Rosetta 3.4
Public Types | Public Member Functions
core::scoring::methods::PeptideBondEnergy Class Reference

PeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment. More...

#include <PeptideBondEnergy.hh>

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List of all members.

Public Types

typedef
ContextIndependentTwoBodyEnergy 
parent

Public Member Functions

 PeptideBondEnergy ()
virtual EnergyMethodOP clone () const
 clone
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 called at the end of energy evaluation
virtual void eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
 Evaluate the intra-residue energy for a given residue.
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const
 called during gradient-based minimization inside dfunc
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 Chainbreak Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies.
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 Distance atomic_interaction_cutoff () const
 how far apart must two heavy atoms be to have a zero interaction energy?
virtual core::Size version () const
 Return the version of the energy method.

Detailed Description

PeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment.


Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::PeptideBondEnergy::PeptideBondEnergy ( )

Referenced by clone().


Member Function Documentation

Distance core::scoring::methods::PeptideBondEnergy::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.

virtual EnergyMethodOP core::scoring::methods::PeptideBondEnergy::clone ( ) const [inline, virtual]
virtual bool core::scoring::methods::PeptideBondEnergy::defines_intrares_energy ( EnergyMap const &  weights) const [inline, 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.

void core::scoring::methods::PeptideBondEnergy::eval_atom_derivative ( id::AtomID const &  id,
pose::Pose const &  pose,
kinematics::DomainMap const &  domain_map,
ScoreFunction const &  sfxn,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const [virtual]

called during gradient-based minimization inside dfunc

F1 and F2 are not zeroed -- contributions from this atom are just summed in

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

virtual void core::scoring::methods::PeptideBondEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [inline, virtual]

Evaluate the intra-residue energy for a given residue.

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

void core::scoring::methods::PeptideBondEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  ) const [virtual]

Chainbreak Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies.

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

void core::scoring::methods::PeptideBondEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  ,
EnergyMap emap 
) const [virtual]
core::Size core::scoring::methods::PeptideBondEnergy::version ( ) const [virtual]

Return the version of the energy method.

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


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