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Rosetta 3.4
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Rosetta 3.4
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#include <SurfVolEnergy.hh>
Public Member Functions | |
| SurfVolEnergy () | |
| 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 DOF-derivatives 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. | |
| virtual core::Size | version () const |
| Return the version of the energy method. | |
| 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. | |
Public Attributes | |
| __pad0__:WholeStructureEnergy parent | |
| core::scoring::packing::SurfVolEnergy::SurfVolEnergy | ( | ) |
Referenced by clone().
| virtual methods::EnergyMethodOP core::scoring::packing::SurfVolEnergy::clone | ( | ) | const [inline, virtual] |
Implements core::scoring::methods::EnergyMethod.
References SurfVolEnergy().
| void core::scoring::packing::SurfVolEnergy::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::id::AtomID::atomno(), core::scoring::dab_sasa, core::pose::datacache::CacheableDataType::DAB_SASA_POSE_INFO, core::scoring::dab_sev, core::pose::Pose::data(), core::id::AtomID::rsd(), and core::pose::Pose::xyz().
| void core::scoring::packing::SurfVolEnergy::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::dab_sasa, core::scoring::dab_sev, core::scoring::packing::get_surf_vol(), core::scoring::packing::SurfVol::tot_surf, and core::scoring::packing::SurfVol::tot_vol.
| void core::scoring::packing::SurfVolEnergy::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::packing::SurfVolEnergy::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::datacache::CacheableDataType::DAB_SASA_POSE_INFO, core::pose::datacache::CacheableDataType::DAB_SEV_POSE_INFO, core::pose::Pose::data(), core::scoring::packing::get_surf_vol_deriv(), and core::pose::initialize_atomid_map_heavy_only().
| core::Size core::scoring::packing::SurfVolEnergy::version | ( | ) | const [virtual] |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
1.7.4
