Rosetta 3.4
Public Member Functions | Public Attributes
core::scoring::disulfides::FullatomDisulfideEnergy Class Reference

#include <FullatomDisulfideEnergy.hh>

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List of all members.

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

Constructor & Destructor Documentation

core::scoring::disulfides::FullatomDisulfideEnergy::FullatomDisulfideEnergy ( FullatomDisulfidePotential const &  potential)

Referenced by clone().

core::scoring::disulfides::FullatomDisulfideEnergy::~FullatomDisulfideEnergy ( ) [virtual]

Member Function Documentation

methods::EnergyMethodOP core::scoring::disulfides::FullatomDisulfideEnergy::clone ( ) const [virtual]
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]
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]
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]
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]
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]
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.


Member Data Documentation


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