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Rosetta 3.4
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Rosetta 3.4
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#include <DunbrackEnergy.hh>
Public Types | |
| typedef ContextIndependentOneBodyEnergy | parent |
| typedef dunbrack::RotamerLibrary | RotamerLibrary |
Public Member Functions | |
| DunbrackEnergy () | |
| ctor | |
| virtual | ~DunbrackEnergy () |
| dtor | |
| virtual scoring::methods::EnergyMethodOP | clone () const |
| clone | |
| virtual void | residue_energy (conformation::Residue const &rsd, pose::Pose const &pose, scoring::EnergyMap &emap) const |
| 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 residue-pairs 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 derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-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. | |
| virtual bool | defines_dof_derivatives (pose::Pose const &p) const |
| Yes. The DunbrackEnergy defines derivatives for phi/psi and the chi dihedrals. | |
| Real | eval_residue_dof_derivative (conformation::Residue const &rsd, scoring::ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap const &weights) const |
| Evaluate the phi/psi and chi dihedral derivatives for the input residue. | |
| virtual Real | eval_dof_derivative (id::DOF_ID const &dof_id, id::TorsionID const &tor_id, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::EnergyMap const &weights) const |
| Deprecated. | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| DunbrackEnergy is context independent; indicates that no context graphs are required. | |
Reimplemented from core::scoring::methods::ContextIndependentOneBodyEnergy.
| core::pack::dunbrack::DunbrackEnergy::DunbrackEnergy | ( | ) |
ctor
Referenced by clone().
| core::pack::dunbrack::DunbrackEnergy::~DunbrackEnergy | ( | ) | [virtual] |
dtor
| EnergyMethodOP core::pack::dunbrack::DunbrackEnergy::clone | ( | ) | const [virtual] |
| bool core::pack::dunbrack::DunbrackEnergy::defines_dof_derivatives | ( | pose::Pose const & | p | ) | const [virtual] |
Yes. The DunbrackEnergy defines derivatives for phi/psi and the chi dihedrals.
Reimplemented from core::scoring::methods::OneBodyEnergy.
| Real core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative | ( | id::DOF_ID const & | dof_id, |
| id::TorsionID const & | tor_id, | ||
| pose::Pose const & | pose, | ||
| scoring::ScoreFunction const & | sfxn, | ||
| scoring::EnergyMap const & | weights | ||
| ) | const [virtual] |
Deprecated.
References core::id::BB, core::id::CHI, core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb(), core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi(), core::pack::dunbrack::DUNBRACK_MAX_BBTOR, core::pack::dunbrack::DUNBRACK_MAX_SCTOR, core::scoring::fa_dun, core::pack::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), core::id::TorsionID::type(), and core::id::TorsionID::valid().
| Real core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative | ( | conformation::Residue const & | rsd, |
| scoring::ResSingleMinimizationData const & | min_data, | ||
| id::DOF_ID const & | dof_id, | ||
| id::TorsionID const & | torsion_id, | ||
| pose::Pose const & | pose, | ||
| scoring::ScoreFunction const & | sfxn, | ||
| scoring::EnergyMap const & | weights | ||
| ) | const [virtual] |
Evaluate the phi/psi and chi dihedral derivatives for the input residue.
Reimplemented from core::scoring::methods::OneBodyEnergy.
References core::id::BB, core::id::CHI, core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dbb(), core::pack::dunbrack::RotamerLibraryScratchSpace::dE_dchi(), core::pack::dunbrack::DUNBRACK_MAX_BBTOR, core::pack::dunbrack::DUNBRACK_MAX_SCTOR, core::scoring::fa_dun, core::pack::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_protein(), core::id::TorsionID::rsd(), core::conformation::Residue::seqpos(), core::id::TorsionID::torsion(), core::id::TorsionID::type(), core::conformation::Residue::type(), and core::id::TorsionID::valid().
| void core::pack::dunbrack::DunbrackEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | ) | const [virtual] |
DunbrackEnergy is context independent; indicates that no context graphs are required.
Implements core::scoring::methods::EnergyMethod.
| bool core::pack::dunbrack::DunbrackEnergy::minimize_in_whole_structure_context | ( | pose::Pose const & | ) | const [inline, virtual] |
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 residue-pairs 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 derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-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.
Reimplemented from core::scoring::methods::EnergyMethod.
| void core::pack::dunbrack::DunbrackEnergy::residue_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| scoring::EnergyMap & | emap | ||
| ) | const [virtual] |
Allocate the scratch space object on the stack to alieviate thread-safety concerns. Scratch does not use new.
Implements core::scoring::methods::ContextIndependentOneBodyEnergy.
References core::scoring::fa_dun, core::pack::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_virtual_residue(), and core::conformation::Residue::type().
1.7.4
