Rosetta 3.4
Public Member Functions | Public Attributes
core::scoring::orbitals::OrbitalsScore Class Reference

#include <OrbitalsScore.hh>

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List of all members.

Public Member Functions

 OrbitalsScore (methods::EnergyMethodOptions const &)
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 eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &, pose::Pose const &, EnergyMap const &, 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 finalize_after_derivatives (pose::Pose &pose, ScoreFunction const &) const
 called at the end of derivatives evaluation
virtual void eval_intrares_energy (core::conformation::Residue const &, core::pose::Pose const &, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &) const
 Evaluate the intra-residue energy for a given residue.
virtual bool defines_intrares_energy (const core::scoring::EnergyMap &) 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 residue_pair_energy (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::pose::Pose const &, core::scoring::ScoreFunction const &, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual core::Real atomic_interaction_cutoff () const
 This is very wrong.
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 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 void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
virtual void update_residue_for_packing (pose::Pose &, Size resid) const
void get_E_haro_one_way (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Real &HARO_sc_H_sc_orb_E) const
void get_E_hpol_one_way (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Real &HPOL_sc_H_sc_orb_E, core::Real &HPOL_bb_H_sc_orb_energy) const
void get_orb_H_distance_and_energy (core::conformation::Residue const &res1, core::Size const &Aindex, numeric::xyzVector< core::Real > const &Axyz, numeric::xyzVector< core::Real > const &Hxyz, numeric::xyzVector< core::Real > const &Dxyz, core::Real &sc_energy, core::Real &bb_h_energy, OrbitalsLookup::h_type htype, bool bb_h_flag) const
void assign_haro_derivs_one_way (core::conformation::Residue const &res1, core::conformation::Residue const &res2, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
void assign_hpol_derivs_one_way (core::conformation::Residue const &res1, core::conformation::Residue const &res2, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
bool cation_pi_rules (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Size const &Aindex, core::Size const &Dindex) const
void assign_orb_H_derivs (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Size &atom_index, numeric::xyzVector< core::Real > const &atom_xyz, core::Size const &H_index, numeric::xyzVector< core::Real > const &H_xyz, OrbitalsLookup::h_type htype, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const

Public Attributes

 __pad0__:ContextDependentTwoBodyEnergy parent

Constructor & Destructor Documentation

core::scoring::orbitals::OrbitalsScore::OrbitalsScore ( methods::EnergyMethodOptions const &  )

Referenced by clone().


Member Function Documentation

void core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way ( core::conformation::Residue const &  res1,
core::conformation::Residue const &  res2,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const
void core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way ( core::conformation::Residue const &  res1,
core::conformation::Residue const &  res2,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const
void core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs ( core::conformation::Residue const &  res1,
core::conformation::Residue const &  res2,
core::Size atom_index,
numeric::xyzVector< core::Real > const &  atom_xyz,
core::Size const &  H_index,
numeric::xyzVector< core::Real > const &  H_xyz,
OrbitalsLookup::h_type  htype,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  r1_atom_derivs,
utility::vector1< DerivVectorPair > &  r2_atom_derivs 
) const
core::Distance core::scoring::orbitals::OrbitalsScore::atomic_interaction_cutoff ( ) const [virtual]

This is very wrong.

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

bool core::scoring::orbitals::OrbitalsScore::cation_pi_rules ( core::conformation::Residue const &  res1,
core::conformation::Residue const &  res2,
core::Size const &  Aindex,
core::Size const &  Dindex 
) const
methods::EnergyMethodOP core::scoring::orbitals::OrbitalsScore::clone ( ) const [virtual]
bool core::scoring::orbitals::OrbitalsScore::defines_intrares_energy ( const core::scoring::EnergyMap 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.

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

Evaluate the intra-residue energy for a given residue.

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

void core::scoring::orbitals::OrbitalsScore::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.

References assign_haro_derivs_one_way(), assign_hpol_derivs_one_way(), and core::conformation::Residue::is_aromatic().

void core::scoring::orbitals::OrbitalsScore::finalize_after_derivatives ( pose::Pose ,
ScoreFunction const &   
) const [virtual]

called at the end of derivatives evaluation

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

void core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way ( core::conformation::Residue const &  res1,
core::conformation::Residue const &  res2,
core::Real HARO_sc_H_sc_orb_E 
) const
void core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way ( core::conformation::Residue const &  res1,
core::conformation::Residue const &  res2,
core::Real HPOL_sc_H_sc_orb_E,
core::Real HPOL_bb_H_sc_orb_energy 
) const
void core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy ( core::conformation::Residue const &  res1,
core::Size const &  Aindex,
numeric::xyzVector< core::Real > const &  Axyz,
numeric::xyzVector< core::Real > const &  Hxyz,
numeric::xyzVector< core::Real > const &  Dxyz,
core::Real sc_energy,
core::Real bb_h_energy,
OrbitalsLookup::h_type  htype,
bool  bb_h_flag 
) const
void core::scoring::orbitals::OrbitalsScore::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.

virtual bool core::scoring::orbitals::OrbitalsScore::minimize_in_whole_structure_context ( pose::Pose const &  ) const [inline, 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::orbitals::OrbitalsScore::prepare_rotamers_for_packing ( pose::Pose const &  ,
conformation::RotamerSetBase  
) const [virtual]

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

void core::scoring::orbitals::OrbitalsScore::residue_pair_energy ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2,
core::pose::Pose const &  pose,
core::scoring::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 get_E_haro_one_way(), get_E_hpol_one_way(), core::conformation::Residue::is_aromatic(), core::scoring::orbitals_haro, core::scoring::orbitals_hpol, and core::scoring::orbitals_hpol_bb.

void core::scoring::orbitals::OrbitalsScore::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::n_residue(), and core::pose::Pose::update_orbital_coords().

void core::scoring::orbitals::OrbitalsScore::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]
void core::scoring::orbitals::OrbitalsScore::update_residue_for_packing ( pose::Pose pose,
Size  resid 
) const [virtual]

Member Data Documentation


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