Rosetta 3.4
Public Types | Public Member Functions
core::scoring::methods::LK_BallEnergy Class Reference

#include <LK_BallEnergy.hh>

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List of all members.

Public Types

typedef
ContextIndependentTwoBodyEnergy 
parent
typedef chemical::ResidueType ResidueType
 convenience typedefs
typedef utility::vector1< SizeSizes
typedef utility::vector1< VectorVectors

Public Member Functions

 LK_BallEnergy (EnergyMethodOptions const &options)
 HACKING //////////////////////////.
virtual EnergyMethodOP clone () const
 clone
 LK_BallEnergy (LK_BallEnergy const &src)
virtual void setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &rotamer_set) const
virtual void update_residue_for_packing (pose::Pose &, Size resid) const
 ensure this function gets called. The default behavior is to do nothing.
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
Real calculate_lk_desolvation_of_single_atom_by_residue (Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)
 helper function for outside use
Real calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair (Size const atom1, conformation::Residue const &rsd1, conformation::Residue const &rsd2)
void calculate_lk_ball_atom_energies (Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, Real &lk_desolvation_of_atom1_by_atom2, Real &lk_ball_desolvation_of_atom1_by_atom2) const
 get the lk-ball desolvation of atom1 by atom2, and the unoriented lk desolvation of atom1 by atom2
Real get_lk_fractional_contribution_for_single_water (Vector const &atom2_xyz, Size const atom2_type, Vector const &atom1_water) const
void eval_desolvation_derivs_no_count_pair (Real const d2, Size const atom1, conformation::Residue const &rsd1, Size const atom2, conformation::Residue const &rsd2, Real &atom1_lk_desolvation_by_atom2_deriv, Real &atom2_lk_desolvation_by_atom1_deriv)
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
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 This guy is used during scoring.
void residue_pair_energy (conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, EnergyMap &emap) const
void accumulate_single_atom_contributions (Size const atom1, Size const atom1_type_index, Vectors const &atom1_waters, conformation::Residue const &rsd1, Size const atom2_type_index, Vector const &atom2_xyz, Real const lk_desolvation_of_atom1_by_atom2, EnergyMap &emap) const
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 Distance atomic_interaction_cutoff () const
 how far apart must two heavy atoms be to have a zero interaction energy?
void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) 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.
Real eval_lk_fraction (Real const d2_delta) const
Real eval_d_lk_fraction_dr_over_r (Real const d2_delta) const
Real get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters, Size &closest_water, Real &closest_water_dis2) const
Real get_lk_fractional_contribution (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters) const
Real eval_lk_ball_fraction_deriv (Vector const &atom2_xyz, Size const atom2_type_index, Vectors const &atom1_waters, bool const evaluate_deriv, Vector &f1, Vector &f2) const
 for external use
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 derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
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 rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.
void sum_contributions_for_atom_pair_one_way (Size const atom1, conformation::Residue const &rsd1, Vectors const &atom1_waters, Size const atom2, conformation::Residue const &rsd2, scoring::EnergyMap const &weights, Real const weight_factor, Real const d2, Vector &F1, Vector &F2) const
void sum_contributions_for_atom_pair (Size const atom1, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, Size const atom2, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, pose::Pose const &pose, scoring::EnergyMap const &weights, Real const cp_weight, Vector &F1, Vector &F2) const
void setup_d2_bounds ()

Member Typedef Documentation

convenience typedefs


Constructor & Destructor Documentation

core::scoring::methods::LK_BallEnergy::LK_BallEnergy ( EnergyMethodOptions const &  options)

HACKING //////////////////////////.

References setup_d2_bounds().

Referenced by clone().

core::scoring::methods::LK_BallEnergy::LK_BallEnergy ( LK_BallEnergy const &  src)

References setup_d2_bounds().


Member Function Documentation

void core::scoring::methods::LK_BallEnergy::accumulate_single_atom_contributions ( Size const  atom1,
Size const  atom1_type_index,
Vectors const &  atom1_waters,
conformation::Residue const &  rsd1,
Size const  atom2_type_index,
Vector const &  atom2_xyz,
Real const  lk_desolvation_of_atom1_by_atom2,
EnergyMap emap 
) const
Distance core::scoring::methods::LK_BallEnergy::atomic_interaction_cutoff ( ) const [virtual]

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

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

References core::scoring::etable::Etable::max_dis().

void core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies ( Size const  atom1,
conformation::Residue const &  rsd1,
Vectors const &  atom1_waters,
Size const  atom2,
conformation::Residue const &  rsd2,
Real lk_desolvation_of_atom1_by_atom2,
Real lk_ball_desolvation_of_atom1_by_atom2 
) const

get the lk-ball desolvation of atom1 by atom2, and the unoriented lk desolvation of atom1 by atom2

References core::conformation::Residue::atom(), core::scoring::etable::count_pair::CP_CROSSOVER_4, get_lk_fractional_contribution(), core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Real core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue ( Size const  atom1,
conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
)
Real core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair ( Size const  atom1,
conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2 
)
EnergyMethodOP core::scoring::methods::LK_BallEnergy::clone ( ) const [virtual]
virtual bool core::scoring::methods::LK_BallEnergy::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.

Real core::scoring::methods::LK_BallEnergy::eval_d_lk_fraction_dr_over_r ( Real const  d2_delta) const
void core::scoring::methods::LK_BallEnergy::eval_desolvation_derivs_no_count_pair ( Real const  d2,
Size const  atom1,
conformation::Residue const &  rsd1,
Size const  atom2,
conformation::Residue const &  rsd2,
Real atom1_lk_desolvation_by_atom2_deriv,
Real atom2_lk_desolvation_by_atom1_deriv 
)
virtual void core::scoring::methods::LK_BallEnergy::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.

Real core::scoring::methods::LK_BallEnergy::eval_lk_ball_fraction_deriv ( Vector const &  atom2_xyz,
Size const  atom2_type,
Vectors const &  atom1_waters,
bool const  evaluate_deriv,
Vector f1,
Vector f2 
) const

for external use

Note that we calculate the lk_ball_iso derivative as well as the lk_ball derivative...

Derivatives are only included for heavyatoms.

For a non-polar heavyatom, the derivs are for all polar atoms that it desolvates

For a polar heavyatom, derivs are for all polar atoms that it desolvates as well as all atoms it's being desolvated by.

Given an atom desolvating a polar atom: the lk_ball_iso deriv is the standard lk deriv, but make sure we use the correct array! (see LK_hack code)

the lk_ball score = wt * lk_polar, so the derivs have two components. One looks like wt * lk_polar deriv contribution. The other looks like the lk_polar term * the derivative of the wt. The derivative of the wt is found by getting the closest water, taking the derivative of the wt term wrt distance and using f1/f2 contributions for the desolvating atom xyz and the water xyz.

Compute the f1 and f2 vectors for the derivative of the lk_fraction term for atom2 desolvating atom1

Note:
f1 and f2 are zeroed and filled within this function, rather than being accumulated into
We pretend that atom1 is the "moving" atom Should eliminate code duplication with next routine... currently this is for outside use.

References eval_d_lk_fraction_dr_over_r(), and get_lk_fractional_contribution().

Referenced by core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds().

Real core::scoring::methods::LK_BallEnergy::eval_lk_fraction ( Real const  d2_delta) const

Stolen from LK_SigmoidalFunc in lk_hack d2_delta = d2 - d2_low

Referenced by get_lk_fractional_contribution(), and get_lk_fractional_contribution_for_single_water().

void core::scoring::methods::LK_BallEnergy::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]
void core::scoring::methods::LK_BallEnergy::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 [virtual]

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 rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

References core::scoring::EMapVector::dot(), core::scoring::methods::LKB_ResidueInfo::has_waters(), residue_pair_energy(), core::scoring::methods::retrieve_residue_info(), core::scoring::methods::retrieve_rotamer_set_info(), and core::conformation::Residue::seqpos().

void core::scoring::methods::LK_BallEnergy::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 [virtual]

Batch computation of rotamer pair energies. Need not be overriden in derived class -- by default, iterates over all pairs of rotamers, and calls derived class's residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range.

Reimplemented from core::scoring::methods::ShortRangeTwoBodyEnergy.

References core::scoring::EMapVector::dot(), core::conformation::RotamerSetBase::get_n_residue_types(), core::conformation::RotamerSetBase::get_n_rotamers_for_residue_type(), core::conformation::RotamerSetBase::get_residue_type_begin(), residue_pair_energy(), core::scoring::methods::retrieve_rotamer_set_info(), and core::conformation::RotamerSetBase::rotamer().

Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution ( Vector const &  atom2_xyz,
Size const  atom2_type_index,
Vectors const &  atom1_waters 
) const
Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution ( Vector const &  atom2_xyz,
Size const  atom2_type,
Vectors const &  atom1_waters,
Size closest_water,
Real closest_water_d2_delta 
) const
Note:
closest_water may be set to 0 upon return if none of the waters are within ramp_width_A2_

References eval_lk_fraction().

Referenced by accumulate_single_atom_contributions(), calculate_lk_ball_atom_energies(), eval_lk_ball_fraction_deriv(), get_lk_fractional_contribution(), and sum_contributions_for_atom_pair_one_way().

Real core::scoring::methods::LK_BallEnergy::get_lk_fractional_contribution_for_single_water ( Vector const &  atom2_xyz,
Size const  atom2_type,
Vector const &  atom1_water 
) const

References eval_lk_fraction().

void core::scoring::methods::LK_BallEnergy::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.

void core::scoring::methods::LK_BallEnergy::prepare_rotamers_for_packing ( pose::Pose const &  ,
conformation::RotamerSetBase  
) const [virtual]
void core::scoring::methods::LK_BallEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  ,
EnergyMap emap 
) const [virtual]
void core::scoring::methods::LK_BallEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
LKB_ResidueInfo const &  rsd1_info,
conformation::Residue const &  rsd2,
LKB_ResidueInfo const &  rsd2_info,
EnergyMap emap 
) const
void core::scoring::methods::LK_BallEnergy::setup_d2_bounds ( )
void core::scoring::methods::LK_BallEnergy::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::scoring::methods::compute_and_store_pose_waters(), and core::pose::Pose::update_residue_neighbors().

void core::scoring::methods::LK_BallEnergy::setup_for_packing ( pose::Pose ,
utility::vector1< bool > const &  ,
utility::vector1< bool > const &   
) const [virtual]
void core::scoring::methods::LK_BallEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]
void core::scoring::methods::LK_BallEnergy::sum_contributions_for_atom_pair ( Size const  atom1,
conformation::Residue const &  rsd1,
LKB_ResidueInfo const &  rsd1_info,
Size const  atom2,
conformation::Residue const &  rsd2,
LKB_ResidueInfo const &  rsd2_info,
pose::Pose const &  pose,
scoring::EnergyMap const &  weights,
Real const  cp_weight,
Vector F1,
Vector F2 
) const
Note:
Assumes that atom1 is the "moving" atom, ie the atom for which eval_atom_derivative was called
Calculates the water positions for atom2 if d2 < safe_max_dis2

References sum_contributions_for_atom_pair_one_way(), core::scoring::methods::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().

Referenced by eval_residue_pair_derivatives().

void core::scoring::methods::LK_BallEnergy::sum_contributions_for_atom_pair_one_way ( Size const  atom1,
conformation::Residue const &  rsd1,
Vectors const &  atom1_waters,
Size const  atom2,
conformation::Residue const &  rsd2,
scoring::EnergyMap const &  weights,
Real const  weight_factor,
Real const  d2,
Vector F1,
Vector F2 
) const
Note:
atom2 is desolvating atom1. atom1_waters is non-empty
Pretend that atom1 is the atom whose derivs are being calculated. weight_factor may include -1 term to switch the order...

References core::conformation::Residue::atom(), eval_d_lk_fraction_dr_over_r(), get_lk_fractional_contribution(), core::scoring::lk_ball, core::scoring::lk_ball_iso, core::conformation::Atom::type(), and core::conformation::Residue::xyz().

Referenced by sum_contributions_for_atom_pair().

void core::scoring::methods::LK_BallEnergy::update_residue_for_packing ( pose::Pose ,
Size  resid 
) const [virtual]

ensure this function gets called. The default behavior is to do nothing.

default implementation noop

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

References core::scoring::methods::LKB_ResidueInfo::build_waters(), core::pose::Pose::residue(), and core::scoring::methods::retrieve_nonconst_residue_info().


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