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Rosetta 3.4
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Rosetta 3.4
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#include <FullatomDisulfideEnergy.hh>
Public Member Functions | |
| FullatomDisulfideEnergy (FullatomDisulfidePotential const &potential) | |
| virtual | ~FullatomDisulfideEnergy () |
| virtual methods::EnergyMethodOP | clone () const |
| virtual void | setup_for_scoring (pose::Pose &, ScoreFunction const &) const |
| virtual bool | defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const |
| Returns true only for disulfide-bonded residue pairs. | |
| 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 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 | use_extended_residue_pair_energy_interface () const |
| During minimization, access atom-index information from the ResPairMinimizationData. | |
| virtual void | residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Pull the atom-index information out of min_data object, and use those indices to score the disulfide bond. | |
| virtual void | setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &data_cache) const |
| Initialize the atom-index information for a particular residue pair and store those indices in the ResPairMinimizationData data_cache. | |
| virtual void | eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const |
| Retrieve the atom-index information for this residue pair from the minpair_data object and evaluate the derivatives for a particular atom. | |
| virtual void | old_eval_atom_derivative (id::AtomID const &, pose::Pose const &, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &, Vector &, Vector &) const |
| virtual Real | eval_dof_derivative (id::DOF_ID const &, id::TorsionID const &, pose::Pose const &, ScoreFunction const &, EnergyMap const &) const |
| 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. | |
| virtual void | residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. | |
| virtual bool | defines_intrares_energy (EnergyMap const &weights) const |
| Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not. | |
| virtual void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the intra-residue energy for a given residue. | |
| virtual methods::LongRangeEnergyType | long_range_type () const |
| virtual bool | defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const |
Public Attributes | |
| __pad0__:ContextIndependentLRTwoBodyEnergy parent | |
| core::scoring::disulfides::FullatomDisulfideEnergy::FullatomDisulfideEnergy | ( | FullatomDisulfidePotential const & | potential | ) |
Referenced by clone().
| core::scoring::disulfides::FullatomDisulfideEnergy::~FullatomDisulfideEnergy | ( | ) | [virtual] |
| methods::EnergyMethodOP core::scoring::disulfides::FullatomDisulfideEnergy::clone | ( | ) | const [virtual] |
Implements core::scoring::methods::EnergyMethod.
References FullatomDisulfideEnergy().
| bool core::scoring::disulfides::FullatomDisulfideEnergy::defines_intrares_energy | ( | EnergyMap const & | weights | ) | const [virtual] |
Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.
For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.
Implements core::scoring::methods::TwoBodyEnergy.
| bool core::scoring::disulfides::FullatomDisulfideEnergy::defines_residue_pair_energy | ( | pose::Pose const & | pose, |
| Size | res1, | ||
| Size | res2 | ||
| ) | const [virtual] |
| bool core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair | ( | conformation::Residue const & | res1, |
| conformation::Residue const & | res2, | ||
| bool | res_moving_wrt_eachother | ||
| ) | const [virtual] |
Returns true only for disulfide-bonded residue pairs.
returns true if both residues are cys, if both are disulfide-cys, and then if all of these conditions have been satisfied, if residue1's SG atom connects to residue 2, and if residue 2's SG atom connects to residue 1
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::conformation::Residue::aa(), core::chemical::aa_cys, core::conformation::Residue::atom_index(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::has_variant_type(), core::chemical::ResConnID::resid(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::conformation::Residue::seqpos(), and core::conformation::Residue::type().
| Real core::scoring::disulfides::FullatomDisulfideEnergy::eval_dof_derivative | ( | id::DOF_ID const & | , |
| id::TorsionID const & | , | ||
| pose::Pose const & | , | ||
| ScoreFunction const & | , | ||
| EnergyMap const & | |||
| ) | const [virtual] |
| void core::scoring::disulfides::FullatomDisulfideEnergy::eval_intrares_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
Evaluate the intra-residue energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
| void core::scoring::disulfides::FullatomDisulfideEnergy::eval_residue_pair_derivatives | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| ResSingleMinimizationData const & | , | ||
| ResSingleMinimizationData const & | , | ||
| ResPairMinimizationData const & | min_data, | ||
| pose::Pose const & | pose, | ||
| EnergyMap const & | weights, | ||
| utility::vector1< DerivVectorPair > & | r1_atom_derivs, | ||
| utility::vector1< DerivVectorPair > & | r2_atom_derivs | ||
| ) | const [virtual] |
Retrieve the atom-index information for this residue pair from the minpair_data object and evaluate the derivatives for a particular atom.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::fa_dslf_respair_data, core::scoring::ResPairMinimizationData::get_data(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), and core::conformation::Residue::has_variant_type().
| void core::scoring::disulfides::FullatomDisulfideEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [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.
| methods::LongRangeEnergyType core::scoring::disulfides::FullatomDisulfideEnergy::long_range_type | ( | ) | const [virtual] |
Implements core::scoring::methods::LongRangeTwoBodyEnergy.
References core::scoring::methods::fa_disulfide_energy.
| bool core::scoring::disulfides::FullatomDisulfideEnergy::minimize_in_whole_structure_context | ( | pose::Pose const & | ) | const [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::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative | ( | id::AtomID const & | atomid, |
| pose::Pose const & | pose, | ||
| kinematics::DomainMap const & | , | ||
| ScoreFunction const & | , | ||
| EnergyMap const & | weights, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const [virtual] |
References core::id::AtomID::atomno(), core::pose::Pose::energies(), core::scoring::methods::fa_disulfide_energy, core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::Energies::long_range_container(), core::pose::Pose::residue(), and core::id::AtomID::rsd().
| void core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
Implements core::scoring::methods::TwoBodyEnergy.
References core::conformation::Residue::aa(), core::chemical::aa_cys, core::scoring::dslf_ca_dih, core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dih, core::scoring::dslf_ss_dst, core::pose::Pose::energies(), core::scoring::methods::fa_disulfide_energy, core::conformation::Residue::has_variant_type(), core::scoring::Energies::long_range_container(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), and core::conformation::Residue::seqpos().
| void core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| ResPairMinimizationData const & | min_data, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
Pull the atom-index information out of min_data object, and use those indices to score the disulfide bond.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::dslf_ca_dih, core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dih, core::scoring::dslf_ss_dst, core::scoring::fa_dslf_respair_data, core::scoring::ResPairMinimizationData::get_data(), core::conformation::Residue::has_variant_type(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), and core::conformation::Residue::seqpos().
| void core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| kinematics::MinimizerMapBase const & | minmap, | ||
| ResSingleMinimizationData const & | res1_data_cache, | ||
| ResSingleMinimizationData const & | res2_data_cache, | ||
| ResPairMinimizationData & | data_cache | ||
| ) | const [virtual] |
Initialize the atom-index information for a particular residue pair and store those indices in the ResPairMinimizationData data_cache.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
References core::scoring::fa_dslf_respair_data, core::conformation::Residue::has_variant_type(), core::conformation::Residue::seqpos(), and core::scoring::ResPairMinimizationData::set_data().
| void core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| ScoreFunction const & | |||
| ) | const [virtual] |
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::methods::fa_disulfide_energy, core::scoring::Energies::long_range_container(), core::scoring::Energies::nonconst_long_range_container(), core::scoring::Energies::set_long_range_container(), and core::conformation::Conformation::size().
| bool core::scoring::disulfides::FullatomDisulfideEnergy::use_extended_residue_pair_energy_interface | ( | ) | const [virtual] |
During minimization, access atom-index information from the ResPairMinimizationData.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
1.7.4
