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Rosetta 3.4
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Rosetta 3.4
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#include <RamachandranEnergy.hh>
Public Types | |
| typedef ContextIndependentOneBodyEnergy | parent |
Public Member Functions | |
| RamachandranEnergy () | |
| ctor | |
| virtual EnergyMethodOP | clone () const |
| clone | |
| virtual void | residue_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap) const |
| Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them). | |
| 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 |
| The ramachandran energy defines derivatives for protein backbone torsion angles. | |
| virtual Real | eval_residue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const |
| Evaluate the phi or psi derivative for a particular residue. | |
| Real | eval_dof_derivative (id::DOF_ID const &, id::TorsionID const &tor_id, pose::Pose const &pose, ScoreFunction const &, EnergyMap const &weights) const |
| NOTE: non-virtual function interface. | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| Ramachandran Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies. | |
Reimplemented from core::scoring::methods::ContextIndependentOneBodyEnergy.
| core::scoring::methods::RamachandranEnergy::RamachandranEnergy | ( | ) |
ctor
Referenced by clone().
| EnergyMethodOP core::scoring::methods::RamachandranEnergy::clone | ( | ) | const [virtual] |
| bool core::scoring::methods::RamachandranEnergy::defines_dof_derivatives | ( | pose::Pose const & | p | ) | const [virtual] |
The ramachandran energy defines derivatives for protein backbone torsion angles.
Reimplemented from core::scoring::methods::OneBodyEnergy.
| Real core::scoring::methods::RamachandranEnergy::eval_dof_derivative | ( | id::DOF_ID const & | , |
| id::TorsionID const & | tor_id, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | , | ||
| EnergyMap const & | weights | ||
| ) | const |
NOTE: non-virtual function interface.
References core::id::BB, core::scoring::Ramachandran::eval_rama_score_residue(), core::conformation::Residue::is_protein(), core::scoring::rama, core::pose::Pose::residue(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), core::id::TorsionID::type(), and core::id::TorsionID::valid().
| Real core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative | ( | conformation::Residue const & | rsd, |
| ResSingleMinimizationData const & | min_data, | ||
| id::DOF_ID const & | dof_id, | ||
| id::TorsionID const & | torsion_id, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap const & | weights | ||
| ) | const [virtual] |
Evaluate the phi or psi derivative for a particular residue.
Reimplemented from core::scoring::methods::OneBodyEnergy.
References core::conformation::Residue::aa(), core::chemical::aa_unk, core::id::BB, core::scoring::Ramachandran::eval_rama_score_residue(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_protein(), core::scoring::rama, core::id::TorsionID::torsion(), core::id::TorsionID::type(), and core::id::TorsionID::valid().
| void core::scoring::methods::RamachandranEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | ) | const [virtual] |
Ramachandran Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies.
Implements core::scoring::methods::EnergyMethod.
| bool core::scoring::methods::RamachandranEnergy::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::scoring::methods::RamachandranEnergy::residue_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them).
Implements core::scoring::methods::ContextIndependentOneBodyEnergy.
References core::conformation::Residue::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_protein(), core::chemical::num_canonical_aas, and core::scoring::rama.
1.7.4
