![]() |
Rosetta
2020.50
|
#include <DEEREnergy.hh>
Public Member Functions | |
DEEREnergy (scoring::methods::EnergyMethodCreatorOP energymethodcreator) | |
Constructor. More... | |
DEEREnergy (scoring::methods::EnergyMethodOptions const &) | |
Constructor for obtaining command-line options. More... | |
DEEREnergy () | |
Default Constructor. More... | |
DEEREnergy (DEEREnergy const &other) | |
Copy constructor. More... | |
core::scoring::methods::EnergyMethodOP | clone () const override |
Copy function. More... | |
~DEEREnergy () override | |
Destructor. More... | |
scoring::epr_deer::DEERDataCacheCOP const | get_const_deer_data (pose::Pose const &pose) const |
Returns the parsed input file (const) More... | |
scoring::epr_deer::DEERDataCacheOP | get_deer_data (pose::Pose &pose) const |
Returns the parsed input file (non-const) More... | |
Real | get_score (pose::Pose &pose, scoring::epr_deer::EPRSpinLabel &sl, Size const &edge_id, Real const &modifier=0.0) const |
Calculates the score for a specific data set Called by setup_for_scoring() and setup_for_derivatives. EPRSpinLabel is used to calculate where the spin label is/can be. Edge ID corresponds to the specific set of data being interrogated/scored. Modifier is used for derivative calculation since the determination of derivatives is not analytically solvable in many cases. More... | |
void | setup_for_scoring (pose::Pose &pose, scoring::ScoreFunction const &) const override |
Overrides virtual fxn for finding scores for a given pose. More... | |
void | initialize_energy_method (pose::Pose &pose) const |
Initialize energy method. More... | |
scoring::methods::LongRangeEnergyType | long_range_type () const override |
Derived function for specifying where the data is getting stored. More... | |
void | setup_for_minimizing (pose::Pose &, scoring::ScoreFunction const &, kinematics::MinimizerMapBase const &) const override |
A declared but unused function. More... | |
bool | defines_intrares_energy (scoring::EnergyMap const &) const override |
Returns "false" by default. More... | |
bool | defines_residue_pair_energy (pose::Pose const &pose, Size rsd1, Size rsd2) const override |
Fetches if two residues are "connected" (i.e. there is a score) More... | |
void | residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, scoring::ScoreFunction const &, scoring::EnergyMap &emap) const override |
Get energy/score for a given pair of residues. Because some sets of data may be between more than two residues, this function looks at a map kept in DEERDataCache specifically maintained for this purpose. More... | |
void | setup_for_derivatives (pose::Pose &pose, scoring::ScoreFunction const &) const override |
Calculates the derivatives for minimization. Done numerically. More... | |
void | eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, scoring::ScoreFunction const &, scoring::EnergyMap const &emap, numeric::xyzVector< Real > &F1, numeric::xyzVector< Real > &F2) const override |
Returns the res-specific F1 and F2 vectors saved in DEERDataCache. More... | |
void | eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, scoring::ScoreFunction const &, scoring::EnergyMap &emap) const override |
A declared but unused function. More... | |
void | finalize_total_energy (pose::Pose &, scoring::ScoreFunction const &, scoring::EnergyMap &) const override |
A declared but unused function. More... | |
void | indicate_required_context_graphs (utility::vector1< bool > &) const override |
A declared but unused function. More... | |
Size | version () const override |
Version 1 (as of 30 January 2017) More... | |
![]() | |
ContextDependentLRTwoBodyEnergy (EnergyMethodCreatorOP) | |
Constructor to inform the EnergyMethod ancestor which ScoreTypes this EnergyMethod is responsible for computing. More... | |
~ContextDependentLRTwoBodyEnergy () override | |
EnergyMethodType | method_type () const override |
Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More... | |
![]() | |
LongRangeTwoBodyEnergy (EnergyMethodCreatorOP creator) | |
Constructor with an EnergyMethodCreator to inform the grandparent EnergyMethod class which ScoreTypes this EnergyMethod computes. More... | |
~LongRangeTwoBodyEnergy () override | |
![]() | |
TwoBodyEnergy (EnergyMethodCreatorOP) | |
Constructor, requiring an EnergyMethodCreator. No default constructor provided to force EnergyMethod writers to provide an energy-method-creator at construction time. More... | |
~TwoBodyEnergy () override | |
virtual bool | defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const |
During minimization, energy methods are allowed to decide that they say nothing about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns "true" for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning "false" for residue pairs that do no move wrt each other. More... | |
virtual bool | use_extended_residue_pair_energy_interface () const |
Rely on the extended version of the residue_pair_energy function during score-function evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return 'true' from this function to use the extended interface. The default method implemented in this class returns 'false'. More... | |
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 |
Evaluate the two-body energies for a particular residue, in the context of a given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit(). More... | |
virtual void | setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, basic::datacache::BasicDataCache &residue_data_cache, ResSingleMinimizationData &res_data_cache) const |
Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More... | |
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 |
Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More... | |
virtual bool | requires_a_setup_for_scoring_for_residue_opportunity_during_minimization (pose::Pose const &pose) const |
Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More... | |
virtual void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const |
Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup. More... | |
virtual bool | requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const |
Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More... | |
virtual void | setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data, basic::datacache::BasicDataCache &res_data_cache) const |
Do any setup work necessary before evaluating the derivatives for this residue. More... | |
virtual bool | requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const |
Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More... | |
virtual void | setup_for_scoring_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const |
Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More... | |
virtual bool | requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const |
Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More... | |
virtual void | setup_for_derivatives_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const |
Do any setup work necessary before evaluating the derivatives for this residue pair. More... | |
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%. More... | |
virtual void | backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
Evaluate the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
virtual void | backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
Evaluate the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
virtual void | sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
Evaluate the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
virtual bool | defines_intrares_energy_for_residue (conformation::Residue const &res) const |
If a score function defines no intra-residue scores for a particular residue, then it may opt-out of being asked during minimization to evaluate the score for this residue. More... | |
virtual bool | use_extended_intrares_energy_interface () const |
Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy during minimization routines should return "true" when this function is invoked on them. This class provides a default "return false" implementation so that classes not desiring to take advantage of this alternate interface need to do nothing. More... | |
virtual void | eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
Evaluate the intra-residue energy for a given residue using the data held within the ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return "true" in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies. More... | |
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. More... | |
virtual bool | defines_intrares_dof_derivatives (pose::Pose const &p) const |
Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More... | |
virtual utility::vector1 < id::PartialAtomID > | atoms_with_dof_derivatives (conformation::Residue const &res, pose::Pose const &p) const |
For a particular residue, list which atoms go into defining the DOF derivatives, including any atoms on adjacent residues. The Pose is provided for context, but there is no requirement that res be a member of that Pose. More... | |
virtual Real | eval_intraresidue_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 DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More... | |
virtual void | bump_energy_full (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const |
virtual void | bump_energy_backbone (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const |
virtual void | evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const |
Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More... | |
virtual void | evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const |
Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More... | |
virtual void | evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const |
Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls the derived class's residue_pair_energy method. More... | |
virtual void | evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const |
Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamr. More... | |
virtual void | evaluate_rotamer_background_energy_maps (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const |
Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamr. More... | |
![]() | |
EnergyMethod (EnergyMethodCreatorOP creator) | |
Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More... | |
virtual void | setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const |
if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More... | |
virtual void | setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const |
if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More... | |
virtual void | prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const |
If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More... | |
virtual void | update_residue_for_packing (pose::Pose &, Size resid) const |
If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More... | |
virtual bool | requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const |
Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More... | |
virtual void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const |
Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More... | |
virtual void | finalize_after_minimizing (pose::Pose &pose) const |
Called after minimization, allowing a derived class to do some teardown steps. 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... | |
virtual void | show_additional_info (std::ostream &, pose::Pose &, bool) const |
show additional information of the energy method More... | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Additional Inherited Members | |
![]() | |
typedef LongRangeTwoBodyEnergy | parent |
![]() | |
typedef TwoBodyEnergy | parent |
![]() | |
typedef EnergyMethod | parent |
![]() | |
typedef utility::VirtualBase | parent |
![]() | |
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... | |
core::energy_methods::DEEREnergy::DEEREnergy | ( | scoring::methods::EnergyMethodCreatorOP | energymethodcreator | ) |
Constructor.
core::energy_methods::DEEREnergy::DEEREnergy | ( | scoring::methods::EnergyMethodOptions const & | ) |
Constructor for obtaining command-line options.
core::energy_methods::DEEREnergy::DEEREnergy | ( | ) |
Default Constructor.
Referenced by clone().
core::energy_methods::DEEREnergy::DEEREnergy | ( | DEEREnergy const & | other | ) |
Copy constructor.
|
override |
Destructor.
|
overridevirtual |
|
overridevirtual |
Returns "false" by default.
Implements core::scoring::methods::TwoBodyEnergy.
|
overridevirtual |
Fetches if two residues are "connected" (i.e. there is a score)
Implements core::scoring::methods::LongRangeTwoBodyEnergy.
References get_const_deer_data().
|
override |
Returns the res-specific F1 and F2 vectors saved in DEERDataCache.
References core::scoring::epr_deer_score, and get_const_deer_data().
|
overridevirtual |
A declared but unused function.
Implements core::scoring::methods::TwoBodyEnergy.
|
overridevirtual |
A declared but unused function.
Reimplemented from core::scoring::methods::EnergyMethod.
scoring::epr_deer::DEERDataCacheCOP const core::energy_methods::DEEREnergy::get_const_deer_data | ( | pose::Pose const & | pose | ) | const |
Returns the parsed input file (const)
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::EPR_DEER_DATA.
Referenced by defines_residue_pair_energy(), eval_atom_derivative(), residue_pair_energy(), setup_for_derivatives(), and setup_for_scoring().
scoring::epr_deer::DEERDataCacheOP core::energy_methods::DEEREnergy::get_deer_data | ( | pose::Pose & | pose | ) | const |
Returns the parsed input file (non-const)
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::EPR_DEER_DATA.
Referenced by get_score(), setup_for_derivatives(), and setup_for_scoring().
Real core::energy_methods::DEEREnergy::get_score | ( | pose::Pose & | pose, |
scoring::epr_deer::EPRSpinLabel & | sl, | ||
Size const & | edge_id, | ||
Real const & | modifier = 0.0 |
||
) | const |
Calculates the score for a specific data set Called by setup_for_scoring() and setup_for_derivatives. EPRSpinLabel is used to calculate where the spin label is/can be. Edge ID corresponds to the specific set of data being interrogated/scored. Modifier is used for derivative calculation since the determination of derivatives is not analytically solvable in many cases.
Calculates the score for a specific data set.
References get_deer_data(), core::scoring::epr_deer::EPRSpinLabel::histogram(), and core::scoring::epr_deer::EPRSpinLabel::label().
Referenced by setup_for_derivatives(), and setup_for_scoring().
|
overridevirtual |
A declared but unused function.
Implements core::scoring::methods::EnergyMethod.
void core::energy_methods::DEEREnergy::initialize_energy_method | ( | pose::Pose & | pose | ) | const |
Initialize energy method.
Initializes energy method.
References core::pose::Pose::data(), core::pose::Pose::energies(), core::pose::datacache::CacheableDataType::EPR_DEER_DATA, core::scoring::epr_deer_score, long_range_type(), core::pose::Pose::size(), and core::pose::Pose::update_residue_neighbors().
Referenced by setup_for_scoring().
|
overridevirtual |
Derived function for specifying where the data is getting stored.
Implements core::scoring::methods::LongRangeTwoBodyEnergy.
References core::scoring::methods::epr_deer_lr.
Referenced by initialize_energy_method().
|
overridevirtual |
Get energy/score for a given pair of residues. Because some sets of data may be between more than two residues, this function looks at a map kept in DEERDataCache specifically maintained for this purpose.
Get energy/score for a given pair of residues.
Implements core::scoring::methods::TwoBodyEnergy.
References core::scoring::epr_deer_score, get_const_deer_data(), protocols::hybridization::score, and core::conformation::Residue::seqpos().
|
overridevirtual |
Calculates the derivatives for minimization. Done numerically.
Reimplemented from core::scoring::methods::EnergyMethod.
References get_const_deer_data(), get_deer_data(), get_score(), core::scoring::epr_deer::EPRSpinLabel::label(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().
|
overridevirtual |
A declared but unused function.
Reimplemented from core::scoring::methods::EnergyMethod.
|
overridevirtual |
Overrides virtual fxn for finding scores for a given pose.
Reimplemented from core::scoring::methods::EnergyMethod.
References get_const_deer_data(), get_deer_data(), get_score(), and initialize_energy_method().
|
overridevirtual |
Version 1 (as of 30 January 2017)
Version 1 (as of 20 November 2017)
Implements core::scoring::methods::EnergyMethod.