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

#include <CenHBEnergy.hh>

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List of all members.

Public Types

typedef
ContextIndependentTwoBodyEnergy 
parent

Public Member Functions

 CenHBEnergy ()
 C-tor, requires options to tell us the atom_type_set_name for the AtomVDW data.
virtual EnergyMethodOP clone () const
 clone
 CenHBEnergy (CenHBEnergy const &src)
 COPY C-TOR.
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
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 the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. 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 ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.
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.
void eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
 Evaluate the intra-residue energy for a given residue.
virtual Distance atomic_interaction_cutoff () const
 CenHBEnergy distance cutoff.
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 CenHBEnergy.

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::CenHBEnergy::CenHBEnergy ( )

C-tor, requires options to tell us the atom_type_set_name for the AtomVDW data.

C-TOR with method options object

Referenced by clone().

core::scoring::methods::CenHBEnergy::CenHBEnergy ( CenHBEnergy const &  src)

COPY C-TOR.

copy c-tor


Member Function Documentation

Distance core::scoring::methods::CenHBEnergy::atomic_interaction_cutoff ( ) const [virtual]
EnergyMethodOP core::scoring::methods::CenHBEnergy::clone ( ) const [virtual]

clone

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

References CenHBEnergy().

virtual bool core::scoring::methods::CenHBEnergy::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::CenHBEnergy::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::CenHBEnergy::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 the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. 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 ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

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

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::scoring::cen_hb, core::conformation::Residue::polymeric_sequence_distance(), and core::conformation::Atom::xyz().

void core::scoring::methods::CenHBEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [virtual]
void core::scoring::methods::CenHBEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
void core::scoring::methods::CenHBEnergy::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  sfxn 
) const [virtual]

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

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

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

void core::scoring::methods::CenHBEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]

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