Rosetta 3.4
Public Member Functions | Public Attributes
core::scoring::carbon_hbonds::CarbonHBondEnergy Class Reference

#include <CarbonHBondEnergy.hh>

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List of all members.

Public Member Functions

 CarbonHBondEnergy ()
 copy c-tor
 CarbonHBondEnergy (CarbonHBondEnergy const &src)
 copy c-tor
virtual methods::EnergyMethodOP clone () const
 clone
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 Evaluate the cbond energy between two residues.
virtual void backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Splitting out based on bb/bb for the OnTheFly IGs.
virtual void backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.
virtual void sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.
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.
virtual void eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
 Evaluate all atom-pair derivatives for any interactions between the two residues.
virtual void eval_intrares_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 the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. 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 calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.
virtual bool defines_intrares_energy (EnergyMap const &) const
 Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.
virtual void eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the intra-residue energy for a given residue.
virtual Distance atomic_interaction_cutoff () const
 how far apart must two heavy atoms be to have a zero interaction energy?
virtual bool divides_backbone_and_sidechain_energetics () const
 A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method.
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 CarbonHBondEnergy is context sensitive.
bool use_orientation_dep_rna_ch_o_bonds (conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd) const

Public Attributes

 __pad0__:ContextIndependentTwoBodyEnergy parent

Constructor & Destructor Documentation

core::scoring::carbon_hbonds::CarbonHBondEnergy::CarbonHBondEnergy ( )

copy c-tor

Referenced by clone().

core::scoring::carbon_hbonds::CarbonHBondEnergy::CarbonHBondEnergy ( CarbonHBondEnergy const &  src)

copy c-tor

copy ctor


Member Function Documentation

Distance core::scoring::carbon_hbonds::CarbonHBondEnergy::atomic_interaction_cutoff ( ) const [virtual]

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

void core::scoring::carbon_hbonds::CarbonHBondEnergy::backbone_backbone_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Splitting out based on bb/bb for the OnTheFly IGs.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::ch_bond, and core::scoring::ch_bond_bb_bb.

void core::scoring::carbon_hbonds::CarbonHBondEnergy::backbone_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluate the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::ch_bond, and core::scoring::ch_bond_bb_sc.

methods::EnergyMethodOP core::scoring::carbon_hbonds::CarbonHBondEnergy::clone ( ) const [virtual]
bool core::scoring::carbon_hbonds::CarbonHBondEnergy::defines_intrares_energy ( EnergyMap const &  weights) const [virtual]

Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.

For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

Implements core::scoring::methods::TwoBodyEnergy.

virtual bool core::scoring::carbon_hbonds::CarbonHBondEnergy::divides_backbone_and_sidechain_energetics ( ) const [inline, virtual]

A derived class should return true for this function if it implements its own versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are "provably distant" based on a pair of bounding spheres for a sidechains and backbones and this method's atomic_interaction_cutoff energy method.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

void core::scoring::carbon_hbonds::CarbonHBondEnergy::eval_intrares_derivatives ( conformation::Residue const &  rsd,
ResSingleMinimizationData const &  min_data,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  atom_derivs 
) const [virtual]

Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. 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 calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::carbon_hbonds::CarbonHBondEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
void core::scoring::carbon_hbonds::CarbonHBondEnergy::eval_residue_pair_derivatives ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
ResSingleMinimizationData const &  ,
ResSingleMinimizationData const &  ,
ResPairMinimizationData const &  min_data,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const [virtual]

Evaluate all atom-pair derivatives for any interactions between the two residues.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

void core::scoring::carbon_hbonds::CarbonHBondEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [virtual]

CarbonHBondEnergy is context sensitive.

CarbonHBondEnergy is not context sensitive.

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

bool core::scoring::carbon_hbonds::CarbonHBondEnergy::minimize_in_whole_structure_context ( pose::Pose const &  ) const [virtual]

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.

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

void core::scoring::carbon_hbonds::CarbonHBondEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  ,
EnergyMap emap 
) const [virtual]
void core::scoring::carbon_hbonds::CarbonHBondEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]
void core::scoring::carbon_hbonds::CarbonHBondEnergy::sidechain_sidechain_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluate the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::ch_bond, and core::scoring::ch_bond_sc_sc.

bool core::scoring::carbon_hbonds::CarbonHBondEnergy::use_orientation_dep_rna_ch_o_bonds ( conformation::Residue const &  don_rsd,
conformation::Residue const &  acc_rsd 
) const

Member Data Documentation


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