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Rosetta 3.5
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Rosetta 3.5
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#include <PDDFEnergy.hh>
Public Member Functions | |
| PDDFEnergy () | |
| PDDFEnergy (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &) | |
| c-tors More... | |
| virtual | ~PDDFEnergy () |
| virtual core::scoring::methods::EnergyMethodOP | clone () const |
| virtual void | finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::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. More... | |
| 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. More... | |
| core::scoring::methods::EnergyMethodOP | create_energy_method (core::scoring::methods::EnergyMethodOptions const &) const |
| utility::vector1< core::Real > & | get_pddf () |
| utility::vector1< core::Real > & | get_dist_bins () |
| utility::vector1< core::Real > & | compute_pddf (const core::pose::Pose &) const |
| utility::vector1< core::Real > & | compute_pddf_without_ff (const core::pose::Pose &) const |
| core::Real | compute_chi (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &) const |
| core::Real | compute_L1 (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &) const |
| void | create_pddf (core::pose::Pose &, core::Real, core::Real, core::Real) |
| core::Real | evaluate_pddf_energy (const core::pose::Pose &pose) const |
 Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy | |
| WholeStructureEnergy (EnergyMethodCreatorOP) | |
| Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More... | |
| virtual | ~WholeStructureEnergy () |
| EnergyMethodType | method_type () const |
| Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More... | |
| virtual Distance | atomic_interaction_cutoff () const |
| how far apart must two heavy atoms be to have a zero interaction energy? More... | |
| Public Member Functions inherited from core::scoring::methods::EnergyMethod | |
| EnergyMethod (EnergyMethodCreatorOP creator) | |
| Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More... | |
| EnergyMethod (EnergyMethod const &src) | |
| Copy constructor copies over the score types of the source. More... | |
| virtual | ~EnergyMethod () |
| virtual void | setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const |
| virtual void | prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const |
| virtual void | update_residue_for_packing (pose::Pose &, Size resid) const |
| ensure this function gets called. The default behavior is to do nothing. More... | |
| virtual void | setup_for_scoring (pose::Pose &, ScoreFunction const &) const |
| virtual void | setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const |
| Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More... | |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const |
| Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More... | |
| virtual void | finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const |
| called at the end of derivatives evaluation More... | |
| 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. More... | |
| virtual bool | defines_high_order_terms (pose::Pose const &) const |
| Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More... | |
| virtual void | 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 |
| 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. More... | |
| ScoreTypes const & | score_types () const |
| Returns the score types that this energy method computes. More... | |
Private Member Functions | |
| void | read_pddf (std::string) |
| virtual core::Size | version () const |
| Return the version of the energy method. More... | |
Additional Inherited Members | |
| Public Types inherited from core::scoring::methods::WholeStructureEnergy | |
| typedef EnergyMethod | parent |
| Protected Member Functions inherited from core::scoring::methods::EnergyMethod | |
| void | set_score_types (EnergyMethodCreatorOP creator) |
| Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More... | |
Definition at line 45 of file PDDFEnergy.hh.
| protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy | ( | ) |
Definition at line 95 of file PDDFEnergy.cc.
References bin_size_, core::chemical::CENTROID, create_pddf(), core::chemical::ChemicalManager::get_instance(), if_fit_area_, if_hydrogens_, max_bin_, min_bin_, norm_, core::import_pose::pose_from_pdb(), read_pddf(), reference_pddf_, core::chemical::ChemicalManager::residue_type_set(), and core::util::switch_to_residue_type_set().
Referenced by clone(), and create_energy_method().
| protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy | ( | utility::vector1< core::Real > const & | reference_d, |
| utility::vector1< core::Real > const & | reference_pddf | ||
| ) |
c-tors
Definition at line 78 of file PDDFEnergy.cc.
References bin_size_, d_, if_fit_area_, max_bin_, min_bin_, pose_pddf_, and reference_pddf_.
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inlinevirtual |
Definition at line 52 of file PDDFEnergy.hh.
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inlinevirtual |
Implements core::scoring::methods::EnergyMethod.
Definition at line 54 of file PDDFEnergy.hh.
References PDDFEnergy().
| core::Real protocols::scoring::methods::saxs::PDDFEnergy::compute_chi | ( | utility::vector1< core::Real > const & | pddf_scored, |
| utility::vector1< core::Real > const & | pddf_reference | ||
| ) | const |
Definition at line 339 of file PDDFEnergy.cc.
References d_, if_fit_area_, max_bin_, and min_bin_.
Referenced by evaluate_pddf_energy(), and finalize_total_energy().
| core::Real protocols::scoring::methods::saxs::PDDFEnergy::compute_L1 | ( | utility::vector1< core::Real > const & | pddf_scored, |
| utility::vector1< core::Real > const & | pddf_reference | ||
| ) | const |
Definition at line 317 of file PDDFEnergy.cc.
| utility::vector1< core::Real > & protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf | ( | const core::pose::Pose & | pose) | const |
Definition at line 258 of file PDDFEnergy.cc.
References a_ids_, core::conformation::Residue::atom_type(), bin_size_, d_, dmatrix_, factors_, ff_manager_, core::scoring::saxs::FormFactorManager::get_ff(), if_hydrogens_, is_glob_, core::chemical::AtomType::is_hydrogen(), core::scoring::saxs::FormFactorManager::is_known_atom(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), pose_pddf_, r_ids_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
| utility::vector1< core::Real > & protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff | ( | const core::pose::Pose & | pose) | const |
Definition at line 217 of file PDDFEnergy.cc.
References a_ids_, core::conformation::Residue::atom_type(), bin_size_, if_hydrogens_, core::chemical::AtomType::is_hydrogen(), core::conformation::Residue::natoms(), pose_pddf_, r_ids_, reference_pddf_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
Referenced by create_pddf(), evaluate_pddf_energy(), and finalize_total_energy().
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inline |
Definition at line 61 of file PDDFEnergy.hh.
References PDDFEnergy().
| void protocols::scoring::methods::saxs::PDDFEnergy::create_pddf | ( | core::pose::Pose & | ref_pose, |
| core::Real | d_min, | ||
| core::Real | d_step, | ||
| core::Real | d_max | ||
| ) |
Definition at line 172 of file PDDFEnergy.cc.
References bin_size_, compute_pddf_without_ff(), d_, pose_pddf_, and reference_pddf_.
Referenced by PDDFEnergy().
| core::Real protocols::scoring::methods::saxs::PDDFEnergy::evaluate_pddf_energy | ( | const core::pose::Pose & | pose) | const |
Definition at line 165 of file PDDFEnergy.cc.
References compute_chi(), compute_pddf_without_ff(), pose_pddf_, and reference_pddf_.
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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.
Definition at line 155 of file PDDFEnergy.cc.
References compute_chi(), compute_pddf_without_ff(), core::scoring::pddf_score, pose_pddf_, and reference_pddf_.
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inline |
Definition at line 69 of file PDDFEnergy.hh.
References d_.
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inline |
Definition at line 65 of file PDDFEnergy.hh.
References pose_pddf_.
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inlinevirtual |
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.
Definition at line 58 of file PDDFEnergy.hh.
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private |
Definition at line 187 of file PDDFEnergy.cc.
References bin_size_, d_, pose_pddf_, and reference_pddf_.
Referenced by PDDFEnergy().
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privatevirtual |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
Definition at line 377 of file PDDFEnergy.cc.
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mutableprivate |
Definition at line 84 of file PDDFEnergy.hh.
Referenced by compute_pddf(), and compute_pddf_without_ff().
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Definition at line 94 of file PDDFEnergy.hh.
Referenced by compute_pddf(), compute_pddf_without_ff(), create_pddf(), PDDFEnergy(), and read_pddf().
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Definition at line 90 of file PDDFEnergy.hh.
Referenced by compute_chi(), compute_pddf(), create_pddf(), get_dist_bins(), PDDFEnergy(), and read_pddf().
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mutableprivate |
Definition at line 85 of file PDDFEnergy.hh.
Referenced by compute_pddf().
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mutableprivate |
Definition at line 82 of file PDDFEnergy.hh.
Referenced by compute_pddf().
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private |
Definition at line 93 of file PDDFEnergy.hh.
Referenced by compute_pddf().
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Definition at line 89 of file PDDFEnergy.hh.
Referenced by compute_chi(), and PDDFEnergy().
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Definition at line 97 of file PDDFEnergy.hh.
Referenced by compute_pddf(), compute_pddf_without_ff(), and PDDFEnergy().
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mutableprivate |
Definition at line 86 of file PDDFEnergy.hh.
Referenced by compute_pddf().
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Definition at line 96 of file PDDFEnergy.hh.
Referenced by compute_chi(), and PDDFEnergy().
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Definition at line 95 of file PDDFEnergy.hh.
Referenced by compute_chi(), and PDDFEnergy().
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Definition at line 88 of file PDDFEnergy.hh.
Referenced by PDDFEnergy().
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mutableprivate |
Definition at line 91 of file PDDFEnergy.hh.
Referenced by compute_pddf(), compute_pddf_without_ff(), create_pddf(), evaluate_pddf_energy(), finalize_total_energy(), get_pddf(), PDDFEnergy(), and read_pddf().
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mutableprivate |
Definition at line 83 of file PDDFEnergy.hh.
Referenced by compute_pddf(), and compute_pddf_without_ff().
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private |
Definition at line 92 of file PDDFEnergy.hh.
Referenced by compute_pddf_without_ff(), create_pddf(), evaluate_pddf_energy(), finalize_total_energy(), PDDFEnergy(), and read_pddf().
1.8.4