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Rosetta 3.4
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Rosetta 3.4
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#include <RNA_BaseBaseEnergy.hh>
Public Member Functions | |
| RNA_BaseBaseEnergy () | |
| c-tor THIS CLASS REQUIRES AN EnergyMethodCreator TO WORK PROPERLY | |
| virtual methods::EnergyMethodOP | clone () const |
| clone | |
| 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 | finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &) 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. | |
| virtual void | eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &, 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. | |
| virtual Distance | atomic_interaction_cutoff () const |
| RNA_BaseBaseEnergy distance cutoff. | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. | |
| core::scoring::rna::RNA_BaseBaseEnergy::RNA_BaseBaseEnergy | ( | ) |
c-tor THIS CLASS REQUIRES AN EnergyMethodCreator TO WORK PROPERLY
Referenced by clone().
| Distance core::scoring::rna::RNA_BaseBaseEnergy::atomic_interaction_cutoff | ( | ) | const [virtual] |
RNA_BaseBaseEnergy distance cutoff.
Reimplemented from core::scoring::methods::WholeStructureEnergy.
| methods::EnergyMethodOP core::scoring::rna::RNA_BaseBaseEnergy::clone | ( | ) | const [virtual] |
| void core::scoring::rna::RNA_BaseBaseEnergy::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. 239-247. 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::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base().
| void core::scoring::rna::RNA_BaseBaseEnergy::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::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering(), core::scoring::rna::RNA_LowResolutionPotential::finalize(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna_base_axis, core::scoring::rna_base_pair, core::scoring::rna_base_stack, core::scoring::rna_base_stack_axis, core::scoring::rna_base_stagger, core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), and core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info().
| virtual void core::scoring::rna::RNA_BaseBaseEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [inline, virtual] |
Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
| void core::scoring::rna::RNA_BaseBaseEnergy::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::scoring::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info(), core::pose::Pose::update_residue_neighbors(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions().
| void core::scoring::rna::RNA_BaseBaseEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| ScoreFunction const & | |||
| ) | const [virtual] |
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_residue_neighbors().
1.7.4
