Rosetta 3.4

#include <HolesEnergy.hh>
Public Member Functions  
HolesEnergy ()  
virtual methods::EnergyMethodOP  clone () const 
void  finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const 
called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.  
void  setup_for_derivatives (pose::Pose &, ScoreFunction const &) const 
Called immediately before atom and DOFderivatives are calculated allowing the derived class a chance to prepare for future calls.  
void  eval_atom_derivative (id::AtomID const &, pose::Pose const &, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &, Vector &, Vector &) 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.  
void  indicate_required_context_graphs (utility::vector1< bool > &) const 
Indicate in the contextgraphsrequired list which contextgraphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.  
Public Attributes  
__pad0__:WholeStructureEnergy parent 
core::scoring::packing::HolesEnergy::HolesEnergy  (  ) 
References core::scoring::packing::HolesParams::read_data_file().
Referenced by clone().
virtual methods::EnergyMethodOP core::scoring::packing::HolesEnergy::clone  (  )  const [inline, virtual] 
Implements core::scoring::methods::EnergyMethod.
References HolesEnergy().
void core::scoring::packing::HolesEnergy::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 [virtual] 
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.
The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) "Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations" Computers & Chemistry 8(4) pp. 239247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.
default implementation does not alter either the F1 or F2 vectors.
Reimplemented from core::scoring::methods::EnergyMethod.
References core::id::AtomID::atomno(), core::pose::Pose::data(), core::scoring::holes_min, core::pose::datacache::CacheableDataType::HOLES_POSE_INFO, core::id::AtomID::rsd(), and core::pose::Pose::xyz().
void core::scoring::packing::HolesEnergy::finalize_total_energy  (  pose::Pose &  pose, 
ScoreFunction const &  sfxn,  
EnergyMap &  total_energy  
)  const [virtual] 
called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.
called at the end of energy evaluation
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::packing::compute_holes_score(), core::scoring::holes, core::scoring::holes_decoy, core::scoring::holes_min, core::scoring::holes_min_mean, core::scoring::holes_resl, core::scoring::packing::PoseBalls::nballs(), and core::scoring::packing::HolesResult::score.
void core::scoring::packing::HolesEnergy::indicate_required_context_graphs  (  utility::vector1< bool > &  context_graphs_required  )  const [inline, virtual] 
Indicate in the contextgraphsrequired list which contextgraphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
void core::scoring::packing::HolesEnergy::setup_for_derivatives  (  pose::Pose &  pose, 
ScoreFunction const &  sfxn  
)  const [virtual] 
Called immediately before atom and DOFderivatives are calculated allowing the derived class a chance to prepare for future calls.
default implementation noop
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::packing::compute_holes_deriv(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::HOLES_POSE_INFO, and core::pose::initialize_atomid_map_heavy_only().