atomic_interaction_cutoff () const
 The NatbiasSecondaryStructureEnergy class requires that the EnergyGraph span 12 Angstroms between centroids. The centroids residues build-in a 3 Angstrom radius each. More...
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 SecondaryStructureEnergy. More...
virtual Size version () const
 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...
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...
- 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_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,, 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 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


Member Typedef Documentation

Constructor & Destructor Documentation

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

default constructor

Referenced by clone().

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

copy constructor

Member Function Documentation

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

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


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


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)

use use original secondary structure potential

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

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

Return the version of the energy method.

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

Member Data Documentation

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

pointer of NatbiasHeliceesSheetPotential

Referenced by finalize_total_energy(), and set_natbias_helices_sheet_pot().

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

native secondary structure

Referenced by finalize_total_energy(), and native_secstruct().

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

use original secondary structure potential if this is true

Referenced by use_nobias().

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

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