
 RG_LocalEnergy () 
 Defines a center of mass based RG calculation that is O(n) rather than O(n^2). More...


virtual EnergyMethodOP  clone () const 
 clone More...


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. More...


core::Real  calculate_rg_score (pose::Pose const &pose) const 

core::Real  calculate_rg_score (pose::Pose const &pose, utility::vector1< bool > const &relevant_residues) const 

virtual void  setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sf) const 
 Called immediately before atom and DOFderivatives are calculated allowing the derived class a chance to prepare for future calls. More...


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 
 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. More...


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. More...


 RG_Energy_Fast () 
 Defines a center of mass based RG calculation that is O(n) rather than O(n^2). More...


core::Real  calculate_rg_score (pose::Pose const &pose) const 

core::Real  calculate_rg_score (pose::Pose const &pose, utility::vector1< bool > const &relevant_residues) const 

virtual core::Size  version () const 
 Return the version of the energy method. More...


 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. contextdependentonebody vs wholestructure. More...


virtual Distance  atomic_interaction_cutoff () const 
 how far apart must two heavy atoms be to have a zero interaction energy? More...


 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_scoring (pose::Pose &, ScoreFunction const &) const 

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  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 residuepairs 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 derivativeevaluation machinery. Methods that return "true" will not have their residueenergy(ext) / residuepairenergy(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 residuepairs? This covers scoring terms like envsmooth 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 residuepair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, highorder constraints (3body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...


ScoreTypes const &  score_types () const 
 Returns the score types that this energy method computes. More...

