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Rosetta 3.4
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Rosetta 3.4
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#include <OccludedHbondSolEnergy.hh>
Public Member Functions | |
| OccludedHbondSolEnergy (methods::EnergyMethodOptions const &options, bool const verbose=false) | |
| OccludedHbondSolEnergy (OccludedHbondSolEnergy const &src) | |
| virtual methods::EnergyMethodOP | clone () const |
| 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 | residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &, ScoreFunction const &, EnergyMap &emap) const |
| Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap. | |
| virtual void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const |
| Evaluate the intra-residue energy for a given residue. | |
| virtual bool | minimize_in_whole_structure_context (pose::Pose const &) const |
| Inform inquiring algorithms that this energy method will opt-in to the residue-pair decomposable derivative evaluation scheme. | |
| virtual bool | defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const |
| 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 |
| Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%. | |
| virtual void | eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const |
| Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd. | |
| virtual bool | defines_intrares_energy (EnergyMap const &) 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 Distance | atomic_interaction_cutoff () const |
| how far apart must two heavy atoms be to have a zero interaction energy? | |
| 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. | |
Public Attributes | |
| __pad0__:ContextIndependentTwoBodyEnergy parent | |
| core::scoring::geometric_solvation::OccludedHbondSolEnergy::OccludedHbondSolEnergy | ( | methods::EnergyMethodOptions const & | options, |
| bool const | verbose = false |
||
| ) |
References core::scoring::geometric_solvation::tr().
Referenced by clone().
| core::scoring::geometric_solvation::OccludedHbondSolEnergy::OccludedHbondSolEnergy | ( | OccludedHbondSolEnergy const & | src | ) |
References core::scoring::geometric_solvation::tr().
| Distance core::scoring::geometric_solvation::OccludedHbondSolEnergy::atomic_interaction_cutoff | ( | ) | const [virtual] |
how far apart must two heavy atoms be to have a zero interaction energy?
If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().
Implements core::scoring::methods::ShortRangeTwoBodyEnergy.
References core::scoring::geometric_solvation::DatabaseOccSolEne::atomic_interaction_cutoff().
| methods::EnergyMethodOP core::scoring::geometric_solvation::OccludedHbondSolEnergy::clone | ( | ) | const [virtual] |
Implements core::scoring::methods::EnergyMethod.
References OccludedHbondSolEnergy().
| virtual bool core::scoring::geometric_solvation::OccludedHbondSolEnergy::defines_intrares_energy | ( | EnergyMap const & | weights | ) | const [inline, 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::geometric_solvation::OccludedHbondSolEnergy::defines_score_for_residue_pair | ( | conformation::Residue const & | res1, |
| conformation::Residue const & | res2, | ||
| bool | res_moving_wrt_eachother | ||
| ) | const [virtual] |
return true if the two residues are moving with respect to each other.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
| void core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_intrares_derivatives | ( | conformation::Residue const & | rsd, |
| ResSingleMinimizationData const & | min_data, | ||
| pose::Pose const & | pose, | ||
| EnergyMap const & | weights, | ||
| utility::vector1< DerivVectorPair > & | atom_derivs | ||
| ) | const [virtual] |
Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
| void core::scoring::geometric_solvation::OccludedHbondSolEnergy::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.
References core::scoring::occ_sol_fitted, and core::scoring::geometric_solvation::tr().
| void core::scoring::geometric_solvation::OccludedHbondSolEnergy::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] |
Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.
Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
| virtual void core::scoring::geometric_solvation::OccludedHbondSolEnergy::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.
| virtual bool core::scoring::geometric_solvation::OccludedHbondSolEnergy::minimize_in_whole_structure_context | ( | pose::Pose const & | ) | const [inline, virtual] |
Inform inquiring algorithms that this energy method will opt-in to the residue-pair decomposable derivative evaluation scheme.
Reimplemented from core::scoring::methods::EnergyMethod.
| void core::scoring::geometric_solvation::OccludedHbondSolEnergy::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::scoring::occ_sol_fitted, core::conformation::Residue::seqpos(), and core::scoring::geometric_solvation::tr().
| void core::scoring::geometric_solvation::OccludedHbondSolEnergy::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::Pose::update_residue_neighbors().
| void core::scoring::geometric_solvation::OccludedHbondSolEnergy::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
