Rosetta 3.4
Public Types | Public Member Functions | Public Attributes
core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy Class Reference

#include <FullatomCustomPairDistanceEnergy.hh>

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List of all members.

Public Types

typedef
utility::fixedsizearray1< Size, 2 > 
ResAtomIndex
typedef utility::OrderedTuple
< ResAtomIndex
ResAtomIndexTuple
typedef std::map
< ResAtomIndexTuple, std::list
< resatom_and_func_struct > > 
ResAtomIndexFuncMap
typedef
utility::fixedsizearray1
< chemical::ResidueTypeCAP, 2 > 
ResTypePair
typedef utility::OrderedTuple
< ResTypePair
ResTypePairTuple
typedef std::map
< ResTypePairTuple,
AtomPairFuncListOP
PairFuncMap

Public Member Functions

 FullatomCustomPairDistanceEnergy ()
 FullatomCustomPairDistanceEnergy (FullatomCustomPairDistanceEnergy const &src)
virtual methods::EnergyMethodOP clone () const
 clone
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 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 void eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
 Evaluate the intra-residue energy for a given residue.
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual Distance atomic_interaction_cutoff () const
 FullatomCustomPairDistanceEnergy distance cutoff.
virtual bool defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const
 Returns true if there are atoms on residue 1 & 2 that have interactions defined between them, and false otherwise. This avoids unnecessary calls to residue_pair_energy_ext during minimization between pairs of atoms that have no interactons.
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
 Returns true. This class takes advantage of the opportunity to store sequence-specific data in a ResiduePairMinimiazationObject listing the atom-pair interactions for a particular residue pair and to extract that data from cache for easy use inside residue_pair_energy_ext.
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
 Extract the cached std::list< atoms_and_func_struct > object from the ResPairMinimizationData object that was stored for this particular residue pair in setup_for_minimizing_for_residue_pair, and use this cached list to evaluate the atom-pair interactions.
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
 Find the list of atom-pair interactions from the pair_and_func_map_ for the given residue-type pair and cache that list in the input ResPairMinimizationData object.
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 all f1/f2 derivative vector pairs for all interacting atoms on the input residue pair.

Public Attributes

 __pad0__:ContextIndependentTwoBodyEnergy parent

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::FullatomCustomPairDistanceEnergy ( )

Referenced by clone().

core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::FullatomCustomPairDistanceEnergy ( FullatomCustomPairDistanceEnergy const &  src)

Member Function Documentation

Distance core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::atomic_interaction_cutoff ( ) const [virtual]
methods::EnergyMethodOP core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::clone ( ) const [virtual]
virtual bool core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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::custom_pair_distance::FullatomCustomPairDistanceEnergy::defines_score_for_residue_pair ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
bool  res_moving_wrt_eachother 
) const [virtual]

Returns true if there are atoms on residue 1 & 2 that have interactions defined between them, and false otherwise. This avoids unnecessary calls to residue_pair_energy_ext during minimization between pairs of atoms that have no interactons.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

virtual void core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [inline, virtual]

Evaluate the intra-residue energy for a given residue.

Implements core::scoring::methods::TwoBodyEnergy.

void core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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]
virtual void core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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.

bool core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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::custom_pair_distance::FullatomCustomPairDistanceEnergy::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::fa_cust_pair_dist, and core::conformation::Residue::xyz().

void core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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]

Extract the cached std::list< atoms_and_func_struct > object from the ResPairMinimizationData object that was stored for this particular residue pair in setup_for_minimizing_for_residue_pair, and use this cached list to evaluate the atom-pair interactions.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::fa_cust_pair_dist, core::scoring::fa_custom_pair_dist_data, core::scoring::ResPairMinimizationData::get_data(), core::scoring::ResPairMinimizationData::get_data_ref(), core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().

void core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::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]

Find the list of atom-pair interactions from the pair_and_func_map_ for the given residue-type pair and cache that list in the input ResPairMinimizationData object.

Reimplemented from core::scoring::methods::TwoBodyEnergy.

References core::scoring::fa_custom_pair_dist_data, core::scoring::ResPairMinimizationData::get_data(), core::conformation::Residue::seqpos(), and core::scoring::ResPairMinimizationData::set_data().

bool core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::use_extended_residue_pair_energy_interface ( ) const [virtual]

Returns true. This class takes advantage of the opportunity to store sequence-specific data in a ResiduePairMinimiazationObject listing the atom-pair interactions for a particular residue pair and to extract that data from cache for easy use inside residue_pair_energy_ext.

Reimplemented from core::scoring::methods::TwoBodyEnergy.


Member Data Documentation


The documentation for this class was generated from the following files:
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